5100000@unknown@formal@none@1@S@Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach@(((:tag . "VBG") (:stem . "mine") (:form . "Mining") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "prokaryotic") (:form . "prokaryotic") (:end . 18)\n (:start . 7) (:id . 43))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 26)\n (:start . 19) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 30) (:start . 27)\n (:id . 45))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 38)\n (:start . 31) (:id . 46))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 44) (:start . 39)\n (:id . 47))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 50) (:start . 45)\n (:id . 48))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 51) (:start . 50)\n (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n (:id . 50))\n ((:tag . "JJ") (:stem . "stop-codon-based") (:form . 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"Background") (:end . 10)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s1.3) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5100003@unknown@formal@none@1@S@Selenocysteine and pyrrolysine are the 21st and 22nd amino acids, which are genetically encoded by stop codons.@(((:tag . "NNP") (:stem . "Selenocysteine") (:form . "Selenocysteine")\n (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 18) (:start . 15)\n (:id . 43))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 30)\n (:start . 19) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 34) (:start . 31)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n (:id . 46))\n ((:tag . "JJ") (:stem . "21st") (:form . "21st") (:end . 43) (:start . 39)\n (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . 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",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n (:id . 66))\n ((:tag . "RB") (:stem . "thereby") (:form . "thereby") (:end . 146)\n (:start . 139) (:id . 67))\n ((:tag . "VBG") (:stem . "render") (:form . "rendering") (:end . 156)\n (:start . 147) (:id . 68))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 162)\n (:start . 157) (:id . 69))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 169)\n (:start . 163) (:id . 70))\n ((:tag . "JJ") (:stem . "inconclusive") (:form . "inconclusive") (:end . 182)\n (:start . 170) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n (:id . 72)))@@@1@31@((:hcues ((:id . :x1.7.2) (:span 130 137)) ((:id . :x1.7.1) (:span 85 88)))\n (:hscopes ((:id . :x1.7.1) (:span 85 125)) ((:id . :x1.7.2) (:span 9 137)))\n (:identifiers (:sid . :s1.7) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100007@unknown@formal@none@1@S@A protein-level study will provide independent insight into the novel amino acid.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "protein-level") (:form . "protein-level")\n (:end . 15) (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 21) (:start . 16)\n (:id . 44))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 26) (:start . 22)\n (:id . 45))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 34)\n (:start . 27) (:id . 46))\n ((:tag . "JJ") (:stem . "independent") (:form . 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"Results") (:end . 7)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s1.9) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5100010@unknown@formal@none@1@S@Since our prediction method relies only on the conservation patterns of primary sequences, it also provides an opportunity to search novel selenoproteins and other readthrough proteins.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 20)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 27)\n (:start . 21) (:id . 45))\n ((:tag . "VBZ") (:stem . "rely") (:form . "relies") (:end . 34) (:start . 28)\n (:id . 46))\n ((:tag . "RB") (:stem . "only") (:form . 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"protein") (:form . "proteins") (:end . 184)\n (:start . 176) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.11) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100011@unknown@formal@none@1@S@It successfully recovered many of currently known selenoproteins and pyrrolysine proteins.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "successfully") (:form . "successfully") (:end . 15)\n (:start . 3) (:id . 43))\n ((:tag . "VBD") (:stem . "recover") (:form . "recovered") (:end . 25)\n (:start . 16) (:id . 44))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 30) (:start . 26)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n (:id . 46))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 43)\n (:start . 34) (:id . 47))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 49) (:start . 44)\n (:id . 48))\n ((:tag . "NNS") (:stem . "selenoprotein") (:form . "selenoproteins")\n (:end . 64) (:start . 50) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n (:id . 50))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 80)\n (:start . 69) (:id . 51))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 89)\n (:start . 81) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s1.12) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100012@unknown@formal@none@1@S@However, no promising candidate for the 23rd amino acid was detected, and only one novel selenoprotein was predicted.@(((:tag . "RB") (:stem . "however") (:form . 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"detect") (:form . "detected") (:end . 68)\n (:start . 60) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n (:id . 55))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 78) (:start . 74)\n (:id . 56))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 82) (:start . 79)\n (:id . 57))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 88) (:start . 83)\n (:id . 58))\n ((:tag . "NN") (:stem . "selenoprotein") (:form . "selenoprotein")\n (:end . 102) (:start . 89) (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 106) (:start . 103)\n (:id . 60))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 116)\n (:start . 107) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n (:id . 62)))@@@1@21@((:ncues ((:id . :x1.13.1) (:span 9 11)))\n (:nscopes ((:id . :x1.13.1) (:span 9 68)))\n (:identifiers (:sid . :s1.13) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100013@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s1.14) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5100014@unknown@formal@none@1@S@Our result suggests that the unknown amino acid encoded by stop codons does not exist, or its phylogenetic distribution is rather limited, which is in agreement with the previous study on tRNA.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "result") (:form . 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"VBZ") (:stem . "do") (:form . "does") (:end . 75) (:start . 71)\n (:id . 54))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 79) (:start . 76)\n (:id . 55))\n ((:tag . "VB") (:stem . "exist") (:form . "exist") (:end . 85) (:start . 80)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 89) (:start . 87)\n (:id . 58))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 93) (:start . 90)\n (:id . 59))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 106)\n (:start . 94) (:id . 60))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 119)\n (:start . 107) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 122) (:start . 120)\n (:id . 62))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 129)\n (:start . 123) (:id . 63))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 137)\n (:start . 130) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n (:id . 65))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 144)\n (:start . 139) (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 147) (:start . 145)\n (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 150) (:start . 148)\n (:id . 68))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 160)\n (:start . 151) (:id . 69))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 165) (:start . 161)\n (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 169) (:start . 166)\n (:id . 71))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 178)\n (:start . 170) (:id . 72))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 184)\n (:start . 179) (:id . 73))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 187) (:start . 185)\n (:id . 74))\n ((:tag . "NNP") (:stem . "tRNA") (:form . "tRNA") (:end . 192) (:start . 188)\n (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n (:id . 76)))@@@1@35@((:hcues ((:id . :x1.15.2) (:span 87 89)) ((:id . :x1.15.3) (:span 11 19)))\n (:ncues ((:id . :x1.15.1) (:span 76 79)))\n (:hscopes ((:id . :x1.15.2) (:span 25 137))\n ((:id . :x1.15.3) (:span 11 137)))\n (:nscopes ((:id . :x1.15.1) (:span 76 85)))\n (:identifiers (:sid . :s1.15) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100015@unknown@formal@none@1@S@The method described here can be used in future studies to explore novel readthrough events from complete genomes, which are rapidly growing.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "VBN") (:stem . "describe") (:form . 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"readthrough") (:form . "readthrough") (:end . 84)\n (:start . 73) (:id . 55))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 91)\n (:start . 85) (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 96) (:start . 92)\n (:id . 57))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 105)\n (:start . 97) (:id . 58))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 113)\n (:start . 106) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n (:id . 60))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 120)\n (:start . 115) (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 124) (:start . 121)\n (:id . 62))\n ((:tag . "RB") (:stem . "rapidly") (:form . "rapidly") (:end . 132)\n (:start . 125) (:id . 63))\n ((:tag . "VBG") (:stem . "grow") (:form . "growing") (:end . 140)\n (:start . 133) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s1.16) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100016@unknown@formal@none@1@S@Background@(((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 10)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s1.17) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011 5100017@unknown@formal@none@1@S@Stop codon readthrough is a phenomenon in which the translation process does not terminate at a stop codon, and an amino acid is inserted there instead 12.@(((:tag . "NNP") (:stem . "Stop") (:form . "Stop") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "readthrough") (:form . "readthrough") (:end . 22)\n (:start . 11) (:id . 44))\n ((:tag . 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"terminate") (:end . 90)\n (:start . 81) (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 93) (:start . 91)\n (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 95) (:start . 94)\n (:id . 57))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 100) (:start . 96)\n (:id . 58))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 106)\n (:start . 101) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n (:id . 61))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 114) (:start . 112)\n (:id . 62))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 120)\n (:start . 115) (:id . 63))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 125) (:start . 121)\n (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 128) (:start . 126)\n (:id . 65))\n ((:tag . "VBN") (:stem . 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"the") (:end . 56) (:start . 53)\n (:id . 54))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 59) (:start . 57)\n (:id . 55))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 65) (:start . 60)\n (:id . 56))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 71) (:start . 66)\n (:id . 57))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 75) (:start . 72)\n (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 77) (:start . 76)\n (:id . 59))\n ((:tag . "JJ") (:stem . "noncanonical") (:form . "noncanonical") (:end . 90)\n (:start . 78) (:id . 60))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 94) (:start . 91)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n (:id . 62)))@@@1@21@((:ncues ((:id . :x1.19.1) (:span 42 45)))\n (:nscopes ((:id . :x1.19.1) (:span 42 71)))\n (:identifiers (:sid . :s1.19) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100020@unknown@formal@none@1@S@Because each of them have specialized tRNA genes for decoding and can be considered extensions of the standard genetic code, they are called the 21st and 22nd amino acids, respectively.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 12) (:start . 8)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 25) (:start . 21)\n (:id . 46))\n ((:tag . "VBN") (:stem . 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"of") (:end . 97) (:start . 95)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n (:id . 58))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 110)\n (:start . 102) (:id . 59))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 118)\n (:start . 111) (:id . 60))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 123) (:start . 119)\n (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n (:id . 62))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 129) (:start . 125)\n (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 133) (:start . 130)\n (:id . 64))\n ((:tag . "VBN") (:stem . "call") (:form . "called") (:end . 140)\n (:start . 134) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n (:id . 66))\n ((:tag . "JJ") (:stem . "21st") (:form . "21st") (:end . 149) (:start . 145)\n (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 153) (:start . 150)\n (:id . 68))\n ((:tag . "JJ") (:stem . "22nd") (:form . "22nd") (:end . 158) (:start . 154)\n (:id . 69))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 164)\n (:start . 159) (:id . 70))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 170)\n (:start . 165) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n (:id . 72))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 184)\n (:start . 172) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s1.21) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100021@unknown@formal@none@1@S@Selenocysteine, the 21st amino acid, is encoded by stop codon UGA, and organisms that use selenocysteine have been found from all three domains of life.@(((:tag . 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(:end . 152) (:start . 151)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s1.22) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100022@unknown@formal@none@1@S@Its insertion into UGA is directed by SECIS (selenocysteine insertion sequence) elements, a stem-loop structure on the selenoprotein mRNA.@(((:tag . "PRP$") (:stem . "its") (:form . "Its") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "insertion") (:form . "insertion") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "NNP") (:stem . "UGA") (:form . "UGA") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n (:id . 46))\n ((:tag . "VBN") (:stem . "direct") (:form . "directed") (:end . 34)\n (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . 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(:end . 138) (:start . 137)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s1.23) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100023@unknown@formal@none@1@S@Along with the progress of genome sequencing projects, computational prediction methods of selenocysteine-containing proteins (selenoproteins) have been developed by several research groups 78910, and the repertoire of selenoproteins has been greatly expanded 1112.@(((:tag . "IN") (:stem . "along") (:form . "Along") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "progress") (:form . "progress") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "NN") (:stem . "genome") (:form . 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(:end . 127) (:start . 126)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.26) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100026@unknown@formal@none@1@S@The limited phylogenetic distribution of pyrrolysine suggests that its incorporation into the genetic code of methanogen is relatively recent, and the insertion mechanism of a novel amino acid can evolve in a shorter period of time than anticipated.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "limited") (:form . "limited") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 24)\n (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 37)\n (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n (:id . 46))\n ((:tag . "NN") (:stem . 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"NN") (:stem . "time") (:form . "time") (:end . 231) (:start . 227)\n (:id . 78))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 236) (:start . 232)\n (:id . 79))\n ((:tag . "VBN") (:stem . "anticipate") (:form . "anticipated") (:end . 248)\n (:start . 237) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 249) (:start . 248)\n (:id . 81)))@@@1@40@((:hcues ((:id . :x1.27.1) (:span 193 196)) ((:id . :x1.27.2) (:span 53 61)))\n (:hscopes ((:id . :x1.27.1) (:span 193 248))\n ((:id . :x1.27.2) (:span 53 248)))\n (:identifiers (:sid . :s1.27) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100027@unknown@formal@none@1@S@This raises an interesting question:: ""Is there a 23rd amino acid"?".@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "raise") (:form . "raises") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . 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"NN") (:stem . "acid") (:form . "acid") (:end . 66) (:start . 62)\n (:id . 55))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 67) (:start . 66)\n (:id . 56))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 68) (:start . 67)\n (:id . 57))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 69) (:start . 68)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n (:id . 59)))@@@1@18@((:hcues ((:id . :x1.28.1) (:span 5 35)))\n (:hscopes ((:id . :x1.28.1) (:span 5 67)))\n (:identifiers (:sid . :s1.28) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100028@unknown@formal@none@1@S@If such an amino acid is discovered, it will deepen our understanding of the evolution and diversity of the genetic code.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "PDT") (:stem . "such") (:form . "such") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 10) (:start . 8)\n (:id . 44))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 16) (:start . 11)\n (:id . 45))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 21) (:start . 17)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 24) (:start . 22)\n (:id . 47))\n ((:tag . "VBN") (:stem . "discover") (:form . "discovered") (:end . 35)\n (:start . 25) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n (:id . 49))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 39) (:start . 37)\n (:id . 50))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 44) (:start . 40)\n (:id . 51))\n ((:tag . "VB") (:stem . "deepen") (:form . "deepen") (:end . 51)\n (:start . 45) (:id . 52))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 55) (:start . 52)\n (:id . 53))\n ((:tag . "NN") (:stem . "understanding") (:form . "understanding")\n (:end . 69) (:start . 56) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n (:id . 56))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 86)\n (:start . 77) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n (:id . 58))\n ((:tag . "NN") (:stem . "diversity") (:form . "diversity") (:end . 100)\n (:start . 91) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n (:id . 61))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 115)\n (:start . 108) (:id . 62))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 120) (:start . 116)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s1.29) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100030@unknown@formal@none@1@S@Since both the 21st and 22nd amino acids are encoded by stop codons, the prime suspect is other stop codons (e.g. stop codon UAA), although the possibility of sense codons certainly remains.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "JJ") (:stem . "21st") (:form . "21st") (:end . 19) (:start . 15)\n (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n (:id . 46))\n ((:tag . "JJ") (:stem . "22nd") (:form . "22nd") (:end . 28) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 34) (:start . 29)\n (:id . 48))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 40) (:start . 35)\n (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 44) (:start . 41)\n (:id . 50))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 52)\n (:start . 45) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 55) (:start . 53)\n (:id . 52))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 60) (:start . 56)\n (:id . 53))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 67)\n (:start . 61) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n (:id . 56))\n ((:tag . "JJ") (:stem . "prime") (:form . "prime") (:end . 78) (:start . 73)\n (:id . 57))\n ((:tag . "NN") (:stem . "suspect") (:form . "suspect") (:end . 86)\n (:start . 79) (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 89) (:start . 87)\n (:id . 59))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 95) (:start . 90)\n (:id . 60))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 100) (:start . 96)\n (:id . 61))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 107)\n (:start . 101) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n (:id . 63))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 113) (:start . 109)\n (:id . 64))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 118) (:start . 114)\n (:id . 65))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 124)\n (:start . 119) (:id . 66))\n ((:tag . "NNP") (:stem . "UAA") (:form . "UAA") (:end . 128) (:start . 125)\n (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n (:id . 69))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 139)\n (:start . 131) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n (:id . 71))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 155)\n (:start . 144) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 158) (:start . 156)\n (:id . 73))\n ((:tag . "NN") (:stem . "sense") (:form . "sense") (:end . 164)\n (:start . 159) (:id . 74))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 171)\n (:start . 165) (:id . 75))\n ((:tag . "RB") (:stem . "certainly") (:form . "certainly") (:end . 181)\n (:start . 172) (:id . 76))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 189)\n (:start . 182) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n (:id . 78)))@@@1@37@((:identifiers (:sid . :s1.31) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100031@unknown@formal@none@1@S@Using this clue, computational screening methods of the 23rd amino acid can be designed.@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "clue") (:form . "clue") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n (:id . 45))\n ((:tag . "JJ") (:stem . "computational") (:form . "computational")\n (:end . 30) (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "screening") (:form . "screening") (:end . 40)\n (:start . 31) (:id . 47))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 48)\n (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n (:id . 50))\n ((:tag . "JJ") (:stem . "23rd") (:form . "23rd") (:end . 60) (:start . 56)\n (:id . 51))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 66) (:start . 61)\n (:id . 52))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 71) (:start . 67)\n (:id . 53))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 75) (:start . 72)\n (:id . 54))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 78) (:start . 76)\n (:id . 55))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 87)\n (:start . 79) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.32) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100032@unknown@formal@none@1@S@Recently, Lobanov et al. addressed this problem by searching tRNAs with anticodons corresponding to stop codons 14.@(((:tag . "RB") (:stem . "recently") (:form . "Recently") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NNP") (:stem . "Lobanov") (:form . "Lobanov") (:end . 17)\n (:start . 10) (:id . 44))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 20) (:start . 18)\n (:id . 45))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 24) (:start . 21)\n (:id . 46))\n ((:tag . "VBN") (:stem . "address") (:form . "addressed") (:end . 34)\n (:start . 25) (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 39) (:start . 35)\n (:id . 48))\n ((:tag . "NN") (:stem . "problem") (:form . "problem") (:end . 47)\n (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 50) (:start . 48)\n (:id . 50))\n ((:tag . "VBG") (:stem . "search") (:form . "searching") (:end . 60)\n (:start . 51) (:id . 51))\n ((:tag . "NNS") (:stem . "trna") (:form . "tRNAs") (:end . 66) (:start . 61)\n (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 71) (:start . 67)\n (:id . 53))\n ((:tag . "NNS") (:stem . "anticodon") (:form . "anticodons") (:end . 82)\n (:start . 72) (:id . 54))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 96)\n (:start . 83) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 99) (:start . 97)\n (:id . 56))\n ((:tag . "VB") (:stem . "stop") (:form . "stop") (:end . 104) (:start . 100)\n (:id . 57))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 111)\n (:start . 105) (:id . 58))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 114) (:start . 112)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.33) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100033@unknown@formal@none@1@S@They analyzed 146 prokaryotic genomes, but no likely tRNA of the novel amino acid was detected.@(((:tag . "PRP") (:stem . "they") (:form . "They") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "analyze") (:form . "analyzed") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "CD") (:stem . "146") (:form . "146") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "JJ") (:stem . "prokaryotic") (:form . "prokaryotic") (:end . 29)\n (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 37)\n (:start . 30) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n (:id . 47))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 42) (:start . 39)\n (:id . 48))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 45) (:start . 43)\n (:id . 49))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 52)\n (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "trna") (:form . "tRNA") (:end . 57) (:start . 53)\n (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n (:id . 53))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 70) (:start . 65)\n (:id . 54))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 76) (:start . 71)\n (:id . 55))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 81) (:start . 77)\n (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 85) (:start . 82)\n (:id . 57))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 94)\n (:start . 86) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n (:id . 59)))@@@1@18@((:ncues ((:id . :x1.34.1) (:span 43 45)))\n (:nscopes ((:id . :x1.34.1) (:span 43 94)))\n (:identifiers (:sid . :s1.34) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100034@unknown@formal@none@1@S@They concluded that the 23rd amino acid would have a limited phylogenetic distribution, if it exists.@(((:tag . "PRP") (:stem . "they") (:form . "They") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "conclude") (:form . "concluded") (:end . 14)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "JJ") (:stem . "23rd") (:form . "23rd") (:end . 28) (:start . 24)\n (:id . 46))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 34) (:start . 29)\n (:id . 47))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 39) (:start . 35)\n (:id . 48))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 45) (:start . 40)\n (:id . 49))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 50) (:start . 46)\n (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n (:id . 51))\n ((:tag . "JJ") (:stem . "limited") (:form . "limited") (:end . 60)\n (:start . 53) (:id . 52))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 73)\n (:start . 61) (:id . 53))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 86)\n (:start . 74) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n (:id . 55))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 90) (:start . 88)\n (:id . 56))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 93) (:start . 91)\n (:id . 57))\n ((:tag . "VBZ") (:stem . "exist") (:form . "exists") (:end . 100)\n (:start . 94) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n (:id . 59)))@@@1@18@((:hcues ((:id . :x1.35.1) (:span 40 45)))\n (:hscopes ((:id . :x1.35.1) (:span 40 100)))\n (:identifiers (:sid . :s1.35) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100035@unknown@formal@none@1@S@However, programs for tRNA identification are based on the features of known tRNAs and do not necessarily perform well on unknown ones.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 17)\n (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 21) (:start . 18)\n (:id . 45))\n ((:tag . "NN") (:stem . "trna") (:form . "tRNA") (:end . 26) (:start . 22)\n (:id . 46))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n (:end . 41) (:start . 27) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 45) (:start . 42)\n (:id . 48))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 51) (:start . 46)\n (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 54) (:start . 52)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n (:id . 51))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 67)\n (:start . 59) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n (:id . 53))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 76) (:start . 71)\n (:id . 54))\n ((:tag . "NNS") (:stem . "trna") (:form . "tRNAs") (:end . 82) (:start . 77)\n (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n (:id . 56))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 89) (:start . 87)\n (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 93) (:start . 90)\n (:id . 58))\n ((:tag . "RB") (:stem . "necessarily") (:form . "necessarily") (:end . 105)\n (:start . 94) (:id . 59))\n ((:tag . "VB") (:stem . "perform") (:form . "perform") (:end . 113)\n (:start . 106) (:id . 60))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 118) (:start . 114)\n (:id . 61))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 121) (:start . 119)\n (:id . 62))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 129)\n (:start . 122) (:id . 63))\n ((:tag . "NNS") (:stem . "one") (:form . "ones") (:end . 134) (:start . 130)\n (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s1.36) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100036@unknown@formal@none@1@S@Actually, tRNASec and tRNAPyl have unusual secondary structures 515 and often escape detection by programs without special consideration.@(((:tag . "RB") (:stem . "actually") (:form . "Actually") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "trnasec") (:form . "tRNASec") (:end . 17)\n (:start . 10) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n (:id . 45))\n ((:tag . "NN") (:stem . "trnapyl") (:form . "tRNAPyl") (:end . 29)\n (:start . 22) (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 34) (:start . 30)\n (:id . 47))\n ((:tag . "JJ") (:stem . "unusual") (:form . "unusual") (:end . 42)\n (:start . 35) (:id . 48))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 52)\n (:start . 43) (:id . 49))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 63)\n (:start . 53) (:id . 50))\n ((:tag . "CD") (:stem . "515") (:form . "515") (:end . 67) (:start . 64)\n (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n (:id . 52))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 77) (:start . 72)\n (:id . 53))\n ((:tag . "VBP") (:stem . "escape") (:form . "escape") (:end . 84)\n (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "detection") (:form . "detection") (:end . 94)\n (:start . 85) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 97) (:start . 95)\n (:id . 56))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 106)\n (:start . 98) (:id . 57))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 114)\n (:start . 107) (:id . 58))\n ((:tag . "JJ") (:stem . "special") (:form . "special") (:end . 122)\n (:start . 115) (:id . 59))\n ((:tag . "NN") (:stem . "consideration") (:form . "consideration")\n (:end . 136) (:start . 123) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n (:id . 61)))@@@1@20@((:ncues ((:id . :x1.37.1) (:span 107 114)))\n (:nscopes ((:id . :x1.37.1) (:span 107 136)))\n (:identifiers (:sid . :s1.37) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100037@unknown@formal@none@1@S@Lobanov et al. thus developed a sensitive search method to deal with this problem, but they also admitted that it would fail to identify highly unusual tRNAs.@(((:tag . "NNP") (:stem . "Lobanov") (:form . "Lobanov") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 10) (:start . 8)\n (:id . 43))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 19) (:start . 15)\n (:id . 45))\n ((:tag . "VBD") (:stem . "develop") (:form . "developed") (:end . 29)\n (:start . 20) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 31) (:start . 30)\n (:id . 47))\n ((:tag . "JJ") (:stem . "sensitive") (:form . "sensitive") (:end . 41)\n (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 48)\n (:start . 42) (:id . 49))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 55)\n (:start . 49) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n (:id . 51))\n ((:tag . "VB") (:stem . "deal") (:form . "deal") (:end . 63) (:start . 59)\n (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 68) (:start . 64)\n (:id . 53))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 73) (:start . 69)\n (:id . 54))\n ((:tag . "NN") (:stem . "problem") (:form . "problem") (:end . 81)\n (:start . 74) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n (:id . 56))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 86) (:start . 83)\n (:id . 57))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 91) (:start . 87)\n (:id . 58))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 96) (:start . 92)\n (:id . 59))\n ((:tag . "VBD") (:stem . "admit") (:form . "admitted") (:end . 105)\n (:start . 97) (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 110) (:start . 106)\n (:id . 61))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 113) (:start . 111)\n (:id . 62))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 119)\n (:start . 114) (:id . 63))\n ((:tag . "VB") (:stem . "fail") (:form . "fail") (:end . 124) (:start . 120)\n (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 127) (:start . 125)\n (:id . 65))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 136)\n (:start . 128) (:id . 66))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 143)\n (:start . 137) (:id . 67))\n ((:tag . "JJ") (:stem . "unusual") (:form . "unusual") (:end . 151)\n (:start . 144) (:id . 68))\n ((:tag . "NNS") (:stem . "trna") (:form . "tRNAs") (:end . 157)\n (:start . 152) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x1.38.2) (:span 114 119)))\n (:ncues ((:id . :x1.38.1) (:span 120 124)))\n (:hscopes ((:id . :x1.38.2) (:span 114 157)))\n (:nscopes ((:id . :x1.38.1) (:span 120 157)))\n (:identifiers (:sid . :s1.38) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100038@unknown@formal@none@1@S@There is another approach to searching for the 23rd amino acid.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n (:id . 43))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 16)\n (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 25)\n (:start . 17) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "VBG") (:stem . "search") (:form . "searching") (:end . 38)\n (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 42) (:start . 39)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n (:id . 49))\n ((:tag . "JJ") (:stem . "23rd") (:form . "23rd") (:end . 51) (:start . 47)\n (:id . 50))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 57) (:start . 52)\n (:id . 51))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 62) (:start . 58)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s1.39) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100040@unknown@formal@none@1@S@Because such an ORF-based study is independent from the tRNA analysis, it can either identify candidate organisms missed by the previous study or strengthen its negative conclusion.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "PDT") (:stem . "such") (:form . "such") (:end . 12) (:start . 8)\n (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "orf-based") (:form . "ORF-based") (:end . 25)\n (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 31) (:start . 26)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 34) (:start . 32)\n (:id . 47))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 46)\n (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 51) (:start . 47)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n (:id . 50))\n ((:tag . "NN") (:stem . "trna") (:form . "tRNA") (:end . 60) (:start . 56)\n (:id . 51))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 69)\n (:start . 61) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n (:id . 53))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 73) (:start . 71)\n (:id . 54))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 77) (:start . 74)\n (:id . 55))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 84)\n (:start . 78) (:id . 56))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 93)\n (:start . 85) (:id . 57))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 103)\n (:start . 94) (:id . 58))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 113)\n (:start . 104) (:id . 59))\n ((:tag . "VBN") (:stem . "miss") (:form . "missed") (:end . 120)\n (:start . 114) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 123) (:start . 121)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n (:id . 62))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 136)\n (:start . 128) (:id . 63))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 142)\n (:start . 137) (:id . 64))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 145) (:start . 143)\n (:id . 65))\n ((:tag . "VB") (:stem . "strengthen") (:form . "strengthen") (:end . 156)\n (:start . 146) (:id . 66))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 160) (:start . 157)\n (:id . 67))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 169)\n (:start . 161) (:id . 68))\n ((:tag . "NN") (:stem . "conclusion") (:form . "conclusion") (:end . 180)\n (:start . 170) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x1.41.1) (:span 78 84 143 145)))\n (:hscopes ((:id . :x1.41.1) (:span 78 180)))\n (:identifiers (:sid . :s1.41) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100041@unknown@formal@none@1@S@Here we report a comprehensive analysis of prokaryotic ORFs that contain an inframe stop codon.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "VBP") (:stem . "report") (:form . "report") (:end . 14)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n (:id . 45))\n ((:tag . "JJ") (:stem . "comprehensive") (:form . "comprehensive")\n (:end . 30) (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 39)\n (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n (:id . 48))\n ((:tag . "JJ") (:stem . "prokaryotic") (:form . "prokaryotic") (:end . 54)\n (:start . 43) (:id . 49))\n ((:tag . "NNS") (:stem . "orf") (:form . "ORFs") (:end . 59) (:start . 55)\n (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 64) (:start . 60)\n (:id . 51))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 72)\n (:start . 65) (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 75) (:start . 73)\n (:id . 53))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 83)\n (:start . 76) (:id . 54))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 88) (:start . 84)\n (:id . 55))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 94) (:start . 89)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.42) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100042@unknown@formal@none@1@S@Through enumeration of theoretical ORFs and inspection of their evolutionary conservation, candidates of readthrough proteins were predicted.@(((:tag . "IN") (:stem . "through") (:form . "Through") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "enumeration") (:form . "enumeration") (:end . 19)\n (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n (:id . 44))\n ((:tag . "JJ") (:stem . "theoretical") (:form . "theoretical") (:end . 34)\n (:start . 23) (:id . 45))\n ((:tag . "NNS") (:stem . "orf") (:form . "ORFs") (:end . 39) (:start . 35)\n (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n (:id . 47))\n ((:tag . "NN") (:stem . "inspection") (:form . "inspection") (:end . 54)\n (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n (:id . 49))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 63)\n (:start . 58) (:id . 50))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 76)\n (:start . 64) (:id . 51))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 89)\n (:start . 77) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n (:id . 53))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 101)\n (:start . 91) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n (:id . 55))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 116)\n (:start . 105) (:id . 56))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 125)\n (:start . 117) (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 130) (:start . 126)\n (:id . 58))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 140)\n (:start . 131) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.43) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100043@unknown@formal@none@1@S@They contained many of the known proteins with stop-codon-encoded amino acids, but almost no novel candidates were identified.@(((:tag . "PRP") (:stem . "they") (:form . "They") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 14)\n (:start . 5) (:id . 43))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 32) (:start . 27)\n (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 41)\n (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 46) (:start . 42)\n (:id . 49))\n ((:tag . "JJ") (:stem . "stop-codon-encoded") (:form . "stop-codon-encoded")\n (:end . 65) (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 71) (:start . 66)\n (:id . 51))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 77) (:start . 72)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n (:id . 53))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 82) (:start . 79)\n (:id . 54))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 89)\n (:start . 83) (:id . 55))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 92) (:start . 90)\n (:id . 56))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 98) (:start . 93)\n (:id . 57))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 109)\n (:start . 99) (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 114) (:start . 110)\n (:id . 59))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 125)\n (:start . 115) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.44) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100044@unknown@formal@none@1@S@Therefore, the unknown amino acid, if it is encoded by a stop codon, is unlikely to exist in the current databases of microbial genomes.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 22)\n (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 28) (:start . 23)\n (:id . 46))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n (:id . 48))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 37) (:start . 35)\n (:id . 49))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 40) (:start . 38)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 43) (:start . 41)\n (:id . 51))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 51)\n (:start . 44) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 54) (:start . 52)\n (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 56) (:start . 55)\n (:id . 54))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 61) (:start . 57)\n (:id . 55))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 67) (:start . 62)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 71) (:start . 69)\n (:id . 58))\n ((:tag . "JJ") (:stem . "unlikely") (:form . "unlikely") (:end . 80)\n (:start . 72) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 83) (:start . 81)\n (:id . 60))\n ((:tag . "VB") (:stem . "exist") (:form . "exist") (:end . 89) (:start . 84)\n (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n (:id . 63))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 104)\n (:start . 97) (:id . 64))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 114)\n (:start . 105) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 117) (:start . 115)\n (:id . 66))\n ((:tag . "JJ") (:stem . "microbial") (:form . "microbial") (:end . 127)\n (:start . 118) (:id . 67))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 135)\n (:start . 128) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n (:id . 69)))@@@1@28@((:hcues ((:id . :x1.45.1) (:span 72 80)))\n (:hscopes ((:id . :x1.45.1) (:span 11 135)))\n (:identifiers (:sid . :s1.45) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100045@unknown@formal@none@1@S@The consequences for selenoproteins and other readthrough genes are also discussed.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "consequence") (:form . "consequences") (:end . 16)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 20) (:start . 17)\n (:id . 44))\n ((:tag . "NNS") (:stem . "selenoprotein") (:form . "selenoproteins")\n (:end . 35) (:start . 21) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n (:id . 46))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 45) (:start . 40)\n (:id . 47))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 57)\n (:start . 46) (:id . 48))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 63) (:start . 58)\n (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 67) (:start . 64)\n (:id . 50))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 72) (:start . 68)\n (:id . 51))\n ((:tag . "VBN") (:stem . "discuss") (:form . "discussed") (:end . 82)\n (:start . 73) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s1.46) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100046@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s1.47) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011 5100047@unknown@formal@none@1@S@Basic ideas@(((:tag . "JJ") (:stem . "basic") (:form . "Basic") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "idea") (:form . "ideas") (:end . 11) (:start . 6)\n (:id . 43)))@@@1@2@((:identifiers (:sid . :s1.48) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100048@unknown@formal@none@1@S@In this study, we focus on theoretical ORFs with one inframe stop codon, termed "interrupted ORFs" (iORFs) (Figure 1a).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n (:id . 46))\n ((:tag . "VBP") (:stem . "focus") (:form . "focus") (:end . 23) (:start . 18)\n (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 26) (:start . 24)\n (:id . 48))\n ((:tag . "JJ") (:stem . "theoretical") (:form . "theoretical") (:end . 38)\n (:start . 27) (:id . 49))\n ((:tag . "NNS") (:stem . "orf") (:form . "ORFs") (:end . 43) (:start . 39)\n (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 48) (:start . 44)\n (:id . 51))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 52) (:start . 49)\n (:id . 52))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 60)\n (:start . 53) (:id . 53))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 65) (:start . 61)\n (:id . 54))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 71) (:start . 66)\n (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n (:id . 56))\n ((:tag . "VBN") (:stem . "term") (:form . "termed") (:end . 79) (:start . 73)\n (:id . 57))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 81) (:start . 80)\n (:id . 58))\n ((:tag . "JJ") (:stem . "interrupted") (:form . "interrupted") (:end . 92)\n (:start . 81) (:id . 59))\n ((:tag . "NNS") (:stem . "orf") (:form . "ORFs") (:end . 97) (:start . 93)\n (:id . 60))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 98) (:start . 97)\n (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n (:id . 62))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 105)\n (:start . 100) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 114)\n (:start . 108) (:id . 66))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 117) (:start . 115)\n (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.49) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100050@unknown@formal@none@1@S@However, the vast majority of the enumerated iORFs will be biologically meaningless.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "JJ") (:stem . "vast") (:form . "vast") (:end . 17) (:start . 13)\n (:id . 45))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 26)\n (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 48))\n ((:tag . "VBN") (:stem . "enumerate") (:form . "enumerated") (:end . 44)\n (:start . 34) (:id . 49))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 50) (:start . 45)\n (:id . 50))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 55) (:start . 51)\n (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 58) (:start . 56)\n (:id . 52))\n ((:tag . "RB") (:stem . "biologically") (:form . "biologically") (:end . 71)\n (:start . 59) (:id . 53))\n ((:tag . "JJ") (:stem . "meaningless") (:form . "meaningless") (:end . 83)\n (:start . 72) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s1.51) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100051@unknown@formal@none@1@S@To filter out such meaningless iORFs, we required the iORFs to have at least one homolog in other genomes, because evolutionary conservation of primary sequence is a strong indicator of functional importance.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "filter") (:form . "filter") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 18) (:start . 14)\n (:id . 45))\n ((:tag . "JJ") (:stem . "meaningless") (:form . "meaningless") (:end . 30)\n (:start . 19) (:id . 46))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 36) (:start . 31)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 40) (:start . 38)\n (:id . 49))\n ((:tag . "VBD") (:stem . "require") (:form . "required") (:end . 49)\n (:start . 41) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n (:id . 51))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 59) (:start . 54)\n (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 62) (:start . 60)\n (:id . 53))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 67) (:start . 63)\n (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 70) (:start . 68)\n (:id . 55))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 76) (:start . 71)\n (:id . 56))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 80) (:start . 77)\n (:id . 57))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 88)\n (:start . 81) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n (:id . 59))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 97) (:start . 92)\n (:id . 60))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 105)\n (:start . 98) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n (:id . 62))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 114)\n (:start . 107) (:id . 63))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 127)\n (:start . 115) (:id . 64))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 140)\n (:start . 128) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 143) (:start . 141)\n (:id . 66))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 151)\n (:start . 144) (:id . 67))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 160)\n (:start . 152) (:id . 68))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 163) (:start . 161)\n (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 165) (:start . 164)\n (:id . 70))\n ((:tag . "JJ") (:stem . "strong") (:form . "strong") (:end . 172)\n (:start . 166) (:id . 71))\n ((:tag . "NN") (:stem . "indicator") (:form . "indicator") (:end . 182)\n (:start . 173) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 185) (:start . 183)\n (:id . 73))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 196)\n (:start . 186) (:id . 74))\n ((:tag . "NN") (:stem . "importance") (:form . "importance") (:end . 207)\n (:start . 197) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s1.52) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100052@unknown@formal@none@1@S@However, this condition is not sufficient, since two major problems remain:: pseudogenes and two adjacent genes.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "condition") (:form . "condition") (:end . 23)\n (:start . 14) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 30) (:start . 27)\n (:id . 47))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 41)\n (:start . 31) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n (:id . 49))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 48) (:start . 43)\n (:id . 50))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 52) (:start . 49)\n (:id . 51))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 58) (:start . 53)\n (:id . 52))\n ((:tag . "NNS") (:stem . "problem") (:form . "problems") (:end . 67)\n (:start . 59) (:id . 53))\n ((:tag . "VBP") (:stem . "remain") (:form . "remain") (:end . 74)\n (:start . 68) (:id . 54))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 75) (:start . 74)\n (:id . 55))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 76) (:start . 75)\n (:id . 56))\n ((:tag . "NNS") (:stem . "pseudogene") (:form . "pseudogenes") (:end . 88)\n (:start . 77) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n (:id . 58))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 96) (:start . 93)\n (:id . 59))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 105)\n (:start . 97) (:id . 60))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 111)\n (:start . 106) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n (:id . 62)))@@@1@21@((:ncues ((:id . :x1.53.1) (:span 27 30)))\n (:nscopes ((:id . :x1.53.1) (:span 27 41)))\n (:identifiers (:sid . :s1.53) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100053@unknown@formal@none@1@S@The first problem is that even if an iORF has homologs in other species, it could be a pseudogene or a product of sequencing error.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "problem") (:form . "problem") (:end . 17)\n (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 20) (:start . 18)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n (:id . 46))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 30) (:start . 26)\n (:id . 47))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 33) (:start . 31)\n (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 36) (:start . 34)\n (:id . 49))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 41) (:start . 37)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 45) (:start . 42)\n (:id . 51))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 54)\n (:start . 46) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n (:id . 53))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 63) (:start . 58)\n (:id . 54))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 71)\n (:start . 64) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n (:id . 56))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 75) (:start . 73)\n (:id . 57))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 81) (:start . 76)\n (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 84) (:start . 82)\n (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 86) (:start . 85)\n (:id . 60))\n ((:tag . "NN") (:stem . "pseudogene") (:form . "pseudogene") (:end . 97)\n (:start . 87) (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 100) (:start . 98)\n (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 102) (:start . 101)\n (:id . 63))\n ((:tag . "NN") (:stem . "product") (:form . "product") (:end . 110)\n (:start . 103) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n (:id . 65))\n ((:tag . "NN") (:stem . "sequencing") (:form . "sequencing") (:end . 124)\n (:start . 114) (:id . 66))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 130)\n (:start . 125) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n (:id . 68)))@@@1@27@((:hcues ((:id . :x1.54.1) (:span 98 100)) ((:id . :x1.54.2) (:span 76 81)))\n (:hscopes ((:id . :x1.54.1) (:span 85 130))\n ((:id . :x1.54.2) (:span 76 130)))\n (:identifiers (:sid . :s1.54) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100054@unknown@formal@none@1@S@The second problem is that adjacent genes on the same reading frame may satisfy the condition of conserved iORFs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "problem") (:form . "problem") (:end . 18)\n (:start . 11) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n (:id . 46))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 35)\n (:start . 27) (:id . 47))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 41) (:start . 36)\n (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 44) (:start . 42)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n (:id . 50))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 53) (:start . 49)\n (:id . 51))\n ((:tag . "NN") (:stem . "reading") (:form . "reading") (:end . 61)\n (:start . 54) (:id . 52))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 67) (:start . 62)\n (:id . 53))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 71) (:start . 68)\n (:id . 54))\n ((:tag . "VB") (:stem . "satisfy") (:form . "satisfy") (:end . 79)\n (:start . 72) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n (:id . 56))\n ((:tag . "NN") (:stem . "condition") (:form . "condition") (:end . 93)\n (:start . 84) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n (:id . 58))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 106)\n (:start . 97) (:id . 59))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 112)\n (:start . 107) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n (:id . 61)))@@@1@20@((:hcues ((:id . :x1.55.1) (:span 68 71)))\n (:hscopes ((:id . :x1.55.1) (:span 68 112)))\n (:identifiers (:sid . :s1.55) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100055@unknown@formal@none@1@S@In particular, gene pairs within an operon are problematic because their gene arrangement is often conserved.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 13)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 44))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 19) (:start . 15)\n (:id . 45))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 25) (:start . 20)\n (:id . 46))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 32)\n (:start . 26) (:id . 47))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 35) (:start . 33)\n (:id . 48))\n ((:tag . "NN") (:stem . "operon") (:form . "operon") (:end . 42)\n (:start . 36) (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 46) (:start . 43)\n (:id . 50))\n ((:tag . "JJ") (:stem . "problematic") (:form . "problematic") (:end . 58)\n (:start . 47) (:id . 51))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 66)\n (:start . 59) (:id . 52))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 72)\n (:start . 67) (:id . 53))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 77) (:start . 73)\n (:id . 54))\n ((:tag . "NN") (:stem . "arrangement") (:form . "arrangement") (:end . 89)\n (:start . 78) (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 92) (:start . 90)\n (:id . 56))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 98) (:start . 93)\n (:id . 57))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 108)\n (:start . 99) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s1.56) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100056@unknown@formal@none@1@S@If the intergenic distance between two genes in an operon happens to be a multiple of three, they look like a conserved readthrough gene.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "intergenic") (:form . "intergenic") (:end . 17)\n (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 26)\n (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 34)\n (:start . 27) (:id . 46))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 38) (:start . 35)\n (:id . 47))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 44) (:start . 39)\n (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 50) (:start . 48)\n (:id . 50))\n ((:tag . "NN") (:stem . "operon") (:form . "operon") (:end . 57)\n (:start . 51) (:id . 51))\n ((:tag . "VBZ") (:stem . "happen") (:form . "happens") (:end . 65)\n (:start . 58) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 71) (:start . 69)\n (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n (:id . 55))\n ((:tag . "NN") (:stem . "multiple") (:form . "multiple") (:end . 82)\n (:start . 74) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n (:id . 57))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 91) (:start . 86)\n (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n (:id . 59))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 97) (:start . 93)\n (:id . 60))\n ((:tag . "VBP") (:stem . "look") (:form . "look") (:end . 102) (:start . 98)\n (:id . 61))\n ((:tag . "IN") (:stem . "like") (:form . "like") (:end . 107) (:start . 103)\n (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 109) (:start . 108)\n (:id . 63))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 119)\n (:start . 110) (:id . 64))\n ((:tag . "NN") (:stem . "readthrough") (:form . "readthrough") (:end . 131)\n (:start . 120) (:id . 65))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 136) (:start . 132)\n (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n (:id . 67)))@@@1@26@((:hcues ((:id . :x1.57.1) (:span 98 107)) ((:id . :x1.57.2) (:span 58 65)))\n (:hscopes ((:id . :x1.57.1) (:span 98 136)) ((:id . :x1.57.2) (:span 3 91)))\n (:identifiers (:sid . :s1.57) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100057@unknown@formal@none@1@S@Basic ideas of the prediction method@(((:tag . "JJ") (:stem . "basic") (:form . "Basic") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "idea") (:form . "ideas") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 29)\n (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 36)\n (:start . 30) (:id . 47)))@@@1@6@((:identifiers (:sid . :s1.58) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5100058@unknown@formal@none@1@S@Basic ideas of the prediction method.@(((:tag . "JJ") (:stem . "basic") (:form . "Basic") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "idea") (:form . "ideas") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 29)\n (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 36)\n (:start . 30) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 37) (:start . 36)\n (:id . 48)))@@@1@7@((:identifiers (:sid . :s1.59) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100060@unknown@formal@none@1@S@(b) Readthrough genes can be distinguished from two adjacent genes based on the results of BLAST searches.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "LS") (:stem . "b") (:form . "b") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "IN") (:stem . "readthrough") (:form . "Readthrough") (:end . 15)\n (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 21) (:start . 16)\n (:id . 46))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 25) (:start . 22)\n (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 28) (:start . 26)\n (:id . 48))\n ((:tag . "VBN") (:stem . "distinguish") (:form . "distinguished") (:end . 42)\n (:start . 29) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 47) (:start . 43)\n (:id . 50))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 51) (:start . 48)\n (:id . 51))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 60)\n (:start . 52) (:id . 52))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 66) (:start . 61)\n (:id . 53))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 72) (:start . 67)\n (:id . 54))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 75) (:start . 73)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n (:id . 56))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 87)\n (:start . 80) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n (:id . 58))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 96) (:start . 91)\n (:id . 59))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 105)\n (:start . 97) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.61) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100061@unknown@formal@none@1@S@Boxes denote iORFs, and × indicates the inframe stop codon.@(((:tag . "NNPS") (:stem . "Box") (:form . "Boxes") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "denote") (:form . "denote") (:end . 12)\n (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n (:id . 46))\n ((:tag . "NNP") (:stem . "×") (:form . "×") (:end . 25) (:start . 24)\n (:id . 47))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 35)\n (:start . 26) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 49))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 47)\n (:start . 40) (:id . 50))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 52) (:start . 48)\n (:id . 51))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 58) (:start . 53)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 59) (:start . 58)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s1.62) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100062@unknown@formal@none@1@S@Shaded regions represent actual protein-coding regions.@(((:tag . "JJ") (:stem . "shaded") (:form . "Shaded") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 14)\n (:start . 7) (:id . 43))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 24)\n (:start . 15) (:id . 44))\n ((:tag . "JJ") (:stem . "actual") (:form . "actual") (:end . 31)\n (:start . 25) (:id . 45))\n ((:tag . "JJ") (:stem . "protein-coding") (:form . "protein-coding")\n (:end . 46) (:start . 32) (:id . 46))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 54)\n (:start . 47) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 55) (:start . 54)\n (:id . 48)))@@@1@7@((:identifiers (:sid . :s1.63) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100063@unknown@formal@none@1@S@If an iORF codes a readthrough protein, BLAST hits from other organisms will cover the inframe stop codon.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 10) (:start . 6)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "cod") (:form . "codes") (:end . 16) (:start . 11)\n (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 18) (:start . 17)\n (:id . 46))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 30)\n (:start . 19) (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 38)\n (:start . 31) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n (:id . 49))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 45) (:start . 40)\n (:id . 50))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 50) (:start . 46)\n (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 55) (:start . 51)\n (:id . 52))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 61) (:start . 56)\n (:id . 53))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 71)\n (:start . 62) (:id . 54))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 76) (:start . 72)\n (:id . 55))\n ((:tag . "VB") (:stem . "cover") (:form . "cover") (:end . 82) (:start . 77)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n (:id . 57))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 94)\n (:start . 87) (:id . 58))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 99) (:start . 95)\n (:id . 59))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 105)\n (:start . 100) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.64) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100064@unknown@formal@none@1@S@In contrast, if the iORF consists of two adjacent genes, many hits that do not cover the inframe stop codon will be found.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 46))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 24) (:start . 20)\n (:id . 47))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 33)\n (:start . 25) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n (:id . 49))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 40) (:start . 37)\n (:id . 50))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 49)\n (:start . 41) (:id . 51))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 55) (:start . 50)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n (:id . 53))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 61) (:start . 57)\n (:id . 54))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 66) (:start . 62)\n (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 71) (:start . 67)\n (:id . 56))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 74) (:start . 72)\n (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 78) (:start . 75)\n (:id . 58))\n ((:tag . "VB") (:stem . "cover") (:form . "cover") (:end . 84) (:start . 79)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n (:id . 60))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 96)\n (:start . 89) (:id . 61))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 101) (:start . 97)\n (:id . 62))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 107)\n (:start . 102) (:id . 63))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 112) (:start . 108)\n (:id . 64))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 115) (:start . 113)\n (:id . 65))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 121)\n (:start . 116) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n (:id . 67)))@@@1@26@((:ncues ((:id . :x1.65.1) (:span 75 78)))\n (:nscopes ((:id . :x1.65.1) (:span 75 107)))\n (:identifiers (:sid . :s1.65) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100065@unknown@formal@none@1@S@To discriminate them from true readthrough genes, evolutionary information was exploited.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "discriminate") (:form . "discriminate") (:end . 15)\n (:start . 3) (:id . 43))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 20) (:start . 16)\n (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 25) (:start . 21)\n (:id . 45))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 30) (:start . 26)\n (:id . 46))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 42)\n (:start . 31) (:id . 47))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 48) (:start . 43)\n (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n (:id . 49))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 62)\n (:start . 50) (:id . 50))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 74)\n (:start . 63) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 78) (:start . 75)\n (:id . 52))\n ((:tag . "VBN") (:stem . "exploit") (:form . "exploited") (:end . 88)\n (:start . 79) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s1.66) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100066@unknown@formal@none@1@S@In order to eliminate pseudogenes and sequencing errors, conservation of iORFs and their inframe stop codons was examined.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "VB") (:stem . "eliminate") (:form . "eliminate") (:end . 21)\n (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "pseudogene") (:form . "pseudogenes") (:end . 33)\n (:start . 22) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n (:id . 47))\n ((:tag . "NN") (:stem . "sequencing") (:form . "sequencing") (:end . 48)\n (:start . 38) (:id . 48))\n ((:tag . "NNS") (:stem . "error") (:form . "errors") (:end . 55)\n (:start . 49) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n (:id . 50))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 69)\n (:start . 57) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n (:id . 52))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 78) (:start . 73)\n (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n (:id . 54))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 88)\n (:start . 83) (:id . 55))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 96)\n (:start . 89) (:id . 56))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 101) (:start . 97)\n (:id . 57))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 108)\n (:start . 102) (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 112) (:start . 109)\n (:id . 59))\n ((:tag . "VBN") (:stem . "examine") (:form . "examined") (:end . 121)\n (:start . 113) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.67) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100067@unknown@formal@none@1@S@Since pseudogenes are less conserved, and sequencing errors are relatively rare events, they will not have homologous iORFs in other species.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "pseudogene") (:form . "pseudogenes") (:end . 17)\n (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 21) (:start . 18)\n (:id . 44))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 26) (:start . 22)\n (:id . 45))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 36)\n (:start . 27) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n (:id . 48))\n ((:tag . "NN") (:stem . "sequencing") (:form . "sequencing") (:end . 52)\n (:start . 42) (:id . 49))\n ((:tag . "NNS") (:stem . "error") (:form . "errors") (:end . 59)\n (:start . 53) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 63) (:start . 60)\n (:id . 51))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 74)\n (:start . 64) (:id . 52))\n ((:tag . "JJ") (:stem . "rare") (:form . "rare") (:end . 79) (:start . 75)\n (:id . 53))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 86)\n (:start . 80) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n (:id . 55))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 92) (:start . 88)\n (:id . 56))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 97) (:start . 93)\n (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 101) (:start . 98)\n (:id . 58))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 106) (:start . 102)\n (:id . 59))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 117)\n (:start . 107) (:id . 60))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 123)\n (:start . 118) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 126) (:start . 124)\n (:id . 62))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 132)\n (:start . 127) (:id . 63))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 140)\n (:start . 133) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n (:id . 65)))@@@1@24@((:ncues ((:id . :x1.68.1) (:span 98 101)))\n (:nscopes ((:id . :x1.68.1) (:span 98 140)))\n (:identifiers (:sid . :s1.68) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100068@unknown@formal@none@1@S@Even if they do, the position or type (UAA, UAG or UGA) of their inframe stop codons will not coincide.@(((:tag . "RB") (:stem . "even") (:form . "Even") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 47))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 29)\n (:start . 21) (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 32) (:start . 30)\n (:id . 49))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 37) (:start . 33)\n (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 39) (:start . 38)\n (:id . 51))\n ((:tag . "NNP") (:stem . "UAA") (:form . "UAA") (:end . 42) (:start . 39)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n (:id . 53))\n ((:tag . "NNP") (:stem . "UAG") (:form . "UAG") (:end . 47) (:start . 44)\n (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 50) (:start . 48)\n (:id . 55))\n ((:tag . "NNP") (:stem . "UGA") (:form . "UGA") (:end . 54) (:start . 51)\n (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n (:id . 58))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 64)\n (:start . 59) (:id . 59))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 72)\n (:start . 65) (:id . 60))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 77) (:start . 73)\n (:id . 61))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 84)\n (:start . 78) (:id . 62))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 89) (:start . 85)\n (:id . 63))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 93) (:start . 90)\n (:id . 64))\n ((:tag . "VB") (:stem . "coincide") (:form . "coincide") (:end . 102)\n (:start . 94) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n (:id . 66)))@@@1@25@((:ncues ((:id . :x1.69.1) (:span 90 93)))\n (:nscopes ((:id . :x1.69.1) (:span 90 102)))\n (:identifiers (:sid . :s1.69) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100070@unknown@formal@none@1@S@A drawback of this criterion is that it limits the target of our study to readthrough genes conserved across two or more species.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "drawback") (:form . "drawback") (:end . 10)\n (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 18) (:start . 14)\n (:id . 45))\n ((:tag . "NN") (:stem . "criterion") (:form . "criterion") (:end . 28)\n (:start . 19) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 31) (:start . 29)\n (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 36) (:start . 32)\n (:id . 48))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 39) (:start . 37)\n (:id . 49))\n ((:tag . "VBZ") (:stem . "limit") (:form . "limits") (:end . 46)\n (:start . 40) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n (:id . 51))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 57)\n (:start . 51) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n (:id . 53))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 64) (:start . 61)\n (:id . 54))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 70) (:start . 65)\n (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n (:id . 56))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 85)\n (:start . 74) (:id . 57))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 91) (:start . 86)\n (:id . 58))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 101)\n (:start . 92) (:id . 59))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 108)\n (:start . 102) (:id . 60))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 112) (:start . 109)\n (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 115) (:start . 113)\n (:id . 62))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 120) (:start . 116)\n (:id . 63))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 128)\n (:start . 121) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s1.71) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100071@unknown@formal@none@1@S@In other words, species-specific readthrough genes are not in the scope of this study.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "NNS") (:stem . "word") (:form . "words") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n (:id . 45))\n ((:tag . "JJ") (:stem . "species-specific") (:form . "species-specific")\n (:end . 32) (:start . 16) (:id . 46))\n ((:tag . "NN") (:stem . "readthrough") (:form . "readthrough") (:end . 44)\n (:start . 33) (:id . 47))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 50) (:start . 45)\n (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 54) (:start . 51)\n (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 58) (:start . 55)\n (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n (:id . 52))\n ((:tag . "NN") (:stem . "scope") (:form . "scope") (:end . 71) (:start . 66)\n (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n (:id . 54))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 79) (:start . 75)\n (:id . 55))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 85) (:start . 80)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n (:id . 57)))@@@1@16@((:ncues ((:id . :x1.72.1) (:span 55 58)))\n (:nscopes ((:id . :x1.72.1) (:span 55 85)))\n (:identifiers (:sid . :s1.72) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100072@unknown@formal@none@1@S@To address the second problem, adjacent gene pairs were filtered out by examining boundaries of sequence alignments between iORFs and its homologs (Figure 1b).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "address") (:form . "address") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 21)\n (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "problem") (:form . "problem") (:end . 29)\n (:start . 22) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n (:id . 47))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 39)\n (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 44) (:start . 40)\n (:id . 49))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 50) (:start . 45)\n (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 55) (:start . 51)\n (:id . 51))\n ((:tag . "VBN") (:stem . "filter") (:form . "filtered") (:end . 64)\n (:start . 56) (:id . 52))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 68) (:start . 65)\n (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 71) (:start . 69)\n (:id . 54))\n ((:tag . "VBG") (:stem . "examine") (:form . "examining") (:end . 81)\n (:start . 72) (:id . 55))\n ((:tag . "NNS") (:stem . "boundary") (:form . "boundaries") (:end . 92)\n (:start . 82) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n (:id . 57))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 104)\n (:start . 96) (:id . 58))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 115)\n (:start . 105) (:id . 59))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 123)\n (:start . 116) (:id . 60))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 129)\n (:start . 124) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 133) (:start . 130)\n (:id . 62))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 137) (:start . 134)\n (:id . 63))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 146)\n (:start . 138) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 154)\n (:start . 148) (:id . 66))\n ((:tag . "NN") (:stem . "1b") (:form . "1b") (:end . 157) (:start . 155)\n (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.73) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100073@unknown@formal@none@1@S@The stop-codon-encoded amino acids of prokaryotes are usually located inside domains, the units of evolutionary sequence conservation.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "stop-codon-encoded") (:form . "stop-codon-encoded")\n (:end . 22) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 28) (:start . 23)\n (:id . 44))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 34) (:start . 29)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n (:id . 46))\n ((:tag . "NNS") (:stem . "prokaryote") (:form . "prokaryotes") (:end . 49)\n (:start . 38) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 53) (:start . 50)\n (:id . 48))\n ((:tag . "RB") (:stem . "usually") (:form . "usually") (:end . 61)\n (:start . 54) (:id . 49))\n ((:tag . "VBN") (:stem . "locate") (:form . "located") (:end . 69)\n (:start . 62) (:id . 50))\n ((:tag . "IN") (:stem . "inside") (:form . "inside") (:end . 76)\n (:start . 70) (:id . 51))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 84)\n (:start . 77) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n (:id . 54))\n ((:tag . "NNS") (:stem . "unit") (:form . "units") (:end . 95) (:start . 90)\n (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n (:id . 56))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 111)\n (:start . 99) (:id . 57))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 120)\n (:start . 112) (:id . 58))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 133)\n (:start . 121) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.74) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100074@unknown@formal@none@1@S@Therefore, the aligned regions of readthrough proteins contain their inframe stop codon.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "JJ") (:stem . "aligned") (:form . "aligned") (:end . 22)\n (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 30)\n (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n (:id . 47))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 45)\n (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 54)\n (:start . 46) (:id . 49))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 62)\n (:start . 55) (:id . 50))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 68)\n (:start . 63) (:id . 51))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 76)\n (:start . 69) (:id . 52))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 81) (:start . 77)\n (:id . 53))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 87) (:start . 82)\n (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s1.75) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100075@unknown@formal@none@1@S@Based on this observation, each iORF was required to have:: (i) at least one homolog from other organisms that covers the inframe stop codon and (ii) no homolog that does not cover the stop codon.@(((:tag . "VBN") (:stem . "base") (:form . "Based") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 8) (:start . 6)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 25)\n (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n (:id . 46))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 31) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 36) (:start . 32)\n (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 40) (:start . 37)\n (:id . 49))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 49)\n (:start . 41) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n (:id . 51))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 57) (:start . 53)\n (:id . 52))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 58) (:start . 57)\n (:id . 53))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 59) (:start . 58)\n (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 61) (:start . 60)\n (:id . 55))\n ((:tag . "LS") (:stem . "i") (:form . "i") (:end . 62) (:start . 61)\n (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 66) (:start . 64)\n (:id . 58))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 72) (:start . 67)\n (:id . 59))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 76) (:start . 73)\n (:id . 60))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 84)\n (:start . 77) (:id . 61))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 89) (:start . 85)\n (:id . 62))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 95) (:start . 90)\n (:id . 63))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 105)\n (:start . 96) (:id . 64))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 110) (:start . 106)\n (:id . 65))\n ((:tag . "VBZ") (:stem . "cover") (:form . "covers") (:end . 117)\n (:start . 111) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n (:id . 67))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 129)\n (:start . 122) (:id . 68))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 134) (:start . 130)\n (:id . 69))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 140)\n (:start . 135) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 144) (:start . 141)\n (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 146) (:start . 145)\n (:id . 72))\n ((:tag . "LS") (:stem . "ii") (:form . "ii") (:end . 148) (:start . 146)\n (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n (:id . 74))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 152) (:start . 150)\n (:id . 75))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 160)\n (:start . 153) (:id . 76))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 165) (:start . 161)\n (:id . 77))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 170) (:start . 166)\n (:id . 78))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 174) (:start . 171)\n (:id . 79))\n ((:tag . "VB") (:stem . "cover") (:form . "cover") (:end . 180)\n (:start . 175) (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 184) (:start . 181)\n (:id . 81))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 189) (:start . 185)\n (:id . 82))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 195)\n (:start . 190) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n (:id . 84)))@@@1@43@((:ncues ((:id . :x1.76.1) (:span 171 174))\n ((:id . :x1.76.2) (:span 150 152)))\n (:nscopes ((:id . :x1.76.1) (:span 171 195))\n ((:id . :x1.76.2) (:span 150 195)))\n (:identifiers (:sid . :s1.76) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100076@unknown@formal@none@1@S@Note that, however, if the whole length of an iORF was used as a query sequence, this procedure will erroneously discard multidomain readthrough proteins.@(((:tag . "VB") (:stem . "note") (:form . "Note") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 44))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 18)\n (:start . 11) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n (:id . 46))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 22) (:start . 20)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 48))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 32) (:start . 27)\n (:id . 49))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 39)\n (:start . 33) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n (:id . 51))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 45) (:start . 43)\n (:id . 52))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 50) (:start . 46)\n (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 54) (:start . 51)\n (:id . 54))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 59) (:start . 55)\n (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 62) (:start . 60)\n (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n (:id . 57))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 70) (:start . 65)\n (:id . 58))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 79)\n (:start . 71) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n (:id . 60))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 85) (:start . 81)\n (:id . 61))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 95)\n (:start . 86) (:id . 62))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 100) (:start . 96)\n (:id . 63))\n ((:tag . "RB") (:stem . "erroneously") (:form . "erroneously") (:end . 112)\n (:start . 101) (:id . 64))\n ((:tag . "VB") (:stem . "discard") (:form . "discard") (:end . 120)\n (:start . 113) (:id . 65))\n ((:tag . "JJ") (:stem . "multidomain") (:form . "multidomain") (:end . 132)\n (:start . 121) (:id . 66))\n ((:tag . "NN") (:stem . "readthrough") (:form . "readthrough") (:end . 144)\n (:start . 133) (:id . 67))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 153)\n (:start . 145) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.77) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100077@unknown@formal@none@1@S@To avoid this problem, a partial sequence around the inframe stop codon was used as a query.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "avoid") (:form . "avoid") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "problem") (:form . "problem") (:end . 21)\n (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 24) (:start . 23)\n (:id . 47))\n ((:tag . "JJ") (:stem . "partial") (:form . "partial") (:end . 32)\n (:start . 25) (:id . 48))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 41)\n (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 48)\n (:start . 42) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n (:id . 51))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 60)\n (:start . 53) (:id . 52))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 65) (:start . 61)\n (:id . 53))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 71) (:start . 66)\n (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 75) (:start . 72)\n (:id . 55))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 80) (:start . 76)\n (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 83) (:start . 81)\n (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 85) (:start . 84)\n (:id . 58))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 91) (:start . 86)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.78) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100078@unknown@formal@none@1@S@Prediction procedure@(((:tag . "NN") (:stem . "prediction") (:form . "Prediction") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 20)\n (:start . 11) (:id . 43)))@@@1@2@((:identifiers (:sid . :s1.79) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100080@unknown@formal@none@1@S@A total of 191 prokaryotes were analyzed in this study, of which 166 are bacteria and 25 are archaea.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "total") (:form . "total") (:end . 7) (:start . 2)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n (:id . 44))\n ((:tag . "CD") (:stem . "191") (:form . "191") (:end . 14) (:start . 11)\n (:id . 45))\n ((:tag . "NNS") (:stem . "prokaryote") (:form . "prokaryotes") (:end . 26)\n (:start . 15) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 31) (:start . 27)\n (:id . 47))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 40)\n (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n (:id . 49))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 48) (:start . 44)\n (:id . 50))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 54) (:start . 49)\n (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 64) (:start . 59)\n (:id . 54))\n ((:tag . "CD") (:stem . "166") (:form . "166") (:end . 68) (:start . 65)\n (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 72) (:start . 69)\n (:id . 56))\n ((:tag . "NNS") (:stem . "bacteria") (:form . "bacteria") (:end . 81)\n (:start . 73) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n (:id . 58))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 88) (:start . 86)\n (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 92) (:start . 89)\n (:id . 60))\n ((:tag . "NN") (:stem . "archaea") (:form . "archaea") (:end . 100)\n (:start . 93) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s1.81) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100081@unknown@formal@none@1@S@They were selected from 328 prokaryotes with completely sequenced genomes by excluding closely related species.@(((:tag . "PRP") (:stem . "they") (:form . "They") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 18)\n (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 23) (:start . 19)\n (:id . 45))\n ((:tag . "CD") (:stem . "328") (:form . "328") (:end . 27) (:start . 24)\n (:id . 46))\n ((:tag . "NNS") (:stem . "prokaryote") (:form . "prokaryotes") (:end . 39)\n (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 44) (:start . 40)\n (:id . 48))\n ((:tag . "RB") (:stem . "completely") (:form . "completely") (:end . 55)\n (:start . 45) (:id . 49))\n ((:tag . "VBN") (:stem . "sequence") (:form . "sequenced") (:end . 65)\n (:start . 56) (:id . 50))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 73)\n (:start . 66) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 76) (:start . 74)\n (:id . 52))\n ((:tag . "VBG") (:stem . "exclude") (:form . "excluding") (:end . 86)\n (:start . 77) (:id . 53))\n ((:tag . "RB") (:stem . "closely") (:form . "closely") (:end . 94)\n (:start . 87) (:id . 54))\n ((:tag . "JJ") (:stem . "related") (:form . "related") (:end . 102)\n (:start . 95) (:id . 55))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 110)\n (:start . 103) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.82) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100082@unknown@formal@none@1@S@From the genome sequences of the 191 organisms, all possible iORFs were enumerated.@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 15) (:start . 9)\n (:id . 44))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 25)\n (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n (:id . 47))\n ((:tag . "CD") (:stem . "191") (:form . "191") (:end . 36) (:start . 33)\n (:id . 48))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 46)\n (:start . 37) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n (:id . 50))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 51) (:start . 48)\n (:id . 51))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 60)\n (:start . 52) (:id . 52))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 66) (:start . 61)\n (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 71) (:start . 67)\n (:id . 54))\n ((:tag . "VBN") (:stem . "enumerate") (:form . "enumerated") (:end . 82)\n (:start . 72) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s1.83) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100083@unknown@formal@none@1@S@Two conditions were imposed on the geometry of the iORFs (Figure 1a).@(((:tag . "CD") (:stem . "two") (:form . "Two") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "VBN") (:stem . "impose") (:form . "imposed") (:end . 27)\n (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "NN") (:stem . "geometry") (:form . "geometry") (:end . 43)\n (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n (:id . 50))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 56) (:start . 51)\n (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n (:id . 52))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 64)\n (:start . 58) (:id . 53))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 67) (:start . 65)\n (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s1.84) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100084@unknown@formal@none@1@S@First, only iORFs longer than 80 codons were extracted.@(((:tag . "RB") (:stem . "first") (:form . "First") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 17) (:start . 12)\n (:id . 45))\n ((:tag . "JJR") (:stem . "long") (:form . "longer") (:end . 24) (:start . 18)\n (:id . 46))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 29) (:start . 25)\n (:id . 47))\n ((:tag . "CD") (:stem . "80") (:form . "80") (:end . 32) (:start . 30)\n (:id . 48))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 39)\n (:start . 33) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 44) (:start . 40)\n (:id . 50))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 54)\n (:start . 45) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 55) (:start . 54)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s1.85) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100085@unknown@formal@none@1@S@Secondly, margins between the inframe stop codon and both termini of the iORF must be longer than 10 codons.@(((:tag . "RB") (:stem . "secondly") (:form . "Secondly") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "margin") (:form . "margins") (:end . 17)\n (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 25)\n (:start . 18) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n (:id . 46))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 37)\n (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 42) (:start . 38)\n (:id . 48))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 48) (:start . 43)\n (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n (:id . 50))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 57) (:start . 53)\n (:id . 51))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 65)\n (:start . 58) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n (:id . 54))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 77) (:start . 73)\n (:id . 55))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 82) (:start . 78)\n (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 85) (:start . 83)\n (:id . 57))\n ((:tag . "JJR") (:stem . "long") (:form . "longer") (:end . 92) (:start . 86)\n (:id . 58))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 97) (:start . 93)\n (:id . 59))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 100) (:start . 98)\n (:id . 60))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 107)\n (:start . 101) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s1.86) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100086@unknown@formal@none@1@S@The total number of iORFs extracted under these conditions was 2,969,958.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 16)\n (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 25) (:start . 20)\n (:id . 46))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 35)\n (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 41) (:start . 36)\n (:id . 48))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 47) (:start . 42)\n (:id . 49))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 58)\n (:start . 48) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 62) (:start . 59)\n (:id . 51))\n ((:tag . "CD") (:stem . "2,969,958") (:form . "2,969,958") (:end . 72)\n (:start . 63) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s1.87) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100087@unknown@formal@none@1@S@Next, iORFs that overlap RNA genes or protein-coding genes in different reading frames were discarded.@(((:tag . "RB") (:stem . "next") (:form . "Next") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 11) (:start . 6)\n (:id . 44))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n (:id . 45))\n ((:tag . "VBP") (:stem . "overlap") (:form . "overlap") (:end . 24)\n (:start . 17) (:id . 46))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 28) (:start . 25)\n (:id . 47))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 34) (:start . 29)\n (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 37) (:start . 35)\n (:id . 49))\n ((:tag . "JJ") (:stem . "protein-coding") (:form . "protein-coding")\n (:end . 52) (:start . 38) (:id . 50))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 58) (:start . 53)\n (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n (:id . 52))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 71)\n (:start . 62) (:id . 53))\n ((:tag . "NN") (:stem . "reading") (:form . "reading") (:end . 79)\n (:start . 72) (:id . 54))\n ((:tag . "NNS") (:stem . "frame") (:form . "frames") (:end . 86)\n (:start . 80) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 91) (:start . 87)\n (:id . 56))\n ((:tag . "VBN") (:stem . "discard") (:form . "discarded") (:end . 101)\n (:start . 92) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.88) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100088@unknown@formal@none@1@S@This test significantly reduced the number of iORFs to 390,926.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 23) (:start . 10) (:id . 44))\n ((:tag . "VBD") (:stem . "reduce") (:form . "reduced") (:end . 31)\n (:start . 24) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n (:id . 46))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 42)\n (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n (:id . 48))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 51) (:start . 46)\n (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 54) (:start . 52)\n (:id . 50))\n ((:tag . "CD") (:stem . "390,926") (:form . "390,926") (:end . 62)\n (:start . 55) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s1.89) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100090@unknown@formal@none@1@S@A flowchart of the prediction procedure.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "flowchart") (:form . "flowchart") (:end . 11)\n (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 29)\n (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 39)\n (:start . 30) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 40) (:start . 39)\n (:id . 48)))@@@1@7@((:identifiers (:sid . :s1.91) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100091@unknown@formal@none@1@S@Several steps are omitted for simplicity.@(((:tag . "JJ") (:stem . "several") (:form . "Several") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "step") (:form . "steps") (:end . 13) (:start . 8)\n (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "VBN") (:stem . "omit") (:form . "omitted") (:end . 25)\n (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 29) (:start . 26)\n (:id . 46))\n ((:tag . "NN") (:stem . "simplicity") (:form . "simplicity") (:end . 40)\n (:start . 30) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 41) (:start . 40)\n (:id . 48)))@@@1@7@((:identifiers (:sid . :s1.92) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100092@unknown@formal@none@1@S@Detailed explanation is given in the text.@(((:tag . "JJ") (:stem . "detailed") (:form . "Detailed") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "explanation") (:form . "explanation") (:end . 20)\n (:start . 9) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 23) (:start . 21)\n (:id . 44))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 29) (:start . 24)\n (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n (:id . 47))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 41) (:start . 37)\n (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 42) (:start . 41)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s1.93) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100093@unknown@formal@none@1@S@As noted above, the target of this study is evolutionarily conserved iORFs.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 46))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 26)\n (:start . 20) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 48))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 34) (:start . 30)\n (:id . 49))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 40) (:start . 35)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 43) (:start . 41)\n (:id . 51))\n ((:tag . "RB") (:stem . "evolutionarily") (:form . "evolutionarily")\n (:end . 58) (:start . 44) (:id . 52))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 68)\n (:start . 59) (:id . 53))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 74) (:start . 69)\n (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s1.94) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100094@unknown@formal@none@1@S@Thus, it was examined whether the iORFs have homologous regions in other genomes.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 8) (:start . 6)\n (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 12) (:start . 9)\n (:id . 45))\n ((:tag . "VBN") (:stem . "examine") (:form . "examined") (:end . 21)\n (:start . 13) (:id . 46))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 29)\n (:start . 22) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 48))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 39) (:start . 34)\n (:id . 49))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 44) (:start . 40)\n (:id . 50))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 55)\n (:start . 45) (:id . 51))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 63)\n (:start . 56) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n (:id . 53))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 72) (:start . 67)\n (:id . 54))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 80)\n (:start . 73) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n (:id . 56)))@@@1@15@((:hcues ((:id . :x1.95.1) (:span 22 29)))\n (:hscopes ((:id . :x1.95.1) (:span 22 80)))\n (:identifiers (:sid . :s1.95) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100095@unknown@formal@none@1@S@The 390,926 iORFs were translated into amino acid sequences and subjected to TBLASTN 16 against the 191 genome sequences.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "390,926") (:form . "390,926") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 17) (:start . 12)\n (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 22) (:start . 18)\n (:id . 45))\n ((:tag . "VBN") (:stem . "translate") (:form . "translated") (:end . 33)\n (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 38) (:start . 34)\n (:id . 47))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 44) (:start . 39)\n (:id . 48))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 49) (:start . 45)\n (:id . 49))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 59)\n (:start . 50) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n (:id . 51))\n ((:tag . "VBN") (:stem . "subject") (:form . "subjected") (:end . 73)\n (:start . 64) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 76) (:start . 74)\n (:id . 53))\n ((:tag . "NNP") (:stem . "TBLASTN") (:form . "TBLASTN") (:end . 84)\n (:start . 77) (:id . 54))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 87) (:start . 85)\n (:id . 55))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 95)\n (:start . 88) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n (:id . 57))\n ((:tag . "CD") (:stem . "191") (:form . "191") (:end . 103) (:start . 100)\n (:id . 58))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 110)\n (:start . 104) (:id . 59))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 120)\n (:start . 111) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.96) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100096@unknown@formal@none@1@S@Instead of the whole length of the amino acid sequence, a window of 101 residues centered at the inframe stop codon was used as a BLAST query.@(((:tag . "RB") (:stem . "instead") (:form . "Instead") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 27)\n (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 48))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 40) (:start . 35)\n (:id . 49))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 45) (:start . 41)\n (:id . 50))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 54)\n (:start . 46) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n (:id . 53))\n ((:tag . "NN") (:stem . "window") (:form . "window") (:end . 64)\n (:start . 58) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n (:id . 55))\n ((:tag . "CD") (:stem . "101") (:form . "101") (:end . 71) (:start . 68)\n (:id . 56))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 80)\n (:start . 72) (:id . 57))\n ((:tag . "VBN") (:stem . "center") (:form . "centered") (:end . 89)\n (:start . 81) (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 92) (:start . 90)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n (:id . 60))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 104)\n (:start . 97) (:id . 61))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 109) (:start . 105)\n (:id . 62))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 115)\n (:start . 110) (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 119) (:start . 116)\n (:id . 64))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 124) (:start . 120)\n (:id . 65))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 127) (:start . 125)\n (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 129) (:start . 128)\n (:id . 67))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 135)\n (:start . 130) (:id . 68))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 141)\n (:start . 136) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n (:id . 70)))@@@1@29@((:ncues ((:id . :x1.97.1) (:span 0 10)))\n (:nscopes ((:id . :x1.97.1) (:span 0 54)))\n (:identifiers (:sid . :s1.97) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100097@unknown@formal@none@1@S@After the BLAST searches, iORFs that have at least one interspecific hit that contains the inframe stop codon were collected.@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 15) (:start . 10)\n (:id . 44))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 24)\n (:start . 16) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n (:id . 46))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 31) (:start . 26)\n (:id . 47))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 36) (:start . 32)\n (:id . 48))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 41) (:start . 37)\n (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 44) (:start . 42)\n (:id . 50))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 50) (:start . 45)\n (:id . 51))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 54) (:start . 51)\n (:id . 52))\n ((:tag . "JJ") (:stem . "interspecific") (:form . "interspecific")\n (:end . 68) (:start . 55) (:id . 53))\n ((:tag . "NN") (:stem . "hit") (:form . "hit") (:end . 72) (:start . 69)\n (:id . 54))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 77) (:start . 73)\n (:id . 55))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 86)\n (:start . 78) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n (:id . 57))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 98)\n (:start . 91) (:id . 58))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 103) (:start . 99)\n (:id . 59))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 109)\n (:start . 104) (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 114) (:start . 110)\n (:id . 61))\n ((:tag . "VBN") (:stem . "collect") (:form . "collected") (:end . 124)\n (:start . 115) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.98) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100098@unknown@formal@none@1@S@Whether the codon aligned to the inframe stop codon is a nonsense codon or not was neglected at this stage.@(((:tag . "IN") (:stem . "whether") (:form . "Whether") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n (:id . 43))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 17) (:start . 12)\n (:id . 44))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 25)\n (:start . 18) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n (:id . 47))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 40)\n (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 45) (:start . 41)\n (:id . 49))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 51) (:start . 46)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 54) (:start . 52)\n (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 56) (:start . 55)\n (:id . 52))\n ((:tag . "JJ") (:stem . "nonsense") (:form . "nonsense") (:end . 65)\n (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 71) (:start . 66)\n (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 74) (:start . 72)\n (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 78) (:start . 75)\n (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 82) (:start . 79)\n (:id . 57))\n ((:tag . "VBN") (:stem . "neglect") (:form . "neglected") (:end . 92)\n (:start . 83) (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 95) (:start . 93)\n (:id . 59))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 100) (:start . 96)\n (:id . 60))\n ((:tag . "NN") (:stem . "stage") (:form . "stage") (:end . 106)\n (:start . 101) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n (:id . 62)))@@@1@21@((:hcues ((:id . :x1.99.2) (:span 72 74)) ((:id . :x1.99.3) (:span 0 7)))\n (:ncues ((:id . :x1.99.1) (:span 75 78)))\n (:hscopes ((:id . :x1.99.2) (:span 55 78)) ((:id . :x1.99.3) (:span 0 78)))\n (:nscopes ((:id . :x1.99.1) (:span 75 78)))\n (:identifiers (:sid . :s1.99) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100100@unknown@formal@none@1@S@The result of the above homology searches was also used for the boundary analysis (Figure 1b).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 45))\n ((:tag . "JJ") (:stem . "above") (:form . "above") (:end . 23) (:start . 18)\n (:id . 46))\n ((:tag . "NN") (:stem . "homology") (:form . "homology") (:end . 32)\n (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 41)\n (:start . 33) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 45) (:start . 42)\n (:id . 49))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 50) (:start . 46)\n (:id . 50))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 55) (:start . 51)\n (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 59) (:start . 56)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n (:id . 53))\n ((:tag . "JJ") (:stem . "boundary") (:form . "boundary") (:end . 72)\n (:start . 64) (:id . 54))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 81)\n (:start . 73) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n (:id . 56))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 89)\n (:start . 83) (:id . 57))\n ((:tag . "NN") (:stem . "1b") (:form . "1b") (:end . 92) (:start . 90)\n (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.101) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100101@unknown@formal@none@1@S@An iORF was discarded if there were any BLAST hits that do not cover the inframe stop codon.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 11) (:start . 8)\n (:id . 44))\n ((:tag . "VBN") (:stem . "discard") (:form . "discarded") (:end . 21)\n (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 24) (:start . 22)\n (:id . 46))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 30) (:start . 25)\n (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 35) (:start . 31)\n (:id . 48))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 39) (:start . 36)\n (:id . 49))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 45) (:start . 40)\n (:id . 50))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 50) (:start . 46)\n (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 55) (:start . 51)\n (:id . 52))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 58) (:start . 56)\n (:id . 53))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 62) (:start . 59)\n (:id . 54))\n ((:tag . "VB") (:stem . "cover") (:form . "cover") (:end . 68) (:start . 63)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n (:id . 56))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 80)\n (:start . 73) (:id . 57))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 85) (:start . 81)\n (:id . 58))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 91) (:start . 86)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n (:id . 60)))@@@1@19@((:ncues ((:id . :x1.102.1) (:span 59 62)))\n (:nscopes ((:id . :x1.102.1) (:span 59 91)))\n (:identifiers (:sid . :s1.102) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100102@unknown@formal@none@1@S@A total of 26,003 iORF satisfied the above criteria.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "total") (:form . "total") (:end . 7) (:start . 2)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n (:id . 44))\n ((:tag . "CD") (:stem . "26,003") (:form . "26,003") (:end . 17)\n (:start . 11) (:id . 45))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 22) (:start . 18)\n (:id . 46))\n ((:tag . "VBD") (:stem . "satisfy") (:form . "satisfied") (:end . 32)\n (:start . 23) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n (:id . 48))\n ((:tag . "JJ") (:stem . "above") (:form . "above") (:end . 42) (:start . 37)\n (:id . 49))\n ((:tag . "NNS") (:stem . "criterion") (:form . "criteria") (:end . 51)\n (:start . 43) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 52) (:start . 51)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s1.103) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100103@unknown@formal@none@1@S@To examine intrafamily conservation of the inframe stop codons, these iORFs were clustered into protein families based on sequence similarity.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "examine") (:form . "examine") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "intrafamily") (:form . "intrafamily") (:end . 22)\n (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 35)\n (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n (:id . 47))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 50)\n (:start . 43) (:id . 48))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 55) (:start . 51)\n (:id . 49))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 62)\n (:start . 56) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n (:id . 51))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 69) (:start . 64)\n (:id . 52))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 75) (:start . 70)\n (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 80) (:start . 76)\n (:id . 54))\n ((:tag . "VBN") (:stem . "cluster") (:form . "clustered") (:end . 90)\n (:start . 81) (:id . 55))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 95) (:start . 91)\n (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 103)\n (:start . 96) (:id . 57))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 112)\n (:start . 104) (:id . 58))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 118)\n (:start . 113) (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 121) (:start . 119)\n (:id . 60))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 130)\n (:start . 122) (:id . 61))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 141)\n (:start . 131) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.104) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100104@unknown@formal@none@1@S@After removal of singletons, 679 clusters with two or more members were obtained.@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "removal") (:form . "removal") (:end . 13)\n (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 44))\n ((:tag . "NNS") (:stem . "singleton") (:form . "singletons") (:end . 27)\n (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n (:id . 46))\n ((:tag . "CD") (:stem . "679") (:form . "679") (:end . 32) (:start . 29)\n (:id . 47))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 41)\n (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 46) (:start . 42)\n (:id . 49))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 50) (:start . 47)\n (:id . 50))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 53) (:start . 51)\n (:id . 51))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 58) (:start . 54)\n (:id . 52))\n ((:tag . "NNS") (:stem . "member") (:form . "members") (:end . 66)\n (:start . 59) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 71) (:start . 67)\n (:id . 54))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 80)\n (:start . 72) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s1.105) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100105@unknown@formal@none@1@S@A cluster was discarded unless all members of the cluster had the same type of inframe stop codons (UAA, UAG or UGA).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 9)\n (:start . 2) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "VBN") (:stem . "discard") (:form . "discarded") (:end . 23)\n (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "unless") (:form . "unless") (:end . 30)\n (:start . 24) (:id . 46))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "NNS") (:stem . "member") (:form . "members") (:end . 42)\n (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n (:id . 50))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 57)\n (:start . 50) (:id . 51))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 61) (:start . 58)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n (:id . 53))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 70) (:start . 66)\n (:id . 54))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 75) (:start . 71)\n (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n (:id . 56))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 86)\n (:start . 79) (:id . 57))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 91) (:start . 87)\n (:id . 58))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 98)\n (:start . 92) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n (:id . 60))\n ((:tag . "NNP") (:stem . "UAA") (:form . "UAA") (:end . 103) (:start . 100)\n (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n (:id . 62))\n ((:tag . "NNP") (:stem . "UAG") (:form . "UAG") (:end . 108) (:start . 105)\n (:id . 63))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 111) (:start . 109)\n (:id . 64))\n ((:tag . "NNP") (:stem . "UGA") (:form . "UGA") (:end . 115) (:start . 112)\n (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s1.106) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100106@unknown@formal@none@1@S@The locations of the inframe stop codons were also required to be identical in the multiple sequence alignment of the cluster members.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "location") (:form . "locations") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 28)\n (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 40)\n (:start . 34) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 45) (:start . 41)\n (:id . 49))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 50) (:start . 46)\n (:id . 50))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 59)\n (:start . 51) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 62) (:start . 60)\n (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 65) (:start . 63)\n (:id . 53))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 75)\n (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n (:id . 56))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 91)\n (:start . 83) (:id . 57))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 100)\n (:start . 92) (:id . 58))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 110)\n (:start . 101) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n (:id . 61))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 125)\n (:start . 118) (:id . 62))\n ((:tag . "NNS") (:stem . "member") (:form . "members") (:end . 133)\n (:start . 126) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s1.107) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100107@unknown@formal@none@1@S@These conditions reduced the number of clusters to 273.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 16)\n (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "reduce") (:form . "reduced") (:end . 24)\n (:start . 17) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 35)\n (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n (:id . 47))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 47)\n (:start . 39) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n (:id . 49))\n ((:tag . "CD") (:stem . "273") (:form . "273") (:end . 54) (:start . 51)\n (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 55) (:start . 54)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s1.108) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100108@unknown@formal@none@1@S@Manual inspection of these 273 clusters revealed that they still contain many false positives that are unrelated to stop-codon-encoded amino acids.@(((:tag . "JJ") (:stem . "manual") (:form . "Manual") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "inspection") (:form . "inspection") (:end . 17)\n (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 26) (:start . 21)\n (:id . 45))\n ((:tag . "CD") (:stem . "273") (:form . "273") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 39)\n (:start . 31) (:id . 47))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 48)\n (:start . 40) (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 53) (:start . 49)\n (:id . 49))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 58) (:start . 54)\n (:id . 50))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 64) (:start . 59)\n (:id . 51))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 72)\n (:start . 65) (:id . 52))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 77) (:start . 73)\n (:id . 53))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 83) (:start . 78)\n (:id . 54))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 93)\n (:start . 84) (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 98) (:start . 94)\n (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 102) (:start . 99)\n (:id . 57))\n ((:tag . "JJ") (:stem . "unrelated") (:form . "unrelated") (:end . 112)\n (:start . 103) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 115) (:start . 113)\n (:id . 59))\n ((:tag . "JJ") (:stem . "stop-codon-encoded") (:form . "stop-codon-encoded")\n (:end . 134) (:start . 116) (:id . 60))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 140)\n (:start . 135) (:id . 61))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 146)\n (:start . 141) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.109) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100110@unknown@formal@none@1@S@Briefly, the first filter assesses protein-likeliness based on the signal of purifying selection, while the second and third filters try to remove adjacent gene pairs using the pattern of BLAST alignments (for details, see Materials and Methods).@(((:tag . "NNP") (:stem . "Briefly") (:form . "Briefly") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 25)\n (:start . 19) (:id . 46))\n ((:tag . "VBZ") (:stem . "assess") (:form . "assesses") (:end . 34)\n (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . "protein-likeliness") (:form . "protein-likeliness")\n (:end . 53) (:start . 35) (:id . 48))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 59) (:start . 54)\n (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 62) (:start . 60)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n (:id . 51))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 73)\n (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n (:id . 53))\n ((:tag . "VBG") (:stem . "purify") (:form . "purifying") (:end . 86)\n (:start . 77) (:id . 54))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 96)\n (:start . 87) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n (:id . 56))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 103) (:start . 98)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n (:id . 58))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 114)\n (:start . 108) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n (:id . 60))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 124)\n (:start . 119) (:id . 61))\n ((:tag . "NNS") (:stem . "filter") (:form . "filters") (:end . 132)\n (:start . 125) (:id . 62))\n ((:tag . "VBP") (:stem . "try") (:form . "try") (:end . 136) (:start . 133)\n (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 139) (:start . 137)\n (:id . 64))\n ((:tag . "VB") (:stem . "remove") (:form . "remove") (:end . 146)\n (:start . 140) (:id . 65))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 155)\n (:start . 147) (:id . 66))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 160) (:start . 156)\n (:id . 67))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 166)\n (:start . 161) (:id . 68))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 172) (:start . 167)\n (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 176) (:start . 173)\n (:id . 70))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 184)\n (:start . 177) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 187) (:start . 185)\n (:id . 72))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 193)\n (:start . 188) (:id . 73))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 204)\n (:start . 194) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 206) (:start . 205)\n (:id . 75))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 209) (:start . 206)\n (:id . 76))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 217)\n (:start . 210) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 218) (:start . 217)\n (:id . 78))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 222) (:start . 219)\n (:id . 79))\n ((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 232)\n (:start . 223) (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 236) (:start . 233)\n (:id . 81))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 244)\n (:start . 237) (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 245) (:start . 244)\n (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 246) (:start . 245)\n (:id . 84)))@@@1@43@((:identifiers (:sid . :s1.111) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100111@unknown@formal@none@1@S@As a result of the filtering, the number of candidate clusters was reduced to 32.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 11) (:start . 5)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 46))\n ((:tag . "NN") (:stem . "filtering") (:form . "filtering") (:end . 28)\n (:start . 19) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 49))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 40)\n (:start . 34) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n (:id . 51))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 53)\n (:start . 44) (:id . 52))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 62)\n (:start . 54) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 66) (:start . 63)\n (:id . 54))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 74)\n (:start . 67) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 77) (:start . 75)\n (:id . 56))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 80) (:start . 78)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.112) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100112@unknown@formal@none@1@S@Through manual inspection of the BLAST alignments, 11 clusters were discarded because they are highly unlikely to code readthrough proteins.@(((:tag . "IN") (:stem . "through") (:form . "Through") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "manual") (:form . "manual") (:end . 14) (:start . 8)\n (:id . 43))\n ((:tag . "NN") (:stem . "inspection") (:form . "inspection") (:end . 25)\n (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n (:id . 46))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 38) (:start . 33)\n (:id . 47))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 49)\n (:start . 39) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n (:id . 49))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 53) (:start . 51)\n (:id . 50))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 62)\n (:start . 54) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 67) (:start . 63)\n (:id . 52))\n ((:tag . "VBN") (:stem . "discard") (:form . "discarded") (:end . 77)\n (:start . 68) (:id . 53))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 85)\n (:start . 78) (:id . 54))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 90) (:start . 86)\n (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 94) (:start . 91)\n (:id . 56))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 101)\n (:start . 95) (:id . 57))\n ((:tag . "JJ") (:stem . "unlikely") (:form . "unlikely") (:end . 110)\n (:start . 102) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 113) (:start . 111)\n (:id . 59))\n ((:tag . "VB") (:stem . "code") (:form . "code") (:end . 118) (:start . 114)\n (:id . 60))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 130)\n (:start . 119) (:id . 61))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 139)\n (:start . 131) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n (:id . 63)))@@@1@22@((:hcues ((:id . :x1.113.1) (:span 102 110)))\n (:hscopes ((:id . :x1.113.1) (:span 86 139)))\n (:identifiers (:sid . :s1.113) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100113@unknown@formal@none@1@S@Known proteins in the predicted clusters@(((:tag . "NN") (:stem . "known") (:form . "Known") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 14)\n (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 17) (:start . 15)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n (:id . 45))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 31)\n (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 40)\n (:start . 32) (:id . 47)))@@@1@6@((:identifiers (:sid . :s1.114) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100114@unknown@formal@none@1@S@The clusters predicted by our method are summarized in Table 1.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 22)\n (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 25) (:start . 23)\n (:id . 45))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 29) (:start . 26)\n (:id . 46))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 36)\n (:start . 30) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 40) (:start . 37)\n (:id . 48))\n ((:tag . "VBN") (:stem . "summarize") (:form . "summarized") (:end . 51)\n (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n (:id . 50))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 60) (:start . 55)\n (:id . 51))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 62) (:start . 61)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s1.115) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100115@unknown@formal@none@1@S@Of the 21 clusters, 15 were known selenoproteins, and four were known pyrrolysine proteins.@(((:tag . "IN") (:stem . "of") (:form . "Of") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 9) (:start . 7)\n (:id . 44))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 18)\n (:start . 10) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n (:id . 46))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 22) (:start . 20)\n (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 27) (:start . 23)\n (:id . 48))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 33) (:start . 28)\n (:id . 49))\n ((:tag . "NNS") (:stem . "selenoprotein") (:form . "selenoproteins")\n (:end . 48) (:start . 34) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n (:id . 52))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 58) (:start . 54)\n (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 63) (:start . 59)\n (:id . 54))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 69) (:start . 64)\n (:id . 55))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 81)\n (:start . 70) (:id . 56))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 90)\n (:start . 82) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.116) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100116@unknown@formal@none@1@S@To assess the sensitivity of our method, the result was compared with a list of prokaryotic selenoproteins reported by Kryukov and Gladyshev 12.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "assess") (:form . "assess") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 25)\n (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 32) (:start . 29)\n (:id . 47))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 39)\n (:start . 33) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n (:id . 50))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 51)\n (:start . 45) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 55) (:start . 52)\n (:id . 52))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 64)\n (:start . 56) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 69) (:start . 65)\n (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 71) (:start . 70)\n (:id . 55))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 76) (:start . 72)\n (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n (:id . 57))\n ((:tag . "JJ") (:stem . "prokaryotic") (:form . "prokaryotic") (:end . 91)\n (:start . 80) (:id . 58))\n ((:tag . "NNS") (:stem . "selenoprotein") (:form . "selenoproteins")\n (:end . 106) (:start . 92) (:id . 59))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 115)\n (:start . 107) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 118) (:start . 116)\n (:id . 61))\n ((:tag . "NNP") (:stem . "Kryukov") (:form . "Kryukov") (:end . 126)\n (:start . 119) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n (:id . 63))\n ((:tag . "NNP") (:stem . "Gladyshev") (:form . "Gladyshev") (:end . 140)\n (:start . 131) (:id . 64))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 143) (:start . 141)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s1.117) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100117@unknown@formal@none@1@S@Since our target is readthrough genes conserved across two or more species, such selenoprotein families were selected from their list.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 16)\n (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 31)\n (:start . 20) (:id . 46))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 37) (:start . 32)\n (:id . 47))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 47)\n (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 54)\n (:start . 48) (:id . 49))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 58) (:start . 55)\n (:id . 50))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 61) (:start . 59)\n (:id . 51))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 66) (:start . 62)\n (:id . 52))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 74)\n (:start . 67) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n (:id . 54))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 80) (:start . 76)\n (:id . 55))\n ((:tag . "NN") (:stem . "selenoprotein") (:form . "selenoprotein")\n (:end . 94) (:start . 81) (:id . 56))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 103)\n (:start . 95) (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 108) (:start . 104)\n (:id . 58))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 117)\n (:start . 109) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 122) (:start . 118)\n (:id . 60))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 128)\n (:start . 123) (:id . 61))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 133) (:start . 129)\n (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.118) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100118@unknown@formal@none@1@S@There were 15 families satisfying this criterion, but one family, proline reductase, was excluded because it was found in only one organism in our dataset.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 22)\n (:start . 14) (:id . 45))\n ((:tag . "VBG") (:stem . "satisfy") (:form . "satisfying") (:end . 33)\n (:start . 23) (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 38) (:start . 34)\n (:id . 47))\n ((:tag . "NN") (:stem . "criterion") (:form . "criterion") (:end . 48)\n (:start . 39) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n (:id . 49))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 53) (:start . 50)\n (:id . 50))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 57) (:start . 54)\n (:id . 51))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 64)\n (:start . 58) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n (:id . 53))\n ((:tag . "NN") (:stem . "proline") (:form . "proline") (:end . 73)\n (:start . 66) (:id . 54))\n ((:tag . "NN") (:stem . "reductase") (:form . "reductase") (:end . 83)\n (:start . 74) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 88) (:start . 85)\n (:id . 57))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 97)\n (:start . 89) (:id . 58))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 105)\n (:start . 98) (:id . 59))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 108) (:start . 106)\n (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 112) (:start . 109)\n (:id . 61))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 118)\n (:start . 113) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n (:id . 63))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 126) (:start . 122)\n (:id . 64))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 130) (:start . 127)\n (:id . 65))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 139)\n (:start . 131) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 142) (:start . 140)\n (:id . 67))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 146) (:start . 143)\n (:id . 68))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 154)\n (:start . 147) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s1.119) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100120@unknown@formal@none@1@S@The three families we failed to find were SelW-like protein, peroxiredoxin and thiol:protein disulphide oxidoreductase.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 18)\n (:start . 10) (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "VBD") (:stem . "fail") (:form . "failed") (:end . 28) (:start . 22)\n (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n (:id . 47))\n ((:tag . "VB") (:stem . "find") (:form . "find") (:end . 36) (:start . 32)\n (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 41) (:start . 37)\n (:id . 49))\n ((:tag . "JJ") (:stem . "selw-like") (:form . "SelW-like") (:end . 51)\n (:start . 42) (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 59)\n (:start . 52) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n (:id . 52))\n ((:tag . "NN") (:stem . "peroxiredoxin") (:form . "peroxiredoxin")\n (:end . 74) (:start . 61) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n (:id . 54))\n ((:tag . "NN") (:stem . "thiol:protein") (:form . "thiol:protein")\n (:end . 92) (:start . 79) (:id . 55))\n ((:tag . "NN") (:stem . "disulphide") (:form . "disulphide") (:end . 103)\n (:start . 93) (:id . 56))\n ((:tag . "NN") (:stem . "oxidoreductase") (:form . "oxidoreductase")\n (:end . 118) (:start . 104) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n (:id . 58)))@@@1@17@((:ncues ((:id . :x1.121.1) (:span 22 28)))\n (:nscopes ((:id . :x1.121.1) (:span 22 36)))\n (:identifiers (:sid . :s1.121) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100121@unknown@formal@none@1@S@SelW-like protein was below the threshold of detection, because its stop codon is near the N-terminus and the amino acid sequences of its members are too divergent.@(((:tag . "JJ") (:stem . "selw-like") (:form . "SelW-like") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 17)\n (:start . 10) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 21) (:start . 18)\n (:id . 44))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 27) (:start . 22)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n (:id . 46))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 41)\n (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n (:id . 48))\n ((:tag . "NN") (:stem . "detection") (:form . "detection") (:end . 54)\n (:start . 45) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n (:id . 50))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 63)\n (:start . 56) (:id . 51))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 67) (:start . 64)\n (:id . 52))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 72) (:start . 68)\n (:id . 53))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 78) (:start . 73)\n (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 81) (:start . 79)\n (:id . 55))\n ((:tag . "IN") (:stem . "near") (:form . "near") (:end . 86) (:start . 82)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n (:id . 57))\n ((:tag . "NNP") (:stem . "N-terminus") (:form . "N-terminus") (:end . 101)\n (:start . 91) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 105) (:start . 102)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n (:id . 60))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 115)\n (:start . 110) (:id . 61))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 120) (:start . 116)\n (:id . 62))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 130)\n (:start . 121) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 133) (:start . 131)\n (:id . 64))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 137) (:start . 134)\n (:id . 65))\n ((:tag . "NNS") (:stem . "member") (:form . "members") (:end . 145)\n (:start . 138) (:id . 66))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 149) (:start . 146)\n (:id . 67))\n ((:tag . "RB") (:stem . "too") (:form . "too") (:end . 153) (:start . 150)\n (:id . 68))\n ((:tag . "JJ") (:stem . "divergent") (:form . "divergent") (:end . 163)\n (:start . 154) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s1.122) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100122@unknown@formal@none@1@S@The reason why the two other families were not detected is more complex.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "reason") (:form . "reason") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "WRB") (:stem . "why") (:form . "why") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 22) (:start . 19)\n (:id . 46))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 28) (:start . 23)\n (:id . 47))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 37)\n (:start . 29) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 42) (:start . 38)\n (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 46) (:start . 43)\n (:id . 50))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 55)\n (:start . 47) (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 58) (:start . 56)\n (:id . 52))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 63) (:start . 59)\n (:id . 53))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 71)\n (:start . 64) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n (:id . 55)))@@@1@14@((:ncues ((:id . :x1.123.1) (:span 43 46)))\n (:nscopes ((:id . :x1.123.1) (:span 15 55)))\n (:identifiers (:sid . :s1.123) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100123@unknown@formal@none@1@S@Since these two families are homologous, they were grouped into an identical cluster at the clustering stage of our method.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 24)\n (:start . 16) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 39)\n (:start . 29) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n (:id . 48))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 45) (:start . 41)\n (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 50) (:start . 46)\n (:id . 50))\n ((:tag . "VBN") (:stem . "group") (:form . "grouped") (:end . 58)\n (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 63) (:start . 59)\n (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 66) (:start . 64)\n (:id . 53))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 76)\n (:start . 67) (:id . 54))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 84)\n (:start . 77) (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 87) (:start . 85)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n (:id . 57))\n ((:tag . "NN") (:stem . "clustering") (:form . "clustering") (:end . 102)\n (:start . 92) (:id . 58))\n ((:tag . "NN") (:stem . "stage") (:form . "stage") (:end . 108)\n (:start . 103) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n (:id . 60))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 115) (:start . 112)\n (:id . 61))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 122)\n (:start . 116) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.124) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100124@unknown@formal@none@1@S@However, the positions of selenocysteine were different between the two families (Figure 3).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 22)\n (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n (:id . 46))\n ((:tag . "NN") (:stem . "selenocysteine") (:form . "selenocysteine")\n (:end . 40) (:start . 26) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 45) (:start . 41)\n (:id . 48))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 55)\n (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 63)\n (:start . 56) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n (:id . 51))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 71) (:start . 68)\n (:id . 52))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 80)\n (:start . 72) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 88)\n (:start . 82) (:id . 55))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 90) (:start . 89)\n (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 91) (:start . 90)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.125) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100125@unknown@formal@none@1@S@The cluster was thus discarded because of an apparent lack of stop codon conservation.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "VBN") (:stem . "discard") (:form . "discarded") (:end . 30)\n (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 38)\n (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 44) (:start . 42)\n (:id . 49))\n ((:tag . "JJ") (:stem . "apparent") (:form . "apparent") (:end . 53)\n (:start . 45) (:id . 50))\n ((:tag . "NN") (:stem . "lack") (:form . "lack") (:end . 58) (:start . 54)\n (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n (:id . 52))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 66) (:start . 62)\n (:id . 53))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 72) (:start . 67)\n (:id . 54))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 85)\n (:start . 73) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n (:id . 56)))@@@1@15@((:hcues ((:id . :x1.126.2) (:span 45 53)))\n (:ncues ((:id . :x1.126.1) (:span 54 58)))\n (:hscopes ((:id . :x1.126.2) (:span 45 85)))\n (:nscopes ((:id . :x1.126.1) (:span 54 85)))\n (:identifiers (:sid . :s1.126) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100126@unknown@formal@none@1@S@To deal with a situation like this, a reexamination of the clustering threshold and subdivision of clusters will be required.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "deal") (:form . "deal") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 14) (:start . 13)\n (:id . 45))\n ((:tag . "NN") (:stem . "situation") (:form . "situation") (:end . 24)\n (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "like") (:form . "like") (:end . 29) (:start . 25)\n (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 34) (:start . 30)\n (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n (:id . 50))\n ((:tag . "NN") (:stem . "reexamination") (:form . "reexamination")\n (:end . 51) (:start . 38) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n (:id . 53))\n ((:tag . "NN") (:stem . "clustering") (:form . "clustering") (:end . 69)\n (:start . 59) (:id . 54))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 79)\n (:start . 70) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n (:id . 56))\n ((:tag . "NN") (:stem . "subdivision") (:form . "subdivision") (:end . 95)\n (:start . 84) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n (:id . 58))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 107)\n (:start . 99) (:id . 59))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 112) (:start . 108)\n (:id . 60))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 115) (:start . 113)\n (:id . 61))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 124)\n (:start . 116) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.127) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100127@unknown@formal@none@1@S@Predicted clusters of readthrough proteins@(((:tag . "VBN") (:stem . "predict") (:form . "Predicted") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 18)\n (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 44))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 33)\n (:start . 22) (:id . 45))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 42)\n (:start . 34) (:id . 46)))@@@1@5@((:identifiers (:sid . :s1.128) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|TableLegend|)))@oe@9-2-2011 5100128@unknown@formal@none@1@S@A plus sign in a locus indicates that the genomic coordinates of the iORF can be described by a concatenation of two genes or regions.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 6) (:start . 2)\n (:id . 43))\n ((:tag . "NN") (:stem . "sign") (:form . "sign") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 14) (:start . 12)\n (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n (:id . 46))\n ((:tag . "NN") (:stem . "locus") (:form . "locus") (:end . 22) (:start . 17)\n (:id . 47))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 32)\n (:start . 23) (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 37) (:start . 33)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n (:id . 50))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 49)\n (:start . 42) (:id . 51))\n ((:tag . "NNS") (:stem . "coordinate") (:form . "coordinates") (:end . 61)\n (:start . 50) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n (:id . 54))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 73) (:start . 69)\n (:id . 55))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 77) (:start . 74)\n (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 80) (:start . 78)\n (:id . 57))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 90)\n (:start . 81) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 93) (:start . 91)\n (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 95) (:start . 94)\n (:id . 60))\n ((:tag . "NN") (:stem . "concatenation") (:form . "concatenation")\n (:end . 109) (:start . 96) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n (:id . 62))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 116) (:start . 113)\n (:id . 63))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 122)\n (:start . 117) (:id . 64))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 125) (:start . 123)\n (:id . 65))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 133)\n (:start . 126) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n (:id . 67)))@@@1@26@((:hcues ((:id . :x1.129.1) (:span 123 125))\n ((:id . :x1.129.2) (:span 23 37)))\n (:hscopes ((:id . :x1.129.1) (:span 117 133))\n ((:id . :x1.129.2) (:span 23 133)))\n (:identifiers (:sid . :s1.129) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100130@unknown@formal@none@1@S@HesB family was not clustered into one family, because their sequences were too short and diverged.@(((:tag . "NNP") (:stem . "HesB") (:form . "HesB") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "VBN") (:stem . "cluster") (:form . "clustered") (:end . 29)\n (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 34) (:start . 30)\n (:id . 47))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 38) (:start . 35)\n (:id . 48))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 45)\n (:start . 39) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n (:id . 50))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 54)\n (:start . 47) (:id . 51))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 60)\n (:start . 55) (:id . 52))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 70)\n (:start . 61) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 75) (:start . 71)\n (:id . 54))\n ((:tag . "RB") (:stem . "too") (:form . "too") (:end . 79) (:start . 76)\n (:id . 55))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 85) (:start . 80)\n (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n (:id . 57))\n ((:tag . "JJ") (:stem . "diverged") (:form . "diverged") (:end . 98)\n (:start . 90) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 59)))@@@1@18@((:ncues ((:id . :x1.131.1) (:span 16 19)))\n (:nscopes ((:id . :x1.131.1) (:span 0 45)))\n (:identifiers (:sid . :s1.131) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100131@unknown@formal@none@1@S@Selenoprotein families we failed to detect because of nonconserved location of stop codons@(((:tag . "NNP") (:stem . "Selenoprotein") (:form . "Selenoprotein")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 22)\n (:start . 14) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 25) (:start . 23)\n (:id . 44))\n ((:tag . "VBD") (:stem . "fail") (:form . "failed") (:end . 32) (:start . 26)\n (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n (:id . 46))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 42)\n (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 50)\n (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n (:id . 49))\n ((:tag . "JJ") (:stem . "nonconserved") (:form . "nonconserved") (:end . 66)\n (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "location") (:form . "location") (:end . 75)\n (:start . 67) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n (:id . 52))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 83) (:start . 79)\n (:id . 53))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 90)\n (:start . 84) (:id . 54)))@@@1@13@((:ncues ((:id . :x1.132.1) (:span 26 32)))\n (:nscopes ((:id . :x1.132.1) (:span 0 42)))\n (:identifiers (:sid . :s1.132) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|FigureLegend|)))@oe@9-2-2011 5100132@unknown@formal@none@1@S@Selenoprotein families we failed to detect because of nonconserved location of stop codons.@(((:tag . "NNP") (:stem . "Selenoprotein") (:form . "Selenoprotein")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 22)\n (:start . 14) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 25) (:start . 23)\n (:id . 44))\n ((:tag . "VBD") (:stem . "fail") (:form . "failed") (:end . 32) (:start . 26)\n (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n (:id . 46))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 42)\n (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 50)\n (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n (:id . 49))\n ((:tag . "JJ") (:stem . "nonconserved") (:form . "nonconserved") (:end . 66)\n (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "location") (:form . "location") (:end . 75)\n (:start . 67) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n (:id . 52))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 83) (:start . 79)\n (:id . 53))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 90)\n (:start . 84) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n (:id . 55)))@@@1@14@((:ncues ((:id . :x1.133.1) (:span 26 32)))\n (:nscopes ((:id . :x1.133.1) (:span 0 42)))\n (:identifiers (:sid . :s1.133) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100133@unknown@formal@none@1@S@Selenocysteine residues of Peroxiredoxin-like protein families constitute homologous redox motifs (TXXU and UXXC), but their positions are different between two families.@(((:tag . "NNP") (:stem . "Selenocysteine") (:form . "Selenocysteine")\n (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 23)\n (:start . 15) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 44))\n ((:tag . "JJ") (:stem . "peroxiredoxin-like") (:form . "Peroxiredoxin-like")\n (:end . 45) (:start . 27) (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 53)\n (:start . 46) (:id . 46))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 62)\n (:start . 54) (:id . 47))\n ((:tag . "VBP") (:stem . "constitute") (:form . "constitute") (:end . 73)\n (:start . 63) (:id . 48))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 84)\n (:start . 74) (:id . 49))\n ((:tag . "NN") (:stem . "redox") (:form . "redox") (:end . 90) (:start . 85)\n (:id . 50))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 97)\n (:start . 91) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 99) (:start . 98)\n (:id . 52))\n ((:tag . "NNP") (:stem . "TXXU") (:form . "TXXU") (:end . 103) (:start . 99)\n (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n (:id . 54))\n ((:tag . "NNP") (:stem . "UXXC") (:form . "UXXC") (:end . 112) (:start . 108)\n (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n (:id . 57))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 118) (:start . 115)\n (:id . 58))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 124)\n (:start . 119) (:id . 59))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 134)\n (:start . 125) (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 138) (:start . 135)\n (:id . 61))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 148)\n (:start . 139) (:id . 62))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 156)\n (:start . 149) (:id . 63))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 160) (:start . 157)\n (:id . 64))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 169)\n (:start . 161) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s1.134) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100134@unknown@formal@none@1@S@Columns are colored according to sequence conservation.@(((:tag . "NNS") (:stem . "column") (:form . "Columns") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 11) (:start . 8)\n (:id . 43))\n ((:tag . "VBN") (:stem . "color") (:form . "colored") (:end . 19)\n (:start . 12) (:id . 44))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 29)\n (:start . 20) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 32) (:start . 30)\n (:id . 46))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 41)\n (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 54)\n (:start . 42) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 55) (:start . 54)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s1.135) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100135@unknown@formal@none@1@S@Selenocysteine residues are shown in red, and the other residues in the redox motifs are shown in yellow.@(((:tag . "NNP") (:stem . "Selenocysteine") (:form . "Selenocysteine")\n (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 23)\n (:start . 15) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 27) (:start . 24)\n (:id . 44))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 33) (:start . 28)\n (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n (:id . 46))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 40) (:start . 37)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n (:id . 50))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 55) (:start . 50)\n (:id . 51))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 64)\n (:start . 56) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n (:id . 54))\n ((:tag . "NN") (:stem . "redox") (:form . "redox") (:end . 77) (:start . 72)\n (:id . 55))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 84)\n (:start . 78) (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 88) (:start . 85)\n (:id . 57))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 94) (:start . 89)\n (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 97) (:start . 95)\n (:id . 59))\n ((:tag . "NN") (:stem . "yellow") (:form . "yellow") (:end . 104)\n (:start . 98) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.136) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100136@unknown@formal@none@1@S@Prx; Peroxiredoxin, TPO; thiol:protein disulphide oxidereductase, Adeh; Anaeromyxobacter dehalogenans, Gmet; Geobacter metallireducens, Gsul; G. sulfurreducens, Dpsy; Desulfotalea psychrophila.@(((:tag . "NNP") (:stem . "Prx") (:form . "Prx") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 4) (:start . 3) (:id . 43))\n ((:tag . "NNP") (:stem . "Peroxiredoxin") (:form . "Peroxiredoxin")\n (:end . 18) (:start . 5) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n (:id . 45))\n ((:tag . "NNP") (:stem . "TPO") (:form . "TPO") (:end . 23) (:start . 20)\n (:id . 46))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 24) (:start . 23)\n (:id . 47))\n ((:tag . "JJ") (:stem . "thiol:protein") (:form . "thiol:protein")\n (:end . 38) (:start . 25) (:id . 48))\n ((:tag . "NN") (:stem . "disulphide") (:form . "disulphide") (:end . 49)\n (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "oxidereductase") (:form . "oxidereductase")\n (:end . 64) (:start . 50) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n (:id . 51))\n ((:tag . "NNP") (:stem . "Adeh") (:form . "Adeh") (:end . 70) (:start . 66)\n (:id . 52))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 71) (:start . 70)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Anaeromyxobacter") (:form . "Anaeromyxobacter")\n (:end . 88) (:start . 72) (:id . 54))\n ((:tag . "NNS") (:stem . "dehalogenan") (:form . "dehalogenans") (:end . 101)\n (:start . 89) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n (:id . 56))\n ((:tag . "NNP") (:stem . "Gmet") (:form . "Gmet") (:end . 107) (:start . 103)\n (:id . 57))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 108) (:start . 107)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Geobacter") (:form . "Geobacter") (:end . 118)\n (:start . 109) (:id . 59))\n ((:tag . "NNS") (:stem . "metallireducen") (:form . "metallireducens")\n (:end . 134) (:start . 119) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n (:id . 61))\n ((:tag . "NNP") (:stem . "Gsul") (:form . "Gsul") (:end . 140) (:start . 136)\n (:id . 62))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 141) (:start . 140)\n (:id . 63))\n ((:tag . "NNP") (:stem . "G.") (:form . "G.") (:end . 144) (:start . 142)\n (:id . 64))\n ((:tag . "VBZ") (:stem . "sulfurreducen") (:form . "sulfurreducens")\n (:end . 159) (:start . 145) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n (:id . 66))\n ((:tag . "NNP") (:stem . "Dpsy") (:form . "Dpsy") (:end . 165) (:start . 161)\n (:id . 67))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 166) (:start . 165)\n (:id . 68))\n ((:tag . "NNP") (:stem . "Desulfotalea") (:form . "Desulfotalea")\n (:end . 179) (:start . 167) (:id . 69))\n ((:tag . "NN") (:stem . "psychrophila") (:form . "psychrophila") (:end . 192)\n (:start . 180) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s1.137) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100137@unknown@formal@none@1@S@The alignments were computed using ClustalW, and the figures were generated using Jalview.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "VBN") (:stem . "compute") (:form . "computed") (:end . 28)\n (:start . 20) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 34) (:start . 29)\n (:id . 46))\n ((:tag . "NNP") (:stem . "ClustalW") (:form . "ClustalW") (:end . 43)\n (:start . 35) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n (:id . 50))\n ((:tag . "NNS") (:stem . "figure") (:form . "figures") (:end . 60)\n (:start . 53) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 65) (:start . 61)\n (:id . 52))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 75)\n (:start . 66) (:id . 53))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 81) (:start . 76)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Jalview") (:form . "Jalview") (:end . 89)\n (:start . 82) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s1.138) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100138@unknown@formal@none@1@S@Of the four pyrrolysine proteins detected, three methylamine methyltransferases have been experimentally confirmed to contain pyrrolysine 617.@(((:tag . "IN") (:stem . "of") (:form . "Of") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 23)\n (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 32)\n (:start . 24) (:id . 46))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 41)\n (:start . 33) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n (:id . 48))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 48) (:start . 43)\n (:id . 49))\n ((:tag . "NN") (:stem . "methylamine") (:form . "methylamine") (:end . 60)\n (:start . 49) (:id . 50))\n ((:tag . "NNS") (:stem . "methyltransferas") (:form . "methyltransferases")\n (:end . 79) (:start . 61) (:id . 51))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 84) (:start . 80)\n (:id . 52))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 89) (:start . 85)\n (:id . 53))\n ((:tag . "RB") (:stem . "experimentally") (:form . "experimentally")\n (:end . 104) (:start . 90) (:id . 54))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 114)\n (:start . 105) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 117) (:start . 115)\n (:id . 56))\n ((:tag . "VB") (:stem . "contain") (:form . "contain") (:end . 125)\n (:start . 118) (:id . 57))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 137)\n (:start . 126) (:id . 58))\n ((:tag . "CD") (:stem . "617") (:form . "617") (:end . 141) (:start . 138)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.139) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100140@unknown@formal@none@1@S@Since the genome annotation of M. acetivorans describes this protein as a gene containing an inframe amber codon, we classified it as a ''known'' candidate, although it is still unclear whether it really contains pyrrolysine.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 16)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 27)\n (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "NNP") (:stem . "M.") (:form . "M.") (:end . 33) (:start . 31)\n (:id . 47))\n ((:tag . "NNS") (:stem . "acetivoran") (:form . "acetivorans") (:end . 45)\n (:start . 34) (:id . 48))\n ((:tag . "VBZ") (:stem . "describe") (:form . "describes") (:end . 55)\n (:start . 46) (:id . 49))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 60) (:start . 56)\n (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 68)\n (:start . 61) (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 71) (:start . 69)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n (:id . 53))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 78) (:start . 74)\n (:id . 54))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 89)\n (:start . 79) (:id . 55))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 92) (:start . 90)\n (:id . 56))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 100)\n (:start . 93) (:id . 57))\n ((:tag . "NN") (:stem . "amber") (:form . "amber") (:end . 106)\n (:start . 101) (:id . 58))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 112)\n (:start . 107) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n (:id . 60))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 116) (:start . 114)\n (:id . 61))\n ((:tag . "VBD") (:stem . "classify") (:form . "classified") (:end . 127)\n (:start . 117) (:id . 62))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 130) (:start . 128)\n (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 133) (:start . 131)\n (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 135) (:start . 134)\n (:id . 65))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 135) (:start . 135)\n (:id . 66))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 143)\n (:start . 138) (:id . 67))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 143) (:start . 143)\n (:id . 68))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 155)\n (:start . 146) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n (:id . 70))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 165)\n (:start . 157) (:id . 71))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 168) (:start . 166)\n (:id . 72))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 171) (:start . 169)\n (:id . 73))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 177)\n (:start . 172) (:id . 74))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 185)\n (:start . 178) (:id . 75))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 193)\n (:start . 186) (:id . 76))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 196) (:start . 194)\n (:id . 77))\n ((:tag . "RB") (:stem . "really") (:form . "really") (:end . 203)\n (:start . 197) (:id . 78))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 212)\n (:start . 204) (:id . 79))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 224)\n (:start . 213) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n (:id . 81)))@@@1@40@((:hcues ((:id . :x1.141.1) (:span 186 193))\n ((:id . :x1.141.2) (:span 178 185)))\n (:hscopes ((:id . :x1.141.1) (:span 186 224))\n ((:id . :x1.141.2) (:span 178 224)))\n (:identifiers (:sid . :s1.141) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100141@unknown@formal@none@1@S@The genome annotation of M. acetivorans also includes several amber-containing genes that were absent from our prediction result.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 21)\n (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n (:id . 45))\n ((:tag . "NNP") (:stem . "M.") (:form . "M.") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "NNS") (:stem . "acetivoran") (:form . "acetivorans") (:end . 39)\n (:start . 28) (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 44) (:start . 40)\n (:id . 48))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 53)\n (:start . 45) (:id . 49))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 61)\n (:start . 54) (:id . 50))\n ((:tag . "JJ") (:stem . "amber-containing") (:form . "amber-containing")\n (:end . 78) (:start . 62) (:id . 51))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 84) (:start . 79)\n (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 89) (:start . 85)\n (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 94) (:start . 90)\n (:id . 54))\n ((:tag . "JJ") (:stem . "absent") (:form . "absent") (:end . 101)\n (:start . 95) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 106) (:start . 102)\n (:id . 56))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 110) (:start . 107)\n (:id . 57))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 121)\n (:start . 111) (:id . 58))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 128)\n (:start . 122) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n (:id . 60)))@@@1@19@((:ncues ((:id . :x1.142.1) (:span 95 101)))\n (:nscopes ((:id . :x1.142.1) (:span 85 128)))\n (:identifiers (:sid . :s1.142) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100142@unknown@formal@none@1@S@They are a methlycobamide:CoM methylase and four transposases 18.@(((:tag . "PRP") (:stem . "they") (:form . "They") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n (:id . 44))\n ((:tag . "JJ") (:stem . "methlycobamide:CoM") (:form . "methlycobamide:CoM")\n (:end . 29) (:start . 11) (:id . 45))\n ((:tag . "NN") (:stem . "methylase") (:form . "methylase") (:end . 39)\n (:start . 30) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n (:id . 47))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 48) (:start . 44)\n (:id . 48))\n ((:tag . "NNS") (:stem . "transposas") (:form . "transposases") (:end . 61)\n (:start . 49) (:id . 49))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 64) (:start . 62)\n (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s1.143) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100143@unknown@formal@none@1@S@The reason why they were not detected is that only one species in our dataset had an amber-containing form of these proteins.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "reason") (:form . "reason") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "WRB") (:stem . "why") (:form . "why") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 19) (:start . 15)\n (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 24) (:start . 20)\n (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 28) (:start . 25)\n (:id . 47))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 37)\n (:start . 29) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 40) (:start . 38)\n (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 45) (:start . 41)\n (:id . 50))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 50) (:start . 46)\n (:id . 51))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 54) (:start . 51)\n (:id . 52))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 62)\n (:start . 55) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n (:id . 54))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 69) (:start . 66)\n (:id . 55))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 77)\n (:start . 70) (:id . 56))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 81) (:start . 78)\n (:id . 57))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 84) (:start . 82)\n (:id . 58))\n ((:tag . "JJ") (:stem . "amber-containing") (:form . "amber-containing")\n (:end . 101) (:start . 85) (:id . 59))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 106) (:start . 102)\n (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 109) (:start . 107)\n (:id . 61))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 115)\n (:start . 110) (:id . 62))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 124)\n (:start . 116) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n (:id . 64)))@@@1@23@((:ncues ((:id . :x1.144.1) (:span 25 28)))\n (:nscopes ((:id . :x1.144.1) (:span 15 37)))\n (:identifiers (:sid . :s1.144) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100144@unknown@formal@none@1@S@This is unavoidable because of the inability of our method to detect species-specific readthrough events.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "JJ") (:stem . "unavoidable") (:form . "unavoidable") (:end . 19)\n (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 27)\n (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "NN") (:stem . "inability") (:form . "inability") (:end . 44)\n (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 51) (:start . 48)\n (:id . 50))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 58)\n (:start . 52) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 61) (:start . 59)\n (:id . 52))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 68)\n (:start . 62) (:id . 53))\n ((:tag . "JJ") (:stem . "species-specific") (:form . "species-specific")\n (:end . 85) (:start . 69) (:id . 54))\n ((:tag . "NN") (:stem . "readthrough") (:form . "readthrough") (:end . 97)\n (:start . 86) (:id . 55))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 104)\n (:start . 98) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.145) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100145@unknown@formal@none@1@S@It is the price for reliably excluding pseudogenes and sequencing errors.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n (:id . 44))\n ((:tag . "NN") (:stem . "price") (:form . "price") (:end . 15) (:start . 10)\n (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 19) (:start . 16)\n (:id . 46))\n ((:tag . "RB") (:stem . "reliably") (:form . "reliably") (:end . 28)\n (:start . 20) (:id . 47))\n ((:tag . "VBG") (:stem . "exclude") (:form . "excluding") (:end . 38)\n (:start . 29) (:id . 48))\n ((:tag . "NNS") (:stem . "pseudogene") (:form . "pseudogenes") (:end . 50)\n (:start . 39) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n (:id . 50))\n ((:tag . "NN") (:stem . "sequencing") (:form . "sequencing") (:end . 65)\n (:start . 55) (:id . 51))\n ((:tag . "NNS") (:stem . "error") (:form . "errors") (:end . 72)\n (:start . 66) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s1.146) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100146@unknown@formal@none@1@S@Unknown candidates in the predicted clusters@(((:tag . "JJ") (:stem . "unknown") (:form . "Unknown") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 18)\n (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 21) (:start . 19)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 35)\n (:start . 26) (:id . 46))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 44)\n (:start . 36) (:id . 47)))@@@1@6@((:identifiers (:sid . :s1.147) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100147@unknown@formal@none@1@S@The successful detection of many known proteins is encouraging, because our method relies only on general properties of proteins that contain stop-codon-encoded amino acids, but not on specific features of selenocysteine or pyrrolysine.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "successful") (:form . "successful") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "detection") (:form . "detection") (:end . 24)\n (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n (:id . 45))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 32) (:start . 28)\n (:id . 46))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 38) (:start . 33)\n (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 47)\n (:start . 39) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 50) (:start . 48)\n (:id . 49))\n ((:tag . "VBG") (:stem . "encourage") (:form . "encouraging") (:end . 62)\n (:start . 51) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n (:id . 51))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 71)\n (:start . 64) (:id . 52))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 75) (:start . 72)\n (:id . 53))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 82)\n (:start . 76) (:id . 54))\n ((:tag . "VBZ") (:stem . "rely") (:form . "relies") (:end . 89) (:start . 83)\n (:id . 55))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 94) (:start . 90)\n (:id . 56))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 97) (:start . 95)\n (:id . 57))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 105)\n (:start . 98) (:id . 58))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 116)\n (:start . 106) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n (:id . 60))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 128)\n (:start . 120) (:id . 61))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 133) (:start . 129)\n (:id . 62))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 141)\n (:start . 134) (:id . 63))\n ((:tag . "JJ") (:stem . "stop-codon-encoded") (:form . "stop-codon-encoded")\n (:end . 160) (:start . 142) (:id . 64))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 166)\n (:start . 161) (:id . 65))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 172)\n (:start . 167) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 173) (:start . 172)\n (:id . 67))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 177) (:start . 174)\n (:id . 68))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 181) (:start . 178)\n (:id . 69))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 184) (:start . 182)\n (:id . 70))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 193)\n (:start . 185) (:id . 71))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 202)\n (:start . 194) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 205) (:start . 203)\n (:id . 73))\n ((:tag . "NN") (:stem . "selenocysteine") (:form . "selenocysteine")\n (:end . 220) (:start . 206) (:id . 74))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 223) (:start . 221)\n (:id . 75))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 235)\n (:start . 224) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 236) (:start . 235)\n (:id . 77)))@@@1@36@((:ncues ((:id . :x1.148.1) (:span 178 181)))\n (:nscopes ((:id . :x1.148.1) (:span 178 235)))\n (:identifiers (:sid . :s1.148) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100148@unknown@formal@none@1@S@Therefore, unknown clusters in our candidates have possibilities for the 23rd amino acid or novel readthrough proteins.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 18)\n (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 27)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 45)\n (:start . 35) (:id . 48))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 50) (:start . 46)\n (:id . 49))\n ((:tag . "NNS") (:stem . "possibility") (:form . "possibilities") (:end . 64)\n (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 68) (:start . 65)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n (:id . 52))\n ((:tag . "JJ") (:stem . "23rd") (:form . "23rd") (:end . 77) (:start . 73)\n (:id . 53))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 83) (:start . 78)\n (:id . 54))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 88) (:start . 84)\n (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 91) (:start . 89)\n (:id . 56))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 97) (:start . 92)\n (:id . 57))\n ((:tag . "NN") (:stem . "readthrough") (:form . "readthrough") (:end . 109)\n (:start . 98) (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 118)\n (:start . 110) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.149) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100150@unknown@formal@none@1@S@The first cluster is comprised of c-type cytochromes from δ-proteobacteria Geobacter sulfurreducens and G. metallireducens.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 17)\n (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 20) (:start . 18)\n (:id . 45))\n ((:tag . "VBN") (:stem . "comprise") (:form . "comprised") (:end . 30)\n (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n (:id . 47))\n ((:tag . "JJ") (:stem . "c-type") (:form . "c-type") (:end . 40)\n (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "cytochrome") (:form . "cytochromes") (:end . 52)\n (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 57) (:start . 53)\n (:id . 50))\n ((:tag . "NNP") (:stem . "δ-proteobacteria") (:form . "δ-proteobacteria")\n (:end . 74) (:start . 58) (:id . 51))\n ((:tag . "NNP") (:stem . "Geobacter") (:form . "Geobacter") (:end . 84)\n (:start . 75) (:id . 52))\n ((:tag . "NNS") (:stem . "sulfurreducen") (:form . "sulfurreducens")\n (:end . 99) (:start . 85) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n (:id . 54))\n ((:tag . "NNP") (:stem . "G.") (:form . "G.") (:end . 106) (:start . 104)\n (:id . 55))\n ((:tag . "NNS") (:stem . "metallireducen") (:form . "metallireducens")\n (:end . 122) (:start . 107) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.151) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100151@unknown@formal@none@1@S@The N-terminal part of the sequence contains five CXXCH heme-biding motifs, while the C-terminal part has no similarity with any characterized proteins.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 35)\n (:start . 27) (:id . 47))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 44)\n (:start . 36) (:id . 48))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 49) (:start . 45)\n (:id . 49))\n ((:tag . "NNP") (:stem . "CXXCH") (:form . "CXXCH") (:end . 55) (:start . 50)\n (:id . 50))\n ((:tag . "JJ") (:stem . "heme-biding") (:form . "heme-biding") (:end . 67)\n (:start . 56) (:id . 51))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 74)\n (:start . 68) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n (:id . 53))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 81) (:start . 76)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n (:id . 55))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 96)\n (:start . 86) (:id . 56))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 101) (:start . 97)\n (:id . 57))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 105) (:start . 102)\n (:id . 58))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 108) (:start . 106)\n (:id . 59))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 119)\n (:start . 109) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 124) (:start . 120)\n (:id . 61))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 128) (:start . 125)\n (:id . 62))\n ((:tag . "VBN") (:stem . "characterize") (:form . "characterized")\n (:end . 142) (:start . 129) (:id . 63))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 151)\n (:start . 143) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n (:id . 65)))@@@1@24@((:ncues ((:id . :x1.152.1) (:span 106 108)))\n (:nscopes ((:id . :x1.152.1) (:span 106 151)))\n (:identifiers (:sid . :s1.152) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100152@unknown@formal@none@1@S@Homology search against unfinished microbial genomes identified seven homologous proteins from four other δ-proteobacteria species.@(((:tag . "NNP") (:stem . "Homology") (:form . "Homology") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 15) (:start . 9)\n (:id . 43))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 23)\n (:start . 16) (:id . 44))\n ((:tag . "JJ") (:stem . "unfinished") (:form . "unfinished") (:end . 34)\n (:start . 24) (:id . 45))\n ((:tag . "JJ") (:stem . "microbial") (:form . "microbial") (:end . 44)\n (:start . 35) (:id . 46))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 52)\n (:start . 45) (:id . 47))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 63)\n (:start . 53) (:id . 48))\n ((:tag . "CD") (:stem . "seven") (:form . "seven") (:end . 69) (:start . 64)\n (:id . 49))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 80)\n (:start . 70) (:id . 50))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 89)\n (:start . 81) (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 94) (:start . 90)\n (:id . 52))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 99) (:start . 95)\n (:id . 53))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 105)\n (:start . 100) (:id . 54))\n ((:tag . "NNP") (:stem . "δ-proteobacteria") (:form . "δ-proteobacteria")\n (:end . 122) (:start . 106) (:id . 55))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 130)\n (:start . 123) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.153) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100153@unknown@formal@none@1@S@Multiple sequence alignment of these sequences is shown in Figure 4a.@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 17)\n (:start . 9) (:id . 43))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 27)\n (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 36) (:start . 31)\n (:id . 46))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 46)\n (:start . 37) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 49) (:start . 47)\n (:id . 48))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 55) (:start . 50)\n (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 65)\n (:start . 59) (:id . 51))\n ((:tag . "NN") (:stem . "4a") (:form . "4a") (:end . 68) (:start . 66)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s1.154) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100154@unknown@formal@none@1@S@Multiple sequence alignments of novel candidate proteins@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 17)\n (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 28)\n (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n (:id . 45))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 37) (:start . 32)\n (:id . 46))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 47)\n (:start . 38) (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 56)\n (:start . 48) (:id . 48)))@@@1@7@((:identifiers (:sid . :s1.155) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100155@unknown@formal@none@1@S@Multiple sequence alignments of novel candidate proteins.@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 17)\n (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 28)\n (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n (:id . 45))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 37) (:start . 32)\n (:id . 46))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 47)\n (:start . 38) (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 56)\n (:start . 48) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 57) (:start . 56)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s1.156) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100156@unknown@formal@none@1@S@(a) A selenoprotein candidate from Geobacter sulfurreducens and its homologs.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "LS") (:stem . "a") (:form . "a") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 5) (:start . 4)\n (:id . 45))\n ((:tag . "NN") (:stem . "selenoprotein") (:form . "selenoprotein")\n (:end . 19) (:start . 6) (:id . 46))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 29)\n (:start . 20) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 34) (:start . 30)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Geobacter") (:form . "Geobacter") (:end . 44)\n (:start . 35) (:id . 49))\n ((:tag . "NNS") (:stem . "sulfurreducen") (:form . "sulfurreducens")\n (:end . 59) (:start . 45) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n (:id . 51))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 67) (:start . 64)\n (:id . 52))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 76)\n (:start . 68) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s1.157) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100157@unknown@formal@none@1@S@The possible selenocysteine residues are shown in red, and putative heme-binding motifs are underlined.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "selenocysteine") (:form . "selenocysteine")\n (:end . 27) (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 36)\n (:start . 28) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 40) (:start . 37)\n (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 46) (:start . 41)\n (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n (:id . 48))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 53) (:start . 50)\n (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n (:id . 51))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 67)\n (:start . 59) (:id . 52))\n ((:tag . "JJ") (:stem . "heme-binding") (:form . "heme-binding") (:end . 80)\n (:start . 68) (:id . 53))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 87)\n (:start . 81) (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 91) (:start . 88)\n (:id . 55))\n ((:tag . "VBN") (:stem . "underline") (:form . "underlined") (:end . 102)\n (:start . 92) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n (:id . 57)))@@@1@16@((:hcues ((:id . :x1.158.1) (:span 59 67)) ((:id . :x1.158.2) (:span 4 12)))\n (:hscopes ((:id . :x1.158.1) (:span 59 87)) ((:id . :x1.158.2) (:span 4 36)))\n (:identifiers (:sid . :s1.158) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100158@unknown@formal@none@1@S@Note that sequence conservation near the selenocysteine is comparable to that of the N-terminal cytochrome domain.@(((:tag . "VB") (:stem . "note") (:form . "Note") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 18)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 31)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "near") (:form . "near") (:end . 36) (:start . 32)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n (:id . 47))\n ((:tag . "NN") (:stem . "selenocysteine") (:form . "selenocysteine")\n (:end . 55) (:start . 41) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 58) (:start . 56)\n (:id . 49))\n ((:tag . "JJ") (:stem . "comparable") (:form . "comparable") (:end . 69)\n (:start . 59) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n (:id . 51))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 77) (:start . 73)\n (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n (:id . 54))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 95)\n (:start . 85) (:id . 55))\n ((:tag . "NN") (:stem . "cytochrome") (:form . "cytochrome") (:end . 106)\n (:start . 96) (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 113)\n (:start . 107) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.159) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100160@unknown@formal@none@1@S@It will be either a sequencing error or a pseudogene.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 10) (:start . 8)\n (:id . 44))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 17)\n (:start . 11) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 19) (:start . 18)\n (:id . 46))\n ((:tag . "NN") (:stem . "sequencing") (:form . "sequencing") (:end . 30)\n (:start . 20) (:id . 47))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 36) (:start . 31)\n (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 39) (:start . 37)\n (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 41) (:start . 40)\n (:id . 50))\n ((:tag . "NN") (:stem . "pseudogene") (:form . "pseudogene") (:end . 52)\n (:start . 42) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 53) (:start . 52)\n (:id . 52)))@@@1@11@((:hcues ((:id . :x1.161.1) (:span 11 17 37 39)))\n (:hscopes ((:id . :x1.161.1) (:span 11 52)))\n (:identifiers (:sid . :s1.161) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100161@unknown@formal@none@1@S@Gsul; G. sulfurreducens, Gmet; G. metallireducens, Gura; G. uraniumreducens, Gfrc; Geobacter sp. FRC-32, Dace; Desulfuromonas acetoxidans, Dpro; Delta proteobacterium MLMS-1.@(((:tag . "NNP") (:stem . "Gsul") (:form . "Gsul") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "G.") (:form . "G.") (:end . 8) (:start . 6)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "sulfurreducen") (:form . "sulfurreducens")\n (:end . 23) (:start . 9) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Gmet") (:form . "Gmet") (:end . 29) (:start . 25)\n (:id . 47))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 30) (:start . 29)\n (:id . 48))\n ((:tag . "NNP") (:stem . "G.") (:form . "G.") (:end . 33) (:start . 31)\n (:id . 49))\n ((:tag . "NNS") (:stem . "metallireducen") (:form . "metallireducens")\n (:end . 49) (:start . 34) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n (:id . 51))\n ((:tag . "NNP") (:stem . "Gura") (:form . "Gura") (:end . 55) (:start . 51)\n (:id . 52))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 56) (:start . 55)\n (:id . 53))\n ((:tag . "NNP") (:stem . "G.") (:form . "G.") (:end . 59) (:start . 57)\n (:id . 54))\n ((:tag . "VBZ") (:stem . "uraniumreducen") (:form . "uraniumreducens")\n (:end . 75) (:start . 60) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n (:id . 56))\n ((:tag . "NNP") (:stem . "Gfrc") (:form . "Gfrc") (:end . 81) (:start . 77)\n (:id . 57))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 82) (:start . 81)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Geobacter") (:form . "Geobacter") (:end . 92)\n (:start . 83) (:id . 59))\n ((:tag . "NNP") (:stem . "sp.") (:form . "sp.") (:end . 96) (:start . 93)\n (:id . 60))\n ((:tag . "NNP") (:stem . "FRC-32") (:form . "FRC-32") (:end . 103)\n (:start . 97) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n (:id . 62))\n ((:tag . "NNP") (:stem . "Dace") (:form . "Dace") (:end . 109) (:start . 105)\n (:id . 63))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 110) (:start . 109)\n (:id . 64))\n ((:tag . "NNP") (:stem . "Desulfuromonas") (:form . "Desulfuromonas")\n (:end . 125) (:start . 111) (:id . 65))\n ((:tag . "NNS") (:stem . "acetoxidan") (:form . "acetoxidans") (:end . 137)\n (:start . 126) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n (:id . 67))\n ((:tag . "NNP") (:stem . "Dpro") (:form . "Dpro") (:end . 143) (:start . 139)\n (:id . 68))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 144) (:start . 143)\n (:id . 69))\n ((:tag . "NNP") (:stem . "Delta") (:form . "Delta") (:end . 150)\n (:start . 145) (:id . 70))\n ((:tag . "NN") (:stem . "proteobacterium") (:form . "proteobacterium")\n (:end . 166) (:start . 151) (:id . 71))\n ((:tag . "NN") (:stem . "mlms-1") (:form . "MLMS-1") (:end . 173)\n (:start . 167) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s1.162) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100162@unknown@formal@none@1@S@(b) Hypothetical proteins from Geobacter species.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "b") (:form . "b") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "hypothetical") (:form . "Hypothetical") (:end . 16)\n (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 25)\n (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 30) (:start . 26)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Geobacter") (:form . "Geobacter") (:end . 40)\n (:start . 31) (:id . 48))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 48)\n (:start . 41) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s1.163) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100163@unknown@formal@none@1@S@The inframe stop codons (TAG) are shown in red.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 23)\n (:start . 17) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n (:id . 46))\n ((:tag . "NNP") (:stem . "TAG") (:form . "TAG") (:end . 28) (:start . 25)\n (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 29) (:start . 28)\n (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 33) (:start . 30)\n (:id . 49))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 39) (:start . 34)\n (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n (:id . 51))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 46) (:start . 43)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 47) (:start . 46)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s1.164) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100164@unknown@formal@none@1@S@This cluster is probably an artifact of close phylogenetic relationship.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "RB") (:stem . "probably") (:form . "probably") (:end . 24)\n (:start . 16) (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "NN") (:stem . "artifact") (:form . "artifact") (:end . 36)\n (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n (:id . 48))\n ((:tag . "JJ") (:stem . "close") (:form . "close") (:end . 45) (:start . 40)\n (:id . 49))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 58)\n (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "relationship") (:form . "relationship") (:end . 71)\n (:start . 59) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n (:id . 52)))@@@1@11@((:hcues ((:id . :x1.165.1) (:span 16 24)))\n (:hscopes ((:id . :x1.165.1) (:span 16 71)))\n (:identifiers (:sid . :s1.165) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100165@unknown@formal@none@1@S@We expect that this cluster may represent a novel selenoprotein family.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "expect") (:form . "expect") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 19) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 27)\n (:start . 20) (:id . 46))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 31) (:start . 28)\n (:id . 47))\n ((:tag . "VB") (:stem . "represent") (:form . "represent") (:end . 41)\n (:start . 32) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 43) (:start . 42)\n (:id . 49))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 49) (:start . 44)\n (:id . 50))\n ((:tag . "NN") (:stem . "selenoprotein") (:form . "selenoprotein")\n (:end . 63) (:start . 50) (:id . 51))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 70)\n (:start . 64) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n (:id . 53)))@@@1@12@((:hcues ((:id . :x1.166.1) (:span 28 31)) ((:id . :x1.166.2) (:span 3 9)))\n (:hscopes ((:id . :x1.166.1) (:span 28 70)) ((:id . :x1.166.2) (:span 3 70)))\n (:identifiers (:sid . :s1.166) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100166@unknown@formal@none@1@S@This is because the inframe stop codons of these proteins are exclusively TGA, and all of the above organisms possess selenocysteine insertion machinery (data not shown).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 15)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 27)\n (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 32) (:start . 28)\n (:id . 47))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 39)\n (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n (:id . 49))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 48) (:start . 43)\n (:id . 50))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 57)\n (:start . 49) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 61) (:start . 58)\n (:id . 52))\n ((:tag . "RB") (:stem . "exclusively") (:form . "exclusively") (:end . 73)\n (:start . 62) (:id . 53))\n ((:tag . "NNP") (:stem . "TGA") (:form . "TGA") (:end . 77) (:start . 74)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 86) (:start . 83)\n (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n (:id . 59))\n ((:tag . "JJ") (:stem . "above") (:form . "above") (:end . 99) (:start . 94)\n (:id . 60))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 109)\n (:start . 100) (:id . 61))\n ((:tag . "VBP") (:stem . "possess") (:form . "possess") (:end . 117)\n (:start . 110) (:id . 62))\n ((:tag . "NN") (:stem . "selenocysteine") (:form . "selenocysteine")\n (:end . 132) (:start . 118) (:id . 63))\n ((:tag . "NN") (:stem . "insertion") (:form . "insertion") (:end . 142)\n (:start . 133) (:id . 64))\n ((:tag . "NN") (:stem . "machinery") (:form . "machinery") (:end . 152)\n (:start . 143) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n (:id . 66))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 158)\n (:start . 154) (:id . 67))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 162) (:start . 159)\n (:id . 68))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 168)\n (:start . 163) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n (:id . 71)))@@@1@30@((:ncues ((:id . :x1.167.1) (:span 159 162)))\n (:nscopes ((:id . :x1.167.1) (:span 153 169)))\n (:identifiers (:sid . :s1.167) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100167@unknown@formal@none@1@S@High conservation of residues near the inframe stop codon also suggests the importance of this region.@(((:tag . "JJ") (:stem . "high") (:form . "High") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 17)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 44))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 29)\n (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "near") (:form . "near") (:end . 34) (:start . 30)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n (:id . 47))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 46)\n (:start . 39) (:id . 48))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 51) (:start . 47)\n (:id . 49))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 57) (:start . 52)\n (:id . 50))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 62) (:start . 58)\n (:id . 51))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 71)\n (:start . 63) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n (:id . 53))\n ((:tag . "NN") (:stem . "importance") (:form . "importance") (:end . 86)\n (:start . 76) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n (:id . 55))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 94) (:start . 90)\n (:id . 56))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 101)\n (:start . 95) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n (:id . 58)))@@@1@17@((:hcues ((:id . :x1.168.1) (:span 63 71)))\n (:hscopes ((:id . :x1.168.1) (:span 63 101)))\n (:identifiers (:sid . :s1.168) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100168@unknown@formal@none@1@S@If they are true selenoproteins, this protein family becomes a rare instance of selenoprotein that lacks non-selenocysteine homologs.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 11) (:start . 8)\n (:id . 44))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 16) (:start . 12)\n (:id . 45))\n ((:tag . "NNS") (:stem . "selenoprotein") (:form . "selenoproteins")\n (:end . 31) (:start . 17) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 37) (:start . 33)\n (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 45)\n (:start . 38) (:id . 49))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 52)\n (:start . 46) (:id . 50))\n ((:tag . "VBZ") (:stem . "become") (:form . "becomes") (:end . 60)\n (:start . 53) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 62) (:start . 61)\n (:id . 52))\n ((:tag . "JJ") (:stem . "rare") (:form . "rare") (:end . 67) (:start . 63)\n (:id . 53))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 76)\n (:start . 68) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n (:id . 55))\n ((:tag . "NN") (:stem . "selenoprotein") (:form . "selenoprotein")\n (:end . 93) (:start . 80) (:id . 56))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 98) (:start . 94)\n (:id . 57))\n ((:tag . "VBZ") (:stem . "lack") (:form . "lacks") (:end . 104) (:start . 99)\n (:id . 58))\n ((:tag . "JJ") (:stem . "non-selenocysteine") (:form . "non-selenocysteine")\n (:end . 123) (:start . 105) (:id . 59))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 132)\n (:start . 124) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n (:id . 61)))@@@1@20@((:ncues ((:id . :x1.169.1) (:span 99 104)))\n (:nscopes ((:id . :x1.169.1) (:span 99 132)))\n (:identifiers (:sid . :s1.169) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100170@unknown@formal@none@1@S@Therefore, yet another possibility is that they are a highly conserved operon.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "CC") (:stem . "yet") (:form . "yet") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 22)\n (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 34)\n (:start . 23) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 37) (:start . 35)\n (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 42) (:start . 38)\n (:id . 48))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 47) (:start . 43)\n (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 51) (:start . 48)\n (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n (:id . 51))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 60)\n (:start . 54) (:id . 52))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 70)\n (:start . 61) (:id . 53))\n ((:tag . "NN") (:stem . "operon") (:form . "operon") (:end . 77)\n (:start . 71) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n (:id . 55)))@@@1@14@((:hcues ((:id . :x1.171.1) (:span 23 34)))\n (:hscopes ((:id . :x1.171.1) (:span 23 77)))\n (:identifiers (:sid . :s1.171) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100171@unknown@formal@none@1@S@An experimental verification is necessary to distinguish these two possibilities.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 15)\n (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "verification") (:form . "verification") (:end . 28)\n (:start . 16) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 31) (:start . 29)\n (:id . 45))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 41)\n (:start . 32) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n (:id . 47))\n ((:tag . "VB") (:stem . "distinguish") (:form . "distinguish") (:end . 56)\n (:start . 45) (:id . 48))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 62) (:start . 57)\n (:id . 49))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 66) (:start . 63)\n (:id . 50))\n ((:tag . "NNS") (:stem . "possibility") (:form . "possibilities") (:end . 80)\n (:start . 67) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s1.172) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100172@unknown@formal@none@1@S@The second cluster consists of two hypothetical proteins, again from G. sulfurreducens and G. metallireducens (Figure 4b).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 18)\n (:start . 11) (:id . 44))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 27)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "JJ") (:stem . "hypothetical") (:form . "hypothetical") (:end . 47)\n (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 56)\n (:start . 48) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n (:id . 50))\n ((:tag . "RB") (:stem . "again") (:form . "again") (:end . 63) (:start . 58)\n (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 68) (:start . 64)\n (:id . 52))\n ((:tag . "NNP") (:stem . "G.") (:form . "G.") (:end . 71) (:start . 69)\n (:id . 53))\n ((:tag . "NNP") (:stem . "sulfurreducens") (:form . "sulfurreducens")\n (:end . 86) (:start . 72) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n (:id . 55))\n ((:tag . "NNP") (:stem . "G.") (:form . "G.") (:end . 93) (:start . 91)\n (:id . 56))\n ((:tag . "NNS") (:stem . "metallireducen") (:form . "metallireducens")\n (:end . 109) (:start . 94) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 117)\n (:start . 111) (:id . 59))\n ((:tag . "NNP") (:stem . "4b") (:form . "4b") (:end . 120) (:start . 118)\n (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 121) (:start . 120)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s1.173) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100173@unknown@formal@none@1@S@In contrast to the first cluster, no homolog was identified from other species.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 24) (:start . 19)\n (:id . 46))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 32)\n (:start . 25) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n (:id . 48))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 36) (:start . 34)\n (:id . 49))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 44)\n (:start . 37) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 48) (:start . 45)\n (:id . 51))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 59)\n (:start . 49) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 64) (:start . 60)\n (:id . 53))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 70) (:start . 65)\n (:id . 54))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 78)\n (:start . 71) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n (:id . 56)))@@@1@15@((:ncues ((:id . :x1.174.1) (:span 34 36)))\n (:nscopes ((:id . :x1.174.1) (:span 34 78)))\n (:identifiers (:sid . :s1.174) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100174@unknown@formal@none@1@S@This cluster is probably a false positive and not readthrough proteins.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "RB") (:stem . "probably") (:form . "probably") (:end . 24)\n (:start . 16) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n (:id . 46))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 32) (:start . 27)\n (:id . 47))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 41)\n (:start . 33) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 49) (:start . 46)\n (:id . 50))\n ((:tag . "VB") (:stem . "readthrough") (:form . "readthrough") (:end . 61)\n (:start . 50) (:id . 51))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 70)\n (:start . 62) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n (:id . 53)))@@@1@12@((:hcues ((:id . :x1.175.2) (:span 16 24)))\n (:ncues ((:id . :x1.175.1) (:span 46 49)))\n (:hscopes ((:id . :x1.175.2) (:span 16 70)))\n (:nscopes ((:id . :x1.175.1) (:span 46 70)))\n (:identifiers (:sid . :s1.175) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100175@unknown@formal@none@1@S@This is because the residues near the inframe stop codons are poorly conserved.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 15)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 28)\n (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "near") (:form . "near") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n (:id . 48))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 45)\n (:start . 38) (:id . 49))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 50) (:start . 46)\n (:id . 50))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 57)\n (:start . 51) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 61) (:start . 58)\n (:id . 52))\n ((:tag . "RB") (:stem . "poorly") (:form . "poorly") (:end . 68)\n (:start . 62) (:id . 53))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 78)\n (:start . 69) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s1.176) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100176@unknown@formal@none@1@S@Moreover, the C-terminal extensions are quite short (about 20 aa).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 24)\n (:start . 14) (:id . 45))\n ((:tag . "NNS") (:stem . "extension") (:form . "extensions") (:end . 35)\n (:start . 25) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 39) (:start . 36)\n (:id . 47))\n ((:tag . "RB") (:stem . "quite") (:form . "quite") (:end . 45) (:start . 40)\n (:id . 48))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 51) (:start . 46)\n (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 53) (:start . 52)\n (:id . 50))\n ((:tag . "RB") (:stem . "about") (:form . "about") (:end . 58) (:start . 53)\n (:id . 51))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 61) (:start . 59)\n (:id . 52))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 64) (:start . 62)\n (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 65) (:start . 64)\n (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s1.177) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100177@unknown@formal@none@1@S@The sequence conservation in this region can be easily explained by the close phylogenetic relationship between the two species.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 25)\n (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 28) (:start . 26)\n (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 33) (:start . 29)\n (:id . 46))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 40)\n (:start . 34) (:id . 47))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 44) (:start . 41)\n (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "RB") (:stem . "easily") (:form . "easily") (:end . 54)\n (:start . 48) (:id . 50))\n ((:tag . "VBN") (:stem . "explain") (:form . "explained") (:end . 64)\n (:start . 55) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 67) (:start . 65)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n (:id . 53))\n ((:tag . "JJ") (:stem . "close") (:form . "close") (:end . 77) (:start . 72)\n (:id . 54))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 90)\n (:start . 78) (:id . 55))\n ((:tag . "NN") (:stem . "relationship") (:form . "relationship") (:end . 103)\n (:start . 91) (:id . 56))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 111)\n (:start . 104) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n (:id . 58))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 119) (:start . 116)\n (:id . 59))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 127)\n (:start . 120) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.178) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100178@unknown@formal@none@1@S@In summary, although a possible selenoprotein was newly identified, there was no promising candidate for an unknown amino acid encoded by a stop codon.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "summary") (:form . "summary") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 44))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 20)\n (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n (:id . 46))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 31)\n (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "selenoprotein") (:form . "selenoprotein")\n (:end . 45) (:start . 32) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "RB") (:stem . "newly") (:form . "newly") (:end . 55) (:start . 50)\n (:id . 50))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 66)\n (:start . 56) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n (:id . 52))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 73) (:start . 68)\n (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 77) (:start . 74)\n (:id . 54))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 80) (:start . 78)\n (:id . 55))\n ((:tag . "JJ") (:stem . "promising") (:form . "promising") (:end . 90)\n (:start . 81) (:id . 56))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 100)\n (:start . 91) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 104) (:start . 101)\n (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 107) (:start . 105)\n (:id . 59))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 115)\n (:start . 108) (:id . 60))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 121)\n (:start . 116) (:id . 61))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 126) (:start . 122)\n (:id . 62))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 134)\n (:start . 127) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 137) (:start . 135)\n (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 139) (:start . 138)\n (:id . 65))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 144) (:start . 140)\n (:id . 66))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 150)\n (:start . 145) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n (:id . 68)))@@@1@27@((:ncues ((:id . :x1.179.1) (:span 78 80)))\n (:nscopes ((:id . :x1.179.1) (:span 78 150)))\n (:identifiers (:sid . :s1.179) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100180@unknown@formal@none@1@S@The above negative result could be explained if the filtering process, which is the final step of the prediction method (Figure 2), was too strict.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "above") (:form . "above") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 18)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 25)\n (:start . 19) (:id . 45))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 31) (:start . 26)\n (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 34) (:start . 32)\n (:id . 47))\n ((:tag . "VBN") (:stem . "explain") (:form . "explained") (:end . 44)\n (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n (:id . 50))\n ((:tag . "VBG") (:stem . "filter") (:form . "filtering") (:end . 61)\n (:start . 52) (:id . 51))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 69)\n (:start . 62) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 76) (:start . 71)\n (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 79) (:start . 77)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n (:id . 56))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 89) (:start . 84)\n (:id . 57))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 94) (:start . 90)\n (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n (:id . 60))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 112)\n (:start . 102) (:id . 61))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 119)\n (:start . 113) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n (:id . 63))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 127)\n (:start . 121) (:id . 64))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 129) (:start . 128)\n (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 130) (:start . 129)\n (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n (:id . 67))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 135) (:start . 132)\n (:id . 68))\n ((:tag . "RB") (:stem . "too") (:form . "too") (:end . 139) (:start . 136)\n (:id . 69))\n ((:tag . "JJ") (:stem . "strict") (:form . "strict") (:end . 146)\n (:start . 140) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n (:id . 71)))@@@1@30@((:hcues ((:id . :x1.181.1) (:span 26 31)))\n (:hscopes ((:id . :x1.181.1) (:span 0 146)))\n (:identifiers (:sid . :s1.181) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100181@unknown@formal@none@1@S@Although the raw output of the search for evolutionarily conserved iORFs was 273 clusters, most of them were discarded at the subsequent filtering stage.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 43))\n ((:tag . "JJ") (:stem . "raw") (:form . "raw") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 23)\n (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 37)\n (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 41) (:start . 38)\n (:id . 49))\n ((:tag . "RB") (:stem . "evolutionarily") (:form . "evolutionarily")\n (:end . 56) (:start . 42) (:id . 50))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 66)\n (:start . 57) (:id . 51))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 72) (:start . 67)\n (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 76) (:start . 73)\n (:id . 53))\n ((:tag . "CD") (:stem . "273") (:form . "273") (:end . 80) (:start . 77)\n (:id . 54))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 89)\n (:start . 81) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n (:id . 56))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 95) (:start . 91)\n (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n (:id . 58))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 103) (:start . 99)\n (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 108) (:start . 104)\n (:id . 60))\n ((:tag . "VBN") (:stem . "discard") (:form . "discarded") (:end . 118)\n (:start . 109) (:id . 61))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 121) (:start . 119)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n (:id . 63))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 136)\n (:start . 126) (:id . 64))\n ((:tag . "NN") (:stem . "filtering") (:form . "filtering") (:end . 146)\n (:start . 137) (:id . 65))\n ((:tag . "NN") (:stem . "stage") (:form . "stage") (:end . 152)\n (:start . 147) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s1.182) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100182@unknown@formal@none@1@S@Because we have no a priori knowledge about the 23rd amino acid, cutoff thresholds for the filtering procedures were determined based on the known readthrough proteins.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 10) (:start . 8)\n (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 18) (:start . 16)\n (:id . 45))\n ((:tag . "FW") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n (:id . 46))\n ((:tag . "FW") (:stem . "priori") (:form . "priori") (:end . 27)\n (:start . 21) (:id . 47))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 37)\n (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 43) (:start . 38)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n (:id . 50))\n ((:tag . "JJ") (:stem . "23rd") (:form . "23rd") (:end . 52) (:start . 48)\n (:id . 51))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 58) (:start . 53)\n (:id . 52))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 63) (:start . 59)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n (:id . 54))\n ((:tag . "NN") (:stem . "cutoff") (:form . "cutoff") (:end . 71)\n (:start . 65) (:id . 55))\n ((:tag . "NNS") (:stem . "threshold") (:form . "thresholds") (:end . 82)\n (:start . 72) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 86) (:start . 83)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n (:id . 58))\n ((:tag . "VBG") (:stem . "filter") (:form . "filtering") (:end . 100)\n (:start . 91) (:id . 59))\n ((:tag . "NNS") (:stem . "procedure") (:form . "procedures") (:end . 111)\n (:start . 101) (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 116) (:start . 112)\n (:id . 61))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 127)\n (:start . 117) (:id . 62))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 133)\n (:start . 128) (:id . 63))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 136) (:start . 134)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n (:id . 65))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 146)\n (:start . 141) (:id . 66))\n ((:tag . "NN") (:stem . "readthrough") (:form . "readthrough") (:end . 158)\n (:start . 147) (:id . 67))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 167)\n (:start . 159) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n (:id . 69)))@@@1@28@((:ncues ((:id . :x1.183.1) (:span 16 18)))\n (:nscopes ((:id . :x1.183.1) (:span 16 63)))\n (:identifiers (:sid . :s1.183) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100183@unknown@formal@none@1@S@This is practically indispensable for objective classification of candidates, but there is no guarantee that unknown proteins with the 23rd amino acid will score higher than the thresholds.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "RB") (:stem . "practically") (:form . "practically") (:end . 19)\n (:start . 8) (:id . 44))\n ((:tag . "JJ") (:stem . "indispensable") (:form . "indispensable")\n (:end . 33) (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 37) (:start . 34)\n (:id . 46))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 47)\n (:start . 38) (:id . 47))\n ((:tag . "NN") (:stem . "classification") (:form . "classification")\n (:end . 62) (:start . 48) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n (:id . 49))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 76)\n (:start . 66) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n (:id . 51))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 81) (:start . 78)\n (:id . 52))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 87) (:start . 82)\n (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 90) (:start . 88)\n (:id . 54))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 93) (:start . 91)\n (:id . 55))\n ((:tag . "NN") (:stem . "guarantee") (:form . "guarantee") (:end . 103)\n (:start . 94) (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 108) (:start . 104)\n (:id . 57))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 116)\n (:start . 109) (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 125)\n (:start . 117) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 130) (:start . 126)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n (:id . 61))\n ((:tag . "JJ") (:stem . "23rd") (:form . "23rd") (:end . 139) (:start . 135)\n (:id . 62))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 145)\n (:start . 140) (:id . 63))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 150) (:start . 146)\n (:id . 64))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 155) (:start . 151)\n (:id . 65))\n ((:tag . "VB") (:stem . "score") (:form . "score") (:end . 161)\n (:start . 156) (:id . 66))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 168)\n (:start . 162) (:id . 67))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 173) (:start . 169)\n (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 177) (:start . 174)\n (:id . 69))\n ((:tag . "NNS") (:stem . "threshold") (:form . "thresholds") (:end . 188)\n (:start . 178) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n (:id . 71)))@@@1@30@((:hcues ((:id . :x1.184.1) (:span 91 103)))\n (:hscopes ((:id . :x1.184.1) (:span 91 188)))\n (:identifiers (:sid . :s1.184) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100184@unknown@formal@none@1@S@To explore whether a number of good candidates lie below the thresholds, the 273 clusters were analyzed in a way independent from filtering.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "explore") (:form . "explore") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 18)\n (:start . 11) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 27)\n (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 47))\n ((:tag . "JJ") (:stem . "good") (:form . "good") (:end . 35) (:start . 31)\n (:id . 48))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 46)\n (:start . 36) (:id . 49))\n ((:tag . "VBP") (:stem . "lie") (:form . "lie") (:end . 50) (:start . 47)\n (:id . 50))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 56) (:start . 51)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n (:id . 52))\n ((:tag . "NNS") (:stem . "threshold") (:form . "thresholds") (:end . 71)\n (:start . 61) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n (:id . 55))\n ((:tag . "CD") (:stem . "273") (:form . "273") (:end . 80) (:start . 77)\n (:id . 56))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 89)\n (:start . 81) (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 94) (:start . 90)\n (:id . 58))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 103)\n (:start . 95) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 108) (:start . 107)\n (:id . 61))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 112) (:start . 109)\n (:id . 62))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 124)\n (:start . 113) (:id . 63))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 129) (:start . 125)\n (:id . 64))\n ((:tag . "VBG") (:stem . "filter") (:form . "filtering") (:end . 139)\n (:start . 130) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x1.185.1) (:span 11 18)))\n (:hscopes ((:id . :x1.185.1) (:span 11 71)))\n (:identifiers (:sid . :s1.185) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100185@unknown@formal@none@1@S@If an organism has many readthrough proteins, proteins from the organism will frequently appear in the 273 clusters.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 14)\n (:start . 6) (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 35)\n (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 44)\n (:start . 36) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n (:id . 49))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 54)\n (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 59) (:start . 55)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n (:id . 52))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 72)\n (:start . 64) (:id . 53))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 77) (:start . 73)\n (:id . 54))\n ((:tag . "RB") (:stem . "frequently") (:form . "frequently") (:end . 88)\n (:start . 78) (:id . 55))\n ((:tag . "VB") (:stem . "appear") (:form . "appear") (:end . 95)\n (:start . 89) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n (:id . 58))\n ((:tag . "CD") (:stem . "273") (:form . "273") (:end . 106) (:start . 103)\n (:id . 59))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 115)\n (:start . 107) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.186) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100186@unknown@formal@none@1@S@Moreover, relative usage of the inframe stop codons will deviate from that of usual termination signals in the proteome.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 18)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "usage") (:form . "usage") (:end . 24) (:start . 19)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n (:id . 47))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 39)\n (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 44) (:start . 40)\n (:id . 49))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 51)\n (:start . 45) (:id . 50))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 56) (:start . 52)\n (:id . 51))\n ((:tag . "VB") (:stem . "deviate") (:form . "deviate") (:end . 64)\n (:start . 57) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 69) (:start . 65)\n (:id . 53))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 74) (:start . 70)\n (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n (:id . 55))\n ((:tag . "JJ") (:stem . "usual") (:form . "usual") (:end . 83) (:start . 78)\n (:id . 56))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 95)\n (:start . 84) (:id . 57))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 103)\n (:start . 96) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n (:id . 60))\n ((:tag . "NN") (:stem . "proteome") (:form . "proteome") (:end . 119)\n (:start . 111) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s1.187) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100187@unknown@formal@none@1@S@Figure 5 shows the discrepancies between relative usage of the inframe and C-terminal stop codons of 127 organisms in the pre-filtering clusters.@(((:tag . "NN") (:stem . "figure") (:form . "Figure") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 8) (:start . 7)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "NNS") (:stem . "discrepancy") (:form . "discrepancies") (:end . 32)\n (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 40)\n (:start . 33) (:id . 47))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 49)\n (:start . 41) (:id . 48))\n ((:tag . "NN") (:stem . "usage") (:form . "usage") (:end . 55) (:start . 50)\n (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n (:id . 51))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 70)\n (:start . 63) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n (:id . 53))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 85)\n (:start . 75) (:id . 54))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 90) (:start . 86)\n (:id . 55))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 97)\n (:start . 91) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n (:id . 57))\n ((:tag . "CD") (:stem . "127") (:form . "127") (:end . 104) (:start . 101)\n (:id . 58))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 114)\n (:start . 105) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 117) (:start . 115)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n (:id . 61))\n ((:tag . "JJ") (:stem . "pre-filtering") (:form . "pre-filtering")\n (:end . 135) (:start . 122) (:id . 62))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 144)\n (:start . 136) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s1.188) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100188@unknown@formal@none@1@S@Only seven organisms had statistically significant discrepancies (P < 0.05), and all of them are known to utilize selenocysteine or pyrrolysine.@(((:tag . "RB") (:stem . "only") (:form . "Only") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "seven") (:form . "seven") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 20)\n (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 24) (:start . 21)\n (:id . 45))\n ((:tag . "RB") (:stem . "statistically") (:form . "statistically")\n (:end . 38) (:start . 25) (:id . 46))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 50)\n (:start . 39) (:id . 47))\n ((:tag . "NNS") (:stem . "discrepancy") (:form . "discrepancies") (:end . 64)\n (:start . 51) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 66) (:start . 65)\n (:id . 49))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 67) (:start . 66)\n (:id . 50))\n ((:tag . "SYM") (:stem . "<") (:form . "<") (:end . 69) (:start . 68)\n (:id . 51))\n ((:tag . "CD") (:stem . "0.05") (:form . "0.05") (:end . 74) (:start . 70)\n (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n (:id . 55))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 84) (:start . 81)\n (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n (:id . 57))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 92) (:start . 88)\n (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 96) (:start . 93)\n (:id . 59))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 102) (:start . 97)\n (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 105) (:start . 103)\n (:id . 61))\n ((:tag . "VB") (:stem . "utilize") (:form . "utilize") (:end . 113)\n (:start . 106) (:id . 62))\n ((:tag . "NN") (:stem . "selenocysteine") (:form . "selenocysteine")\n (:end . 128) (:start . 114) (:id . 63))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 131) (:start . 129)\n (:id . 64))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 143)\n (:start . 132) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s1.189) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100190@unknown@formal@none@1@S@Discrepancies of stop codon usages between the inframe and C-terminal stop codons.@(((:tag . "NNS") (:stem . "discrepancy") (:form . "Discrepancies") (:end . 13)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 43))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 21) (:start . 17)\n (:id . 44))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 27) (:start . 22)\n (:id . 45))\n ((:tag . "NNS") (:stem . "usage") (:form . "usages") (:end . 34)\n (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 42)\n (:start . 35) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n (:id . 48))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 54)\n (:start . 47) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n (:id . 50))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 69)\n (:start . 59) (:id . 51))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 74) (:start . 70)\n (:id . 52))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 81)\n (:start . 75) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s1.191) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100191@unknown@formal@none@1@S@The inframe stop codon usage is taken from the pre-filtering clusters, and the C-terminal usage is computed based on the annotated proteins of the organism.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 22) (:start . 17)\n (:id . 45))\n ((:tag . "NN") (:stem . "usage") (:form . "usage") (:end . 28) (:start . 23)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 31) (:start . 29)\n (:id . 47))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 37) (:start . 32)\n (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 42) (:start . 38)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n (:id . 50))\n ((:tag . "JJ") (:stem . "pre-filtering") (:form . "pre-filtering")\n (:end . 60) (:start . 47) (:id . 51))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 69)\n (:start . 61) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n (:id . 55))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 89)\n (:start . 79) (:id . 56))\n ((:tag . "NN") (:stem . "usage") (:form . "usage") (:end . 95) (:start . 90)\n (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 98) (:start . 96)\n (:id . 58))\n ((:tag . "VBN") (:stem . "compute") (:form . "computed") (:end . 107)\n (:start . 99) (:id . 59))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 113)\n (:start . 108) (:id . 60))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 116) (:start . 114)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n (:id . 62))\n ((:tag . "JJ") (:stem . "annotated") (:form . "annotated") (:end . 130)\n (:start . 121) (:id . 63))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 139)\n (:start . 131) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n (:id . 66))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 155)\n (:start . 147) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.192) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100192@unknown@formal@none@1@S@Red circle: an organism with pyrrolysine, blue; selenocysteine, yellow; both pyrrolysine and selenocysteine, white; neither pyrrolysine nor selenocysteine.@(((:tag . "JJ") (:stem . "red") (:form . "Red") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "circle") (:form . "circle") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 11) (:start . 10)\n (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 14) (:start . 12)\n (:id . 45))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 23)\n (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 28) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 40)\n (:start . 29) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n (:id . 49))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 46) (:start . 42)\n (:id . 50))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 47) (:start . 46)\n (:id . 51))\n ((:tag . "NN") (:stem . "selenocysteine") (:form . "selenocysteine")\n (:end . 62) (:start . 48) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n (:id . 53))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 70)\n (:start . 64) (:id . 54))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 71) (:start . 70)\n (:id . 55))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 76) (:start . 72)\n (:id . 56))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 88)\n (:start . 77) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n (:id . 58))\n ((:tag . "NN") (:stem . "selenocysteine") (:form . "selenocysteine")\n (:end . 107) (:start . 93) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n (:id . 60))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 114)\n (:start . 109) (:id . 61))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 115) (:start . 114)\n (:id . 62))\n ((:tag . "CC") (:stem . "neither") (:form . "neither") (:end . 123)\n (:start . 116) (:id . 63))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 135)\n (:start . 124) (:id . 64))\n ((:tag . "CC") (:stem . "nor") (:form . "nor") (:end . 139) (:start . 136)\n (:id . 65))\n ((:tag . "NN") (:stem . "selenocysteine") (:form . "selenocysteine")\n (:end . 154) (:start . 140) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n (:id . 67)))@@@1@26@((:ncues ((:id . :x1.193.1) (:span 116 123 136 139)))\n (:nscopes ((:id . :x1.193.1) (:span 116 154)))\n (:identifiers (:sid . :s1.193) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100193@unknown@formal@none@1@S@The organisms are ordered by their discrepancy scores.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "VBN") (:stem . "order") (:form . "ordered") (:end . 25)\n (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 34)\n (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "discrepancy") (:form . "discrepancy") (:end . 46)\n (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 53)\n (:start . 47) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 54) (:start . 53)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s1.194) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100194@unknown@formal@none@1@S@The discrepancy score is the negative logarithm of a p-value of Fisher's exact test.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "discrepancy") (:form . "discrepancy") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 21) (:start . 16)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 24) (:start . 22)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 37)\n (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "logarithm") (:form . "logarithm") (:end . 47)\n (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n (:id . 50))\n ((:tag . "NN") (:stem . "p-value") (:form . "p-value") (:end . 60)\n (:start . 53) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n (:id . 52))\n ((:tag . "NNP") (:stem . "Fisher") (:form . "Fisher") (:end . 70)\n (:start . 64) (:id . 53))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 72) (:start . 70)\n (:id . 54))\n ((:tag . "JJ") (:stem . "exact") (:form . "exact") (:end . 78) (:start . 73)\n (:id . 55))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 83) (:start . 79)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.195) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100195@unknown@formal@none@1@S@The dotted line indicates significance level 0.05 after a correction for multiple testing.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "dot") (:form . "dotted") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 25)\n (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 38)\n (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 44) (:start . 39)\n (:id . 47))\n ((:tag . "CD") (:stem . "0.05") (:form . "0.05") (:end . 49) (:start . 45)\n (:id . 48))\n ((:tag . 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(:end . 130) (:start . 129)\n (:id . 62)))@@@1@21@((:ncues ((:id . :x1.197.1) (:span 81 84)))\n (:nscopes ((:id . :x1.197.1) (:span 81 129)))\n (:identifiers (:sid . :s1.197) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100197@unknown@formal@none@1@S@An inspection of the G. oxydans iORFs in the 273 clusters revealed that their inframe stop codons are dominated by TAA, but all of them belong to a single protein cluster associated with transposable elements.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "inspection") (:form . "inspection") (:end . 13)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "NNP") (:stem . "G.") (:form . "G.") 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(:end . 191) (:start . 190)\n (:id . 74)))@@@1@33@((:hcues ((:id . :x1.199.2) (:span 137 147)) ((:id . :x1.199.3) (:span 17 25))\n ((:id . :x1.199.4) (:span 11 16)))\n (:ncues ((:id . :x1.199.1) (:span 127 133)))\n (:hscopes ((:id . :x1.199.2) (:span 113 190))\n ((:id . :x1.199.3) (:span 17 111)) ((:id . :x1.199.4) (:span 11 111)))\n (:nscopes ((:id . :x1.199.1) (:span 113 190)))\n (:identifiers (:sid . :s1.199) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100200@unknown@formal@none@1@S@However, the result agrees with the filtering-dependent analysis that no candidate of the novel stop-codon-encoded amino acid is detectable in the current dataset.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . 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(:end . 184) (:start . 183)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s1.203) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100203@unknown@formal@none@1@S@Most of them are aimed at identification of selenoproteins, reflecting concerns from the scientific community and accumulated knowledge on selenocysteine.@(((:tag . "JJS") (:stem . "most") (:form . "Most") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "VBN") (:stem . "aim") (:form . "aimed") (:end . 22) (:start . 17)\n (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 25) (:start . 23)\n (:id . 47))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n (:end . 40) (:start . 26) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n (:id . 49))\n ((:tag . "NNS") (:stem . "selenoprotein") (:form . "selenoproteins")\n (:end . 58) (:start . 44) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n (:id . 51))\n ((:tag . "VBG") (:stem . "reflect") (:form . "reflecting") (:end . 70)\n (:start . 60) (:id . 52))\n ((:tag . "NNS") (:stem . "concern") (:form . "concerns") (:end . 79)\n (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 84) (:start . 80)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n (:id . 55))\n ((:tag . "JJ") (:stem . "scientific") (:form . "scientific") (:end . 99)\n (:start . 89) (:id . 56))\n ((:tag . "NN") (:stem . "community") (:form . "community") (:end . 109)\n (:start . 100) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . 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"of") (:end . 188) (:start . 186)\n (:id . 73))\n ((:tag . "NN") (:stem . "selenocysteine") (:form . "selenocysteine")\n (:end . 203) (:start . 189) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s1.205) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100205@unknown@formal@none@1@S@However, since the target of this study is the 23rd amino acid, and there is no a priori knowledge, only general properties of stop-codon-encoded amino acids can be used for prediction.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . 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(:end . 185) (:start . 184)\n (:id . 76)))@@@1@35@((:ncues ((:id . :x1.206.1) (:span 77 79)))\n (:nscopes ((:id . :x1.206.1) (:span 77 98)))\n (:identifiers (:sid . :s1.206) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100206@unknown@formal@none@1@S@Such general-purpose algorithms have also been developed to date.@(((:tag . "JJ") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "general-purpose") (:form . "general-purpose")\n (:end . 20) (:start . 5) (:id . 43))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 31)\n (:start . 21) (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 36) (:start . 32)\n (:id . 45))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 41) (:start . 37)\n (:id . 46))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 46) (:start . 42)\n (:id . 47))\n ((:tag . "VBN") (:stem . "develop") (:form . "developed") (:end . 56)\n (:start . 47) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n (:id . 49))\n ((:tag . "NN") (:stem . "date") (:form . "date") (:end . 64) (:start . 60)\n (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s1.207) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100207@unknown@formal@none@1@S@The method of Chaudhuri and Yeates 10 extracts iORFs from microbial genomes and analyzes sequence conservation around the inframe stop codon.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Chaudhuri") (:form . 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(:end . 141) (:start . 140)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.208) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100208@unknown@formal@none@1@S@Their method is thus similar to ours and applicable to both selenocysteine and pyrrolysine.@(((:tag . "PRP$") (:stem . "their") (:form . "Their") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 12) (:start . 6)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 28)\n (:start . 21) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n (:id . 47))\n ((:tag . "NNS") (:stem . "our") (:form . "ours") (:end . 36) (:start . 32)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n (:id . 49))\n ((:tag . "JJ") (:stem . "applicable") (:form . "applicable") (:end . 51)\n (:start . 41) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 54) (:start . 52)\n (:id . 51))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 59) (:start . 55)\n (:id . 52))\n ((:tag . "NN") (:stem . "selenocysteine") (:form . "selenocysteine")\n (:end . 74) (:start . 60) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n (:id . 54))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 90)\n (:start . 79) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s1.209) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100210@unknown@formal@none@1@S@Their method is applicable not only to stop codon readthrough but also to frameshift.@(((:tag . "PRP$") (:stem . "their") (:form . "Their") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 12) (:start . 6)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "applicable") (:form . "applicable") (:end . 26)\n (:start . 16) (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 35) (:start . 31)\n (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n (:id . 48))\n ((:tag . "VB") (:stem . "stop") (:form . "stop") (:end . 43) (:start . 39)\n (:id . 49))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 49) (:start . 44)\n (:id . 50))\n ((:tag . "IN") (:stem . "readthrough") (:form . "readthrough") (:end . 61)\n (:start . 50) (:id . 51))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 65) (:start . 62)\n (:id . 52))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 70) (:start . 66)\n (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n (:id . 54))\n ((:tag . "NN") (:stem . "frameshift") (:form . "frameshift") (:end . 84)\n (:start . 74) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s1.211) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100211@unknown@formal@none@1@S@However, both of them did not apply their methods to search for novel amino acids.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 21) (:start . 17)\n (:id . 46))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 25) (:start . 22)\n (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 29) (:start . 26)\n (:id . 48))\n ((:tag . "VB") (:stem . "apply") (:form . "apply") (:end . 35) (:start . 30)\n (:id . 49))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 41)\n (:start . 36) (:id . 50))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 49)\n (:start . 42) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n (:id . 52))\n ((:tag . "VB") (:stem . "search") (:form . "search") (:end . 59)\n (:start . 53) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 63) (:start . 60)\n (:id . 54))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 69) (:start . 64)\n (:id . 55))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 75) (:start . 70)\n (:id . 56))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 81) (:start . 76)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n (:id . 58)))@@@1@17@((:ncues ((:id . :x1.212.1) (:span 26 29)))\n (:nscopes ((:id . :x1.212.1) (:span 26 81)))\n (:identifiers (:sid . :s1.212) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100212@unknown@formal@none@1@S@Therefore, the question of the 23rd amino acid has not been investigated from the viewpoint of coding sequences.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "question") (:form . "question") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n (:id . 47))\n ((:tag . "JJ") (:stem . "23rd") (:form . "23rd") (:end . 35) (:start . 31)\n (:id . 48))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 41) (:start . 36)\n (:id . 49))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 46) (:start . 42)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 50) (:start . 47)\n (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 54) (:start . 51)\n (:id . 52))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 59) (:start . 55)\n (:id . 53))\n ((:tag . "VBN") (:stem . "investigate") (:form . "investigated") (:end . 72)\n (:start . 60) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 77) (:start . 73)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n (:id . 56))\n ((:tag . "NN") (:stem . "viewpoint") (:form . "viewpoint") (:end . 91)\n (:start . 82) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n (:id . 58))\n ((:tag . "VBG") (:stem . "cod") (:form . "coding") (:end . 101) (:start . 95)\n (:id . 59))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 111)\n (:start . 102) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n (:id . 61)))@@@1@20@((:ncues ((:id . :x1.213.1) (:span 51 54)))\n (:nscopes ((:id . :x1.213.1) (:span 11 111)))\n (:identifiers (:sid . :s1.213) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100213@unknown@formal@none@1@S@Additionally, the previous methods cannot effectively discriminate pseudogenes from readthrough genes.@(((:tag . "RB") (:stem . "additionally") (:form . "Additionally") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 26)\n (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 34)\n (:start . 27) (:id . 46))\n ((:tag . "VBP") (:stem . "cannot") (:form . "cannot") (:end . 41)\n (:start . 35) (:id . 47))\n ((:tag . "RB") (:stem . "effectively") (:form . "effectively") (:end . 53)\n (:start . 42) (:id . 48))\n ((:tag . "VB") (:stem . "discriminate") (:form . "discriminate") (:end . 66)\n (:start . 54) (:id . 49))\n ((:tag . "NNS") (:stem . "pseudogene") (:form . "pseudogenes") (:end . 78)\n (:start . 67) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 83) (:start . 79)\n (:id . 51))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 95)\n (:start . 84) (:id . 52))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 101) (:start . 96)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n (:id . 54)))@@@1@13@((:ncues ((:id . :x1.214.1) (:span 35 41)))\n (:nscopes ((:id . :x1.214.1) (:span 35 101)))\n (:identifiers (:sid . :s1.214) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100214@unknown@formal@none@1@S@For instance, Chaudhuri and Yeates reported a homolog of cobalamin biosynthesis protein CobN as a novel candidate of pyrrolysine protein.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Chaudhuri") (:form . "Chaudhuri") (:end . 23)\n (:start . 14) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 27) (:start . 24)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Yeates") (:form . "Yeates") (:end . 34)\n (:start . 28) (:id . 47))\n ((:tag . "VBD") (:stem . "report") (:form . "reported") (:end . 43)\n (:start . 35) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 45) (:start . 44)\n (:id . 49))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 53)\n (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n (:id . 51))\n ((:tag . "NN") (:stem . "cobalamin") (:form . "cobalamin") (:end . 66)\n (:start . 57) (:id . 52))\n ((:tag . "NN") (:stem . "biosynthesis") (:form . "biosynthesis") (:end . 79)\n (:start . 67) (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 87)\n (:start . 80) (:id . 54))\n ((:tag . "NN") (:stem . "cobn") (:form . "CobN") (:end . 92) (:start . 88)\n (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 95) (:start . 93)\n (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 97) (:start . 96)\n (:id . 57))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 103) (:start . 98)\n (:id . 58))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 113)\n (:start . 104) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n (:id . 60))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 128)\n (:start . 117) (:id . 61))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 136)\n (:start . 129) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.215) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100215@unknown@formal@none@1@S@However, the gene is probably a pseudogene because it contains an inframe TAA codon in addition to the TAG codon, and only one species seems to have the amber-containing form of the gene.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 17) (:start . 13)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 20) (:start . 18)\n (:id . 46))\n ((:tag . "RB") (:stem . "probably") (:form . "probably") (:end . 29)\n (:start . 21) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 31) (:start . 30)\n (:id . 48))\n ((:tag . "NN") (:stem . "pseudogene") (:form . "pseudogene") (:end . 42)\n (:start . 32) (:id . 49))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 50)\n (:start . 43) (:id . 50))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 53) (:start . 51)\n (:id . 51))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 62)\n (:start . 54) (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 65) (:start . 63)\n (:id . 53))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 73)\n (:start . 66) (:id . 54))\n ((:tag . "NNP") (:stem . "TAA") (:form . "TAA") (:end . 77) (:start . 74)\n (:id . 55))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 83) (:start . 78)\n (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n (:id . 57))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 95)\n (:start . 87) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 98) (:start . 96)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n (:id . 60))\n ((:tag . "NNP") (:stem . "TAG") (:form . "TAG") (:end . 106) (:start . 103)\n (:id . 61))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 112)\n (:start . 107) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n (:id . 64))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 122) (:start . 118)\n (:id . 65))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 126) (:start . 123)\n (:id . 66))\n ((:tag . "NN") (:stem . "species") (:form . "species") (:end . 134)\n (:start . 127) (:id . 67))\n ((:tag . "VBZ") (:stem . "seem") (:form . "seems") (:end . 140)\n (:start . 135) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 143) (:start . 141)\n (:id . 69))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 148) (:start . 144)\n (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n (:id . 71))\n ((:tag . "JJ") (:stem . "amber-containing") (:form . "amber-containing")\n (:end . 169) (:start . 153) (:id . 72))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 174) (:start . 170)\n (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 177) (:start . 175)\n (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 181) (:start . 178)\n (:id . 75))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 186) (:start . 182)\n (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n (:id . 77)))@@@1@36@((:hcues ((:id . :x1.216.1) (:span 135 140))\n ((:id . :x1.216.2) (:span 21 29)))\n (:hscopes ((:id . :x1.216.1) (:span 123 186))\n ((:id . :x1.216.2) (:span 21 42)))\n (:identifiers (:sid . :s1.216) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100216@unknown@formal@none@1@S@The previous methods also assume that proteins with stop-codon-encoded amino acids will have non-readthrough homologs (i.e., homologous proteins that do not have inframe stop codons).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 20)\n (:start . 13) (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 25) (:start . 21)\n (:id . 45))\n ((:tag . "VBP") (:stem . "assume") (:form . "assume") (:end . 32)\n (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 37) (:start . 33)\n (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 46)\n (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 51) (:start . 47)\n (:id . 49))\n ((:tag . "JJ") (:stem . "stop-codon-encoded") (:form . "stop-codon-encoded")\n (:end . 70) (:start . 52) (:id . 50))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 76) (:start . 71)\n (:id . 51))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 82) (:start . 77)\n (:id . 52))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 87) (:start . 83)\n (:id . 53))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 92) (:start . 88)\n (:id . 54))\n ((:tag . "JJ") (:stem . "non-readthrough") (:form . "non-readthrough")\n (:end . 108) (:start . 93) (:id . 55))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 117)\n (:start . 109) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 119) (:start . 118)\n (:id . 57))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 123) (:start . 119)\n (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n (:id . 59))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 135)\n (:start . 125) (:id . 60))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 144)\n (:start . 136) (:id . 61))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 149) (:start . 145)\n (:id . 62))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 152) (:start . 150)\n (:id . 63))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 156) (:start . 153)\n (:id . 64))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 161) (:start . 157)\n (:id . 65))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 169)\n (:start . 162) (:id . 66))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 174) (:start . 170)\n (:id . 67))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 181)\n (:start . 175) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 182) (:start . 181)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x1.217.2) (:span 26 32)))\n (:ncues ((:id . :x1.217.1) (:span 153 156)))\n (:hscopes ((:id . :x1.217.2) (:span 26 182)))\n (:nscopes ((:id . :x1.217.1) (:span 153 182)))\n (:identifiers (:sid . :s1.217) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100217@unknown@formal@none@1@S@However, that is not necessarily true.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 20) (:start . 17)\n (:id . 46))\n ((:tag . "RB") (:stem . "necessarily") (:form . "necessarily") (:end . 32)\n (:start . 21) (:id . 47))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 37) (:start . 33)\n (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 38) (:start . 37)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s1.218) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100218@unknown@formal@none@1@S@For example, pyrrolysine-containing monomethylamine methyltransferases adopt TIM barrel fold 6, but their primary sequences do not exhibit detectable similarity to other TIM barrel proteins because of evolutionary divergence.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "JJ") (:stem . "pyrrolysine-containing")\n (:form . "pyrrolysine-containing") (:end . 35) (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "monomethylamine") (:form . "monomethylamine")\n (:end . 51) (:start . 36) (:id . 46))\n ((:tag . "NNS") (:stem . "methyltransferas") (:form . "methyltransferases")\n (:end . 70) (:start . 52) (:id . 47))\n ((:tag . "VBP") (:stem . "adopt") (:form . "adopt") (:end . 76) (:start . 71)\n (:id . 48))\n ((:tag . "NNP") (:stem . "TIM") (:form . "TIM") (:end . 80) (:start . 77)\n (:id . 49))\n ((:tag . "NN") (:stem . "barrel") (:form . "barrel") (:end . 87)\n (:start . 81) (:id . 50))\n ((:tag . "RB") (:stem . "fold") (:form . "fold") (:end . 92) (:start . 88)\n (:id . 51))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 94) (:start . 93)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n (:id . 53))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 99) (:start . 96)\n (:id . 54))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 105)\n (:start . 100) (:id . 55))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 113)\n (:start . 106) (:id . 56))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 123)\n (:start . 114) (:id . 57))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 126) (:start . 124)\n (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 130) (:start . 127)\n (:id . 59))\n ((:tag . "VB") (:stem . "exhibit") (:form . "exhibit") (:end . 138)\n (:start . 131) (:id . 60))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 149)\n (:start . 139) (:id . 61))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 160)\n (:start . 150) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 163) (:start . 161)\n (:id . 63))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 169)\n (:start . 164) (:id . 64))\n ((:tag . "NNP") (:stem . "TIM") (:form . "TIM") (:end . 173) (:start . 170)\n (:id . 65))\n ((:tag . "NN") (:stem . "barrel") (:form . "barrel") (:end . 180)\n (:start . 174) (:id . 66))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 189)\n (:start . 181) (:id . 67))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 197)\n (:start . 190) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 200) (:start . 198)\n (:id . 69))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 213)\n (:start . 201) (:id . 70))\n ((:tag . "NN") (:stem . "divergence") (:form . "divergence") (:end . 224)\n (:start . 214) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n (:id . 72)))@@@1@31@((:ncues ((:id . :x1.219.1) (:span 127 130)))\n (:nscopes ((:id . :x1.219.1) (:span 127 189)))\n (:identifiers (:sid . :s1.219) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100220@unknown@formal@none@1@S@Yet another example is glycine reductase selenoprotein A.@(((:tag . "RB") (:stem . "yet") (:form . "Yet") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 19)\n (:start . 12) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 22) (:start . 20)\n (:id . 45))\n ((:tag . "NN") (:stem . "glycine") (:form . "glycine") (:end . 30)\n (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "reductase") (:form . "reductase") (:end . 40)\n (:start . 31) (:id . 47))\n ((:tag . "NN") (:stem . "selenoprotein") (:form . "selenoprotein")\n (:end . 54) (:start . 41) (:id . 48))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 56) (:start . 55)\n (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 57) (:start . 56)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s1.221) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100221@unknown@formal@none@1@S@Only the selenocysteine-containing form of the enzyme is currently known 20.@(((:tag . "RB") (:stem . "only") (:form . "Only") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "JJ") (:stem . "selenocysteine-containing")\n (:form . "selenocysteine-containing") (:end . 34) (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 39) (:start . 35)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n (:id . 47))\n ((:tag . "NN") (:stem . "enzyme") (:form . "enzyme") (:end . 53)\n (:start . 47) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 56) (:start . 54)\n (:id . 49))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 66)\n (:start . 57) (:id . 50))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 72) (:start . 67)\n (:id . 51))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 75) (:start . 73)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s1.222) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100222@unknown@formal@none@1@S@Therefore, it is important not to assume non-readthrough homologs for exploring novel candidates.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 26)\n (:start . 17) (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 30) (:start . 27)\n (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 33) (:start . 31)\n (:id . 48))\n ((:tag . "VB") (:stem . "assume") (:form . "assume") (:end . 40)\n (:start . 34) (:id . 49))\n ((:tag . "JJ") (:stem . "non-readthrough") (:form . "non-readthrough")\n (:end . 56) (:start . 41) (:id . 50))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 65)\n (:start . 57) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 69) (:start . 66)\n (:id . 52))\n ((:tag . "VBG") (:stem . "explore") (:form . "exploring") (:end . 79)\n (:start . 70) (:id . 53))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 85) (:start . 80)\n (:id . 54))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 96)\n (:start . 86) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n (:id . 56)))@@@1@15@((:ncues ((:id . :x1.223.1) (:span 27 30)))\n (:nscopes ((:id . :x1.223.1) (:span 27 96)))\n (:identifiers (:sid . :s1.223) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100223@unknown@formal@none@1@S@If any non-readthrough homologs are registered in public sequence databases, a careful annotation process of a newly sequenced genome will be able to detect readthrough genes, even though they may be annotated as pseudogenes.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "non-readthrough") (:form . "non-readthrough")\n (:end . 22) (:start . 7) (:id . 44))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 31)\n (:start . 23) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n (:id . 46))\n ((:tag . "VBN") (:stem . "register") (:form . "registered") (:end . 46)\n (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n (:id . 48))\n ((:tag . "JJ") (:stem . "public") (:form . "public") (:end . 56)\n (:start . 50) (:id . 49))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 65)\n (:start . 57) (:id . 50))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 75)\n (:start . 66) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 78) (:start . 77)\n (:id . 53))\n ((:tag . "JJ") (:stem . "careful") (:form . "careful") (:end . 86)\n (:start . 79) (:id . 54))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 97)\n (:start . 87) (:id . 55))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 105)\n (:start . 98) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 108) (:start . 106)\n (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 110) (:start . 109)\n (:id . 58))\n ((:tag . "RB") (:stem . "newly") (:form . "newly") (:end . 116)\n (:start . 111) (:id . 59))\n ((:tag . "VBN") (:stem . "sequence") (:form . "sequenced") (:end . 126)\n (:start . 117) (:id . 60))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 133)\n (:start . 127) (:id . 61))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 138) (:start . 134)\n (:id . 62))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 141) (:start . 139)\n (:id . 63))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 146) (:start . 142)\n (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 149) (:start . 147)\n (:id . 65))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 156)\n (:start . 150) (:id . 66))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 168)\n (:start . 157) (:id . 67))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 174)\n (:start . 169) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n (:id . 69))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 180) (:start . 176)\n (:id . 70))\n ((:tag . "IN") (:stem . "though") (:form . "though") (:end . 187)\n (:start . 181) (:id . 71))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 192) (:start . 188)\n (:id . 72))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 196) (:start . 193)\n (:id . 73))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 199) (:start . 197)\n (:id . 74))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 209)\n (:start . 200) (:id . 75))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 212) (:start . 210)\n (:id . 76))\n ((:tag . "NNS") (:stem . "pseudogene") (:form . "pseudogenes") (:end . 224)\n (:start . 213) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n (:id . 78)))@@@1@37@((:hcues ((:id . :x1.224.1) (:span 193 196)))\n (:hscopes ((:id . :x1.224.1) (:span 188 224)))\n (:identifiers (:sid . :s1.224) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100224@unknown@formal@none@1@S@However, if all members of a gene family have stop codon readthrough, correct annotation of their gene structure will be extremely difficult, and all of them will be split into two distinct genes.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 15) (:start . 12)\n (:id . 45))\n ((:tag . "NNS") (:stem . "member") (:form . "members") (:end . 23)\n (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n (:id . 48))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 33) (:start . 29)\n (:id . 49))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 40)\n (:start . 34) (:id . 50))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 45) (:start . 41)\n (:id . 51))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 50) (:start . 46)\n (:id . 52))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 56) (:start . 51)\n (:id . 53))\n ((:tag . "NN") (:stem . "readthrough") (:form . "readthrough") (:end . 68)\n (:start . 57) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n (:id . 55))\n ((:tag . "JJ") (:stem . "correct") (:form . "correct") (:end . 77)\n (:start . 70) (:id . 56))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 88)\n (:start . 78) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n (:id . 58))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 97)\n (:start . 92) (:id . 59))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 102) (:start . 98)\n (:id . 60))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 112)\n (:start . 103) (:id . 61))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 117) (:start . 113)\n (:id . 62))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 120) (:start . 118)\n (:id . 63))\n ((:tag . "RB") (:stem . "extremely") (:form . "extremely") (:end . 130)\n (:start . 121) (:id . 64))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 140)\n (:start . 131) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 145) (:start . 142)\n (:id . 67))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 149) (:start . 146)\n (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 152) (:start . 150)\n (:id . 69))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 157) (:start . 153)\n (:id . 70))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 162) (:start . 158)\n (:id . 71))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 165) (:start . 163)\n (:id . 72))\n ((:tag . "VBN") (:stem . "split") (:form . "split") (:end . 171)\n (:start . 166) (:id . 73))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 176) (:start . 172)\n (:id . 74))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 180) (:start . 177)\n (:id . 75))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 189)\n (:start . 181) (:id . 76))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 195)\n (:start . 190) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n (:id . 78)))@@@1@37@((:identifiers (:sid . :s1.225) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100225@unknown@formal@none@1@S@The method reported here is unique in that it does not assume non-readthrough homologs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 19)\n (:start . 11) (:id . 44))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 24) (:start . 20)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 34)\n (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 42) (:start . 38)\n (:id . 49))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 45) (:start . 43)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 50) (:start . 46)\n (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 54) (:start . 51)\n (:id . 52))\n ((:tag . "VB") (:stem . "assume") (:form . "assume") (:end . 61)\n (:start . 55) (:id . 53))\n ((:tag . "JJ") (:stem . "non-readthrough") (:form . "non-readthrough")\n (:end . 77) (:start . 62) (:id . 54))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 86)\n (:start . 78) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n (:id . 56)))@@@1@15@((:ncues ((:id . :x1.226.1) (:span 51 54)))\n (:nscopes ((:id . :x1.226.1) (:span 51 86)))\n (:identifiers (:sid . :s1.226) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100226@unknown@formal@none@1@S@Using this method, a systematic screening of the 23rd amino acid and other readthrough genes was carried out.@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 17)\n (:start . 11) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n (:id . 46))\n ((:tag . "JJ") (:stem . "systematic") (:form . "systematic") (:end . 31)\n (:start . 21) (:id . 47))\n ((:tag . "NN") (:stem . "screening") (:form . "screening") (:end . 41)\n (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n (:id . 50))\n ((:tag . "JJ") (:stem . "23rd") (:form . "23rd") (:end . 53) (:start . 49)\n (:id . 51))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 59) (:start . 54)\n (:id . 52))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 64) (:start . 60)\n (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n (:id . 54))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 74) (:start . 69)\n (:id . 55))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 86)\n (:start . 75) (:id . 56))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 92) (:start . 87)\n (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 96) (:start . 93)\n (:id . 58))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 104)\n (:start . 97) (:id . 59))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 108) (:start . 105)\n (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.227) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100227@unknown@formal@none@1@S@Many of the currently known selenoproteins and pyrrolysine proteins were recovered, indicating the effectiveness of this approach.@(((:tag . "JJ") (:stem . "many") (:form . "Many") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n (:id . 44))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 21)\n (:start . 12) (:id . 45))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 27) (:start . 22)\n (:id . 46))\n ((:tag . "NNS") (:stem . "selenoprotein") (:form . "selenoproteins")\n (:end . 42) (:start . 28) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n (:id . 48))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 58)\n (:start . 47) (:id . 49))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 67)\n (:start . 59) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 72) (:start . 68)\n (:id . 51))\n ((:tag . "VBN") (:stem . "recover") (:form . "recovered") (:end . 82)\n (:start . 73) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n (:id . 53))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 94)\n (:start . 84) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n (:id . 55))\n ((:tag . "NN") (:stem . "effectiveness") (:form . "effectiveness")\n (:end . 112) (:start . 99) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n (:id . 57))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 120) (:start . 116)\n (:id . 58))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 129)\n (:start . 121) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.228) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100228@unknown@formal@none@1@S@In particular, successful detection of pyrrolysine-containing methyltransferases and selenoprotein A should be noted.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 13)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "successful") (:form . "successful") (:end . 25)\n (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "detection") (:form . "detection") (:end . 35)\n (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n (:id . 47))\n ((:tag . "JJ") (:stem . "pyrrolysine-containing")\n (:form . "pyrrolysine-containing") (:end . 61) (:start . 39) (:id . 48))\n ((:tag . "NNS") (:stem . "methyltransferas") (:form . "methyltransferases")\n (:end . 80) (:start . 62) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n (:id . 50))\n ((:tag . "NN") (:stem . "selenoprotein") (:form . "selenoprotein")\n (:end . 98) (:start . 85) (:id . 51))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 100) (:start . 99)\n (:id . 52))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 107)\n (:start . 101) (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 110) (:start . 108)\n (:id . 54))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 116)\n (:start . 111) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s1.229) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100230@unknown@formal@none@1@S@What can be concluded from this result?@(((:tag . "WP") (:stem . "what") (:form . "What") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "VBN") (:stem . "conclude") (:form . "concluded") (:end . 21)\n (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 26) (:start . 22)\n (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 31) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 38)\n (:start . 32) (:id . 48))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 39) (:start . 38)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s1.231) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100231@unknown@formal@none@1@S@The most likely explanation is that the 23rd amino acid does not exist, or its distribution on the tree of life is rather limited.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 15) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "explanation") (:form . "explanation") (:end . 27)\n (:start . 16) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 35) (:start . 31)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "JJ") (:stem . "23rd") (:form . "23rd") (:end . 44) (:start . 40)\n (:id . 49))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 50) (:start . 45)\n (:id . 50))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 55) (:start . 51)\n (:id . 51))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 60) (:start . 56)\n (:id . 52))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 64) (:start . 61)\n (:id . 53))\n ((:tag . "VB") (:stem . "exist") (:form . "exist") (:end . 70) (:start . 65)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 74) (:start . 72)\n (:id . 56))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 78) (:start . 75)\n (:id . 57))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 91)\n (:start . 79) (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 94) (:start . 92)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n (:id . 60))\n ((:tag . "NN") (:stem . "tree") (:form . "tree") (:end . 103) (:start . 99)\n (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n (:id . 62))\n ((:tag . "NN") (:stem . "life") (:form . "life") (:end . 111) (:start . 107)\n (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 114) (:start . 112)\n (:id . 64))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 121)\n (:start . 115) (:id . 65))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 129)\n (:start . 122) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n (:id . 67)))@@@1@26@((:hcues ((:id . :x1.232.2) (:span 72 74)) ((:id . :x1.232.3) (:span 9 15)))\n (:ncues ((:id . :x1.232.1) (:span 61 64)))\n (:hscopes ((:id . :x1.232.2) (:span 36 129))\n ((:id . :x1.232.3) (:span 9 27)))\n (:nscopes ((:id . :x1.232.1) (:span 61 70)))\n (:identifiers (:sid . :s1.232) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100232@unknown@formal@none@1@S@Although a broad spectrum of taxonomic groups has been subjected to genome sequencing, the genomes of most microbial species on the earth have yet to be determined.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "JJ") (:stem . "broad") (:form . "broad") (:end . 16) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "spectrum") (:form . "spectrum") (:end . 25)\n (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "JJ") (:stem . "taxonomic") (:form . "taxonomic") (:end . 38)\n (:start . 29) (:id . 47))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 45)\n (:start . 39) (:id . 48))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 54) (:start . 50)\n (:id . 50))\n ((:tag . "VBN") (:stem . "subject") (:form . "subjected") (:end . 64)\n (:start . 55) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n (:id . 52))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 74)\n (:start . 68) (:id . 53))\n ((:tag . "NN") (:stem . "sequencing") (:form . "sequencing") (:end . 85)\n (:start . 75) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n (:id . 56))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 98)\n (:start . 91) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 101) (:start . 99)\n (:id . 58))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 106) (:start . 102)\n (:id . 59))\n ((:tag . "JJ") (:stem . "microbial") (:form . "microbial") (:end . 116)\n (:start . 107) (:id . 60))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 124)\n (:start . 117) (:id . 61))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 127) (:start . 125)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n (:id . 63))\n ((:tag . "NN") (:stem . "earth") (:form . "earth") (:end . 137)\n (:start . 132) (:id . 64))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 142) (:start . 138)\n (:id . 65))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 146) (:start . 143)\n (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 149) (:start . 147)\n (:id . 67))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 152) (:start . 150)\n (:id . 68))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 163)\n (:start . 153) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s1.233) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100233@unknown@formal@none@1@S@The unknown amino acid may be used by these species.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 17) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 22) (:start . 18)\n (:id . 45))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 29) (:start . 27)\n (:id . 47))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 34) (:start . 30)\n (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 37) (:start . 35)\n (:id . 49))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 43) (:start . 38)\n (:id . 50))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 51)\n (:start . 44) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 52) (:start . 51)\n (:id . 52)))@@@1@11@((:hcues ((:id . :x1.234.1) (:span 23 26)))\n (:hscopes ((:id . :x1.234.1) (:span 0 51)))\n (:identifiers (:sid . :s1.234) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100234@unknown@formal@none@1@S@Alternatively, only one organism in our dataset may have the 23rd amino acid.@(((:tag . "RB") (:stem . "alternatively") (:form . "Alternatively")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 43))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 32)\n (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n (:id . 47))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 47)\n (:start . 40) (:id . 49))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 51) (:start . 48)\n (:id . 50))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 56) (:start . 52)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n (:id . 52))\n ((:tag . "JJ") (:stem . "23rd") (:form . "23rd") (:end . 65) (:start . 61)\n (:id . 53))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 71) (:start . 66)\n (:id . 54))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 76) (:start . 72)\n (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n (:id . 56)))@@@1@15@((:hcues ((:id . :x1.235.1) (:span 48 51)))\n (:hscopes ((:id . :x1.235.1) (:span 48 76)))\n (:identifiers (:sid . :s1.235) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100235@unknown@formal@none@1@S@This is because our method is limited to readthrough genes conserved across two or more species.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 15)\n (:start . 8) (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 26)\n (:start . 20) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n (:id . 47))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 37)\n (:start . 30) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n (:id . 49))\n ((:tag . "VB") (:stem . "readthrough") (:form . "readthrough") (:end . 52)\n (:start . 41) (:id . 50))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 58) (:start . 53)\n (:id . 51))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 68)\n (:start . 59) (:id . 52))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 75)\n (:start . 69) (:id . 53))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 79) (:start . 76)\n (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 82) (:start . 80)\n (:id . 55))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 87) (:start . 83)\n (:id . 56))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 95)\n (:start . 88) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.236) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100236@unknown@formal@none@1@S@If the novel amino acid appears in younger, non-conserved sequences, our technique will miss them.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 12) (:start . 7)\n (:id . 44))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 31)\n (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n (:id . 48))\n ((:tag . "JJR") (:stem . "young") (:form . "younger") (:end . 42)\n (:start . 35) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n (:id . 50))\n ((:tag . "JJ") (:stem . "non-conserved") (:form . "non-conserved")\n (:end . 57) (:start . 44) (:id . 51))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 67)\n (:start . 58) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n (:id . 53))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 72) (:start . 69)\n (:id . 54))\n ((:tag . "NN") (:stem . "technique") (:form . "technique") (:end . 82)\n (:start . 73) (:id . 55))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 87) (:start . 83)\n (:id . 56))\n ((:tag . "VB") (:stem . "miss") (:form . "miss") (:end . 92) (:start . 88)\n (:id . 57))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 97) (:start . 93)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s1.237) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100237@unknown@formal@none@1@S@In either case, the distribution of the 23rd amino acid will be significantly narrower than that of selenocysteine, which has scattered but wide distribution 21.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "either") (:form . "either") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 46))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 32)\n (:start . 20) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 49))\n ((:tag . "JJ") (:stem . "23rd") (:form . "23rd") (:end . 44) (:start . 40)\n (:id . 50))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 50) (:start . 45)\n (:id . 51))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 55) (:start . 51)\n (:id . 52))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 60) (:start . 56)\n (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 63) (:start . 61)\n (:id . 54))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 77) (:start . 64) (:id . 55))\n ((:tag . "JJR") (:stem . "narrow") (:form . "narrower") (:end . 86)\n (:start . 78) (:id . 56))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 91) (:start . 87)\n (:id . 57))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 96) (:start . 92)\n (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n (:id . 59))\n ((:tag . "NN") (:stem . "selenocysteine") (:form . "selenocysteine")\n (:end . 114) (:start . 100) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 121)\n (:start . 116) (:id . 62))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 125) (:start . 122)\n (:id . 63))\n ((:tag . "VBN") (:stem . "scatter") (:form . "scattered") (:end . 135)\n (:start . 126) (:id . 64))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 139) (:start . 136)\n (:id . 65))\n ((:tag . "JJ") (:stem . "wide") (:form . "wide") (:end . 144) (:start . 140)\n (:id . 66))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 157)\n (:start . 145) (:id . 67))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 160) (:start . 158)\n (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.238) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100238@unknown@formal@none@1@S@This conclusion coincides with and strengthens that of the previous research on tRNA 14.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "conclusion") (:form . "conclusion") (:end . 15)\n (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "coincide") (:form . "coincides") (:end . 25)\n (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 30) (:start . 26)\n (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 34) (:start . 31)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "strengthen") (:form . "strengthens") (:end . 46)\n (:start . 35) (:id . 47))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 51) (:start . 47)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n (:id . 50))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 67)\n (:start . 59) (:id . 51))\n ((:tag . "NN") (:stem . "research") (:form . "research") (:end . 76)\n (:start . 68) (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 79) (:start . 77)\n (:id . 53))\n ((:tag . "NNP") (:stem . "tRNA") (:form . "tRNA") (:end . 84) (:start . 80)\n (:id . 54))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 87) (:start . 85)\n (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s1.239) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100240@unknown@formal@none@1@S@It is well known that the genetic code varies in several organisms 22.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 10) (:start . 6)\n (:id . 44))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 16) (:start . 11)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 47))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 33)\n (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 38) (:start . 34)\n (:id . 49))\n ((:tag . "VBZ") (:stem . "vary") (:form . "varies") (:end . 45) (:start . 39)\n (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n (:id . 51))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 56)\n (:start . 49) (:id . 52))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 66)\n (:start . 57) (:id . 53))\n ((:tag . "CD") (:stem . "22") (:form . "22") (:end . 69) (:start . 67)\n (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s1.241) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100241@unknown@formal@none@1@S@Thus, certain organisms may use one of the sense codons for the novel amino acid.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 13)\n (:start . 6) (:id . 44))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 23)\n (:start . 14) (:id . 45))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 27) (:start . 24)\n (:id . 46))\n ((:tag . "VB") (:stem . "use") (:form . "use") (:end . 31) (:start . 28)\n (:id . 47))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 35) (:start . 32)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n (:id . 50))\n ((:tag . "NN") (:stem . "sense") (:form . "sense") (:end . 48) (:start . 43)\n (:id . 51))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 55)\n (:start . 49) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 59) (:start . 56)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n (:id . 54))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 69) (:start . 64)\n (:id . 55))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 75) (:start . 70)\n (:id . 56))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 80) (:start . 76)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n (:id . 58)))@@@1@17@((:hcues ((:id . :x1.242.1) (:span 24 27)))\n (:hscopes ((:id . :x1.242.1) (:span 24 80)))\n (:identifiers (:sid . :s1.242) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100242@unknown@formal@none@1@S@Because codons for most amino acids are degenerate, redefinition of one of them is feasible.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 14) (:start . 8)\n (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 18) (:start . 15)\n (:id . 44))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 23) (:start . 19)\n (:id . 45))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 29) (:start . 24)\n (:id . 46))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 35) (:start . 30)\n (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "JJ") (:stem . "degenerate") (:form . "degenerate") (:end . 50)\n (:start . 40) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n (:id . 50))\n ((:tag . "NN") (:stem . "redefinition") (:form . "redefinition") (:end . 64)\n (:start . 52) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n (:id . 52))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 71) (:start . 68)\n (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n (:id . 54))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 79) (:start . 75)\n (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 82) (:start . 80)\n (:id . 56))\n ((:tag . "JJ") (:stem . "feasible") (:form . "feasible") (:end . 91)\n (:start . 83) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n (:id . 58)))@@@1@17@((:hcues ((:id . :x1.243.1) (:span 83 91)))\n (:hscopes ((:id . :x1.243.1) (:span 68 91)))\n (:identifiers (:sid . :s1.243) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100243@unknown@formal@none@1@S@However, that possibility is beyond the scope of this study and is left as an open problem.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 25)\n (:start . 14) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "IN") (:stem . "beyond") (:form . "beyond") (:end . 35)\n (:start . 29) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "NN") (:stem . "scope") (:form . "scope") (:end . 45) (:start . 40)\n (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n (:id . 50))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 53) (:start . 49)\n (:id . 51))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 59) (:start . 54)\n (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 66) (:start . 64)\n (:id . 54))\n ((:tag . "VBN") (:stem . "leave") (:form . "left") (:end . 71) (:start . 67)\n (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 74) (:start . 72)\n (:id . 56))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 77) (:start . 75)\n (:id . 57))\n ((:tag . "JJ") (:stem . "open") (:form . "open") (:end . 82) (:start . 78)\n (:id . 58))\n ((:tag . "NN") (:stem . "problem") (:form . "problem") (:end . 90)\n (:start . 83) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.244) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100244@unknown@formal@none@1@S@Bioinformatics analysis of unusual tRNA genes and codon usage may provide insights into this problem.@(((:tag . "NNP") (:stem . "Bioinformatic") (:form . "Bioinformatics")\n (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 23)\n (:start . 15) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 44))\n ((:tag . "JJ") (:stem . "unusual") (:form . "unusual") (:end . 34)\n (:start . 27) (:id . 45))\n ((:tag . "NN") (:stem . "trna") (:form . "tRNA") (:end . 39) (:start . 35)\n (:id . 46))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 45) (:start . 40)\n (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n (:id . 48))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 55) (:start . 50)\n (:id . 49))\n ((:tag . "NN") (:stem . "usage") (:form . "usage") (:end . 61) (:start . 56)\n (:id . 50))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 65) (:start . 62)\n (:id . 51))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 73)\n (:start . 66) (:id . 52))\n ((:tag . "NNS") (:stem . "insight") (:form . "insights") (:end . 82)\n (:start . 74) (:id . 53))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 87) (:start . 83)\n (:id . 54))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 92) (:start . 88)\n (:id . 55))\n ((:tag . "NN") (:stem . "problem") (:form . "problem") (:end . 100)\n (:start . 93) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n (:id . 57)))@@@1@16@((:hcues ((:id . :x1.245.1) (:span 62 65)))\n (:hscopes ((:id . :x1.245.1) (:span 62 100)))\n (:identifiers (:sid . :s1.245) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100245@unknown@formal@none@1@S@In addition to the 23rd amino acid, our method can simultaneously explore selenoproteins and other readthrough proteins.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "JJ") (:stem . "23rd") (:form . "23rd") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 29) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 34) (:start . 30)\n (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n (:id . 49))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 39) (:start . 36)\n (:id . 50))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 46)\n (:start . 40) (:id . 51))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 50) (:start . 47)\n (:id . 52))\n ((:tag . "RB") (:stem . "simultaneously") (:form . "simultaneously")\n (:end . 65) (:start . 51) (:id . 53))\n ((:tag . "VB") (:stem . "explore") (:form . "explore") (:end . 73)\n (:start . 66) (:id . 54))\n ((:tag . "NNS") (:stem . "selenoprotein") (:form . "selenoproteins")\n (:end . 88) (:start . 74) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n (:id . 56))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 98) (:start . 93)\n (:id . 57))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 110)\n (:start . 99) (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 119)\n (:start . 111) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.246) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100246@unknown@formal@none@1@S@A common assumption in microbial selenoprotein predictions is that selenoproteins will have cysteine homologs.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 8) (:start . 2)\n (:id . 43))\n ((:tag . "NN") (:stem . "assumption") (:form . "assumption") (:end . 19)\n (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 22) (:start . 20)\n (:id . 45))\n ((:tag . "JJ") (:stem . "microbial") (:form . "microbial") (:end . 32)\n (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "selenoprotein") (:form . "selenoprotein")\n (:end . 46) (:start . 33) (:id . 47))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 58)\n (:start . 47) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 61) (:start . 59)\n (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 66) (:start . 62)\n (:id . 50))\n ((:tag . "NNS") (:stem . "selenoprotein") (:form . "selenoproteins")\n (:end . 81) (:start . 67) (:id . 51))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 86) (:start . 82)\n (:id . 52))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 91) (:start . 87)\n (:id . 53))\n ((:tag . "NN") (:stem . "cysteine") (:form . "cysteine") (:end . 100)\n (:start . 92) (:id . 54))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 109)\n (:start . 101) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n (:id . 56)))@@@1@15@((:hcues ((:id . :x1.247.1) (:span 9 19)))\n (:hscopes ((:id . :x1.247.1) (:span 9 109)))\n (:identifiers (:sid . :s1.247) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100247@unknown@formal@none@1@S@Zhang et al. 20 examined the validity of this assumption using a SECIS-based method and concluded that selenoproteins without cysteine homologs will be extremely rare.@(((:tag . "NNP") (:stem . "Zhang") (:form . "Zhang") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 8) (:start . 6)\n (:id . 43))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "VBD") (:stem . "examine") (:form . "examined") (:end . 24)\n (:start . 16) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n (:id . 47))\n ((:tag . "NN") (:stem . "validity") (:form . "validity") (:end . 37)\n (:start . 29) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n (:id . 49))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 45) (:start . 41)\n (:id . 50))\n ((:tag . "NN") (:stem . "assumption") (:form . "assumption") (:end . 56)\n (:start . 46) (:id . 51))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 62) (:start . 57)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n (:id . 53))\n ((:tag . "JJ") (:stem . "secis-based") (:form . "SECIS-based") (:end . 76)\n (:start . 65) (:id . 54))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 83)\n (:start . 77) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n (:id . 56))\n ((:tag . "VBD") (:stem . "conclude") (:form . "concluded") (:end . 97)\n (:start . 88) (:id . 57))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 102) (:start . 98)\n (:id . 58))\n ((:tag . "NNS") (:stem . "selenoprotein") (:form . "selenoproteins")\n (:end . 117) (:start . 103) (:id . 59))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 125)\n (:start . 118) (:id . 60))\n ((:tag . "NN") (:stem . "cysteine") (:form . "cysteine") (:end . 134)\n (:start . 126) (:id . 61))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 143)\n (:start . 135) (:id . 62))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 148) (:start . 144)\n (:id . 63))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 151) (:start . 149)\n (:id . 64))\n ((:tag . "RB") (:stem . "extremely") (:form . "extremely") (:end . 161)\n (:start . 152) (:id . 65))\n ((:tag . "JJ") (:stem . "rare") (:form . "rare") (:end . 166) (:start . 162)\n (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n (:id . 67)))@@@1@26@((:ncues ((:id . :x1.248.1) (:span 118 125)))\n (:nscopes ((:id . :x1.248.1) (:span 118 143)))\n (:identifiers (:sid . :s1.248) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100248@unknown@formal@none@1@S@Our method can reassess this assumption in a SECIS-independent way.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "VB") (:stem . "reassess") (:form . "reassess") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 28) (:start . 24)\n (:id . 46))\n ((:tag . "NN") (:stem . "assumption") (:form . "assumption") (:end . 39)\n (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n (:id . 49))\n ((:tag . "JJ") (:stem . "secis-independent") (:form . "SECIS-independent")\n (:end . 62) (:start . 45) (:id . 50))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 66) (:start . 63)\n (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s1.249) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100250@unknown@formal@none@1@S@Therefore, selenoproteins that lack cysteine homologs will be scarce, as previously reported.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "NNS") (:stem . "selenoprotein") (:form . "selenoproteins")\n (:end . 25) (:start . 11) (:id . 44))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n (:id . 45))\n ((:tag . "VBP") (:stem . "lack") (:form . "lack") (:end . 35) (:start . 31)\n (:id . 46))\n ((:tag . "NN") (:stem . "cysteine") (:form . "cysteine") (:end . 44)\n (:start . 36) (:id . 47))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 53)\n (:start . 45) (:id . 48))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 58) (:start . 54)\n (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 61) (:start . 59)\n (:id . 50))\n ((:tag . "JJ") (:stem . "scarce") (:form . "scarce") (:end . 68)\n (:start . 62) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n (:id . 52))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 72) (:start . 70)\n (:id . 53))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 83)\n (:start . 73) (:id . 54))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 92)\n (:start . 84) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n (:id . 56)))@@@1@15@((:ncues ((:id . :x1.251.1) (:span 31 35)))\n (:nscopes ((:id . :x1.251.1) (:span 31 53)))\n (:identifiers (:sid . :s1.251) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100251@unknown@formal@none@1@S@Other readthrough proteins with canonical amino acids (i.e., proteins that have canonical amino acids at their inframe stop codons) are quite rare in prokaryotes 1.@(((:tag . "JJ") (:stem . "other") (:form . "Other") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 17)\n (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 26)\n (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 31) (:start . 27)\n (:id . 45))\n ((:tag . "JJ") (:stem . "canonical") (:form . "canonical") (:end . 41)\n (:start . 32) (:id . 46))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 47) (:start . 42)\n (:id . 47))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 53) (:start . 48)\n (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n (:id . 49))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 59) (:start . 55)\n (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n (:id . 51))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 69)\n (:start . 61) (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 74) (:start . 70)\n (:id . 53))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 79) (:start . 75)\n (:id . 54))\n ((:tag . "JJ") (:stem . "canonical") (:form . "canonical") (:end . 89)\n (:start . 80) (:id . 55))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 95) (:start . 90)\n (:id . 56))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 101) (:start . 96)\n (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 104) (:start . 102)\n (:id . 58))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 110)\n (:start . 105) (:id . 59))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 118)\n (:start . 111) (:id . 60))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 123) (:start . 119)\n (:id . 61))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 130)\n (:start . 124) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 131) (:start . 130)\n (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 135) (:start . 132)\n (:id . 64))\n ((:tag . "RB") (:stem . "quite") (:form . "quite") (:end . 141)\n (:start . 136) (:id . 65))\n ((:tag . "JJ") (:stem . "rare") (:form . "rare") (:end . 146) (:start . 142)\n (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n (:id . 67))\n ((:tag . "NNS") (:stem . "prokaryote") (:form . "prokaryotes") (:end . 161)\n (:start . 150) (:id . 68))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 163) (:start . 162)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s1.252) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100252@unknown@formal@none@1@S@The result reported here is in agreement, but it is not conclusive.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 19)\n (:start . 11) (:id . 44))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 24) (:start . 20)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n (:id . 47))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 40)\n (:start . 31) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n (:id . 49))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 45) (:start . 42)\n (:id . 50))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 48) (:start . 46)\n (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 51) (:start . 49)\n (:id . 52))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 55) (:start . 52)\n (:id . 53))\n ((:tag . "JJ") (:stem . "conclusive") (:form . "conclusive") (:end . 66)\n (:start . 56) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n (:id . 55)))@@@1@14@((:ncues ((:id . :x1.253.1) (:span 52 55)))\n (:nscopes ((:id . :x1.253.1) (:span 52 66)))\n (:identifiers (:sid . :s1.253) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100253@unknown@formal@none@1@S@This is because our method assumes that stop-codon-encoded amino acid is located inside a domain, but it is unclear whether it holds true in prokaryotic readthrough with canonical amino acids.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 15)\n (:start . 8) (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 26)\n (:start . 20) (:id . 46))\n ((:tag . "VBZ") (:stem . "assume") (:form . "assumes") (:end . 34)\n (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 39) (:start . 35)\n (:id . 48))\n ((:tag . "JJ") (:stem . "stop-codon-encoded") (:form . "stop-codon-encoded")\n (:end . 58) (:start . 40) (:id . 49))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 64) (:start . 59)\n (:id . 50))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 69) (:start . 65)\n (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 72) (:start . 70)\n (:id . 52))\n ((:tag . "JJ") (:stem . "located") (:form . "located") (:end . 80)\n (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "inside") (:form . "inside") (:end . 87)\n (:start . 81) (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 89) (:start . 88)\n (:id . 55))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 96)\n (:start . 90) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n (:id . 57))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 101) (:start . 98)\n (:id . 58))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 104) (:start . 102)\n (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 107) (:start . 105)\n (:id . 60))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 115)\n (:start . 108) (:id . 61))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 123)\n (:start . 116) (:id . 62))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 126) (:start . 124)\n (:id . 63))\n ((:tag . "VBZ") (:stem . "hold") (:form . "holds") (:end . 132)\n (:start . 127) (:id . 64))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 137) (:start . 133)\n (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 140) (:start . 138)\n (:id . 66))\n ((:tag . "JJ") (:stem . "prokaryotic") (:form . "prokaryotic") (:end . 152)\n (:start . 141) (:id . 67))\n ((:tag . "NN") (:stem . "readthrough") (:form . "readthrough") (:end . 164)\n (:start . 153) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 169) (:start . 165)\n (:id . 69))\n ((:tag . "JJ") (:stem . "canonical") (:form . "canonical") (:end . 179)\n (:start . 170) (:id . 70))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 185)\n (:start . 180) (:id . 71))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 191)\n (:start . 186) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n (:id . 73)))@@@1@32@((:hcues ((:id . :x1.254.1) (:span 116 123))\n ((:id . :x1.254.2) (:span 108 115)) ((:id . :x1.254.3) (:span 27 34)))\n (:hscopes ((:id . :x1.254.1) (:span 116 191))\n ((:id . :x1.254.2) (:span 108 191)) ((:id . :x1.254.3) (:span 27 96)))\n (:identifiers (:sid . :s1.254) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100254@unknown@formal@none@1@S@At least, only one experimentally-confirmed example from a pathogenic strain of Escherichia coli 23, whose genome is not yet determined, does not obey this rule.@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 14) (:start . 10)\n (:id . 45))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 18) (:start . 15)\n (:id . 46))\n ((:tag . "JJ") (:stem . "experimentally-confirmed")\n (:form . "experimentally-confirmed") (:end . 43) (:start . 19) (:id . 47))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 51)\n (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 56) (:start . 52)\n (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 58) (:start . 57)\n (:id . 50))\n ((:tag . "JJ") (:stem . "pathogenic") (:form . "pathogenic") (:end . 69)\n (:start . 59) (:id . 51))\n ((:tag . "NN") (:stem . "strain") (:form . "strain") (:end . 76)\n (:start . 70) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n (:id . 53))\n ((:tag . "FW") (:stem . "escherichia") (:form . "Escherichia") (:end . 91)\n (:start . 80) (:id . 54))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 96) (:start . 92)\n (:id . 55))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 99) (:start . 97)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n (:id . 57))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 106)\n (:start . 101) (:id . 58))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 113)\n (:start . 107) (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 116) (:start . 114)\n (:id . 60))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 120) (:start . 117)\n (:id . 61))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 124) (:start . 121)\n (:id . 62))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 135)\n (:start . 125) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n (:id . 64))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 141) (:start . 137)\n (:id . 65))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 145) (:start . 142)\n (:id . 66))\n ((:tag . "VB") (:stem . "obey") (:form . "obey") (:end . 150) (:start . 146)\n (:id . 67))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 155) (:start . 151)\n (:id . 68))\n ((:tag . "NN") (:stem . "rule") (:form . "rule") (:end . 160) (:start . 156)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n (:id . 70)))@@@1@29@((:ncues ((:id . :x1.255.1) (:span 142 145))\n ((:id . :x1.255.2) (:span 117 120)))\n (:nscopes ((:id . :x1.255.1) (:span 142 160))\n ((:id . :x1.255.2) (:span 101 135)))\n (:identifiers (:sid . :s1.255) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100255@unknown@formal@none@1@S@What can be concluded from our result is that this type of readthrough will be located outside of domains, such as a linker between two domains.@(((:tag . "WP") (:stem . "what") (:form . "What") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "VBN") (:stem . "conclude") (:form . "concluded") (:end . 21)\n (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 26) (:start . 22)\n (:id . 46))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 30) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 37)\n (:start . 31) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 40) (:start . 38)\n (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 45) (:start . 41)\n (:id . 50))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 50) (:start . 46)\n (:id . 51))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 55) (:start . 51)\n (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n (:id . 53))\n ((:tag . "NN") (:stem . "readthrough") (:form . "readthrough") (:end . 70)\n (:start . 59) (:id . 54))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 75) (:start . 71)\n (:id . 55))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 78) (:start . 76)\n (:id . 56))\n ((:tag . "VBN") (:stem . "locate") (:form . "located") (:end . 86)\n (:start . 79) (:id . 57))\n ((:tag . "IN") (:stem . "outside") (:form . "outside") (:end . 94)\n (:start . 87) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n (:id . 59))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 105)\n (:start . 98) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n (:id . 61))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 111) (:start . 107)\n (:id . 62))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 114) (:start . 112)\n (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 116) (:start . 115)\n (:id . 64))\n ((:tag . "NN") (:stem . "linker") (:form . "linker") (:end . 123)\n (:start . 117) (:id . 65))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 131)\n (:start . 124) (:id . 66))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 135) (:start . 132)\n (:id . 67))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 143)\n (:start . 136) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.256) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100256@unknown@formal@none@1@S@Such a stop codon may behave as a switch that regulates production of short and long isoforms from a single mRNA, as in readthrough genes from viruses 24.@(((:tag . "PDT") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 6) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 17) (:start . 12)\n (:id . 45))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "VB") (:stem . "behave") (:form . "behave") (:end . 28)\n (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 31) (:start . 29)\n (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n (:id . 49))\n ((:tag . "NN") (:stem . "switch") (:form . "switch") (:end . 40)\n (:start . 34) (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 45) (:start . 41)\n (:id . 51))\n ((:tag . "VBZ") (:stem . "regulate") (:form . "regulates") (:end . 55)\n (:start . 46) (:id . 52))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 66)\n (:start . 56) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n (:id . 54))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 75) (:start . 70)\n (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 79) (:start . 76)\n (:id . 56))\n ((:tag . "JJ") (:stem . "long") (:form . "long") (:end . 84) (:start . 80)\n (:id . 57))\n ((:tag . "NNS") (:stem . "isoform") (:form . "isoforms") (:end . 93)\n (:start . 85) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 98) (:start . 94)\n (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 100) (:start . 99)\n (:id . 60))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 107)\n (:start . 101) (:id . 61))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 112) (:start . 108)\n (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 116) (:start . 114)\n (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 119) (:start . 117)\n (:id . 65))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 131)\n (:start . 120) (:id . 66))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 137)\n (:start . 132) (:id . 67))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 142) (:start . 138)\n (:id . 68))\n ((:tag . "NNS") (:stem . "virus") (:form . "viruses") (:end . 150)\n (:start . 143) (:id . 69))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 153) (:start . 151)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n (:id . 71)))@@@1@30@((:hcues ((:id . :x1.257.1) (:span 18 21)))\n (:hscopes ((:id . :x1.257.1) (:span 18 150)))\n (:identifiers (:sid . :s1.257) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100257@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s1.258) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Title|)))@oe@9-2-2011 5100258@unknown@formal@none@1@S@To explore the possibility of a 23rd amino acid, ORFs in prokaryotic genomes were investigated in a comprehensive way.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "explore") (:form . "explore") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 26)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 31) (:start . 30)\n (:id . 47))\n ((:tag . "JJ") (:stem . "23rd") (:form . 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"DT") (:stem . "a") (:form . "a") (:end . 99) (:start . 98)\n (:id . 59))\n ((:tag . "JJ") (:stem . "comprehensive") (:form . "comprehensive")\n (:end . 113) (:start . 100) (:id . 60))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 117) (:start . 114)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s1.259) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100260@unknown@formal@none@1@S@Therefore, if such an amino acid exists, it will have limited distribution in the tree of life.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "PDT") (:stem . "such") (:form . "such") (:end . 18) (:start . 14)\n (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 21) (:start . 19)\n (:id . 46))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 27) (:start . 22)\n (:id . 47))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 32) (:start . 28)\n (:id . 48))\n ((:tag . "VBZ") (:stem . "exist") (:form . "exists") (:end . 39)\n (:start . 33) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n (:id . 50))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 43) (:start . 41)\n (:id . 51))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 48) (:start . 44)\n (:id . 52))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 53) (:start . 49)\n (:id . 53))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 61)\n (:start . 54) (:id . 54))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 74)\n (:start . 62) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n (:id . 57))\n ((:tag . "NN") (:stem . "tree") (:form . "tree") (:end . 86) (:start . 82)\n (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n (:id . 59))\n ((:tag . "NN") (:stem . "life") (:form . "life") (:end . 94) (:start . 90)\n (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.261) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100261@unknown@formal@none@1@S@Alternatively, it may be encoded by one of the sense codons.@(((:tag . "RB") (:stem . "alternatively") (:form . "Alternatively")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 17) (:start . 15)\n (:id . 44))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 21) (:start . 18)\n (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 24) (:start . 22)\n (:id . 46))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 32)\n (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 35) (:start . 33)\n (:id . 48))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 39) (:start . 36)\n (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n (:id . 51))\n ((:tag . "NN") (:stem . "sense") (:form . "sense") (:end . 52) (:start . 47)\n (:id . 52))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 59)\n (:start . 53) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n (:id . 54)))@@@1@13@((:hcues ((:id . :x1.262.1) (:span 18 21)))\n (:hscopes ((:id . :x1.262.1) (:span 15 59)))\n (:identifiers (:sid . :s1.262) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100262@unknown@formal@none@1@S@From the viewpoint of selenoprotein prediction, the sensitivity of our method was lower than an existing method.@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "viewpoint") (:form . "viewpoint") (:end . 18)\n (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "NN") (:stem . "selenoprotein") (:form . "selenoprotein")\n (:end . 35) (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 46)\n (:start . 36) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n (:id . 49))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 63)\n (:start . 52) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n (:id . 51))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 70) (:start . 67)\n (:id . 52))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 77)\n (:start . 71) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 81) (:start . 78)\n (:id . 54))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 87) (:start . 82)\n (:id . 55))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 92) (:start . 88)\n (:id . 56))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 95) (:start . 93)\n (:id . 57))\n ((:tag . "VBG") (:stem . "exist") (:form . "existing") (:end . 104)\n (:start . 96) (:id . 58))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 111)\n (:start . 105) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.263) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100263@unknown@formal@none@1@S@However, our method has several unique features.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 19)\n (:start . 13) (:id . 45))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 23) (:start . 20)\n (:id . 46))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 31)\n (:start . 24) (:id . 47))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 38)\n (:start . 32) (:id . 48))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 47)\n (:start . 39) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 48) (:start . 47)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s1.264) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100264@unknown@formal@none@1@S@It is applicable to general readthrough genes and rigorously excludes pseudogenes and sequencing errors.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "applicable") (:form . "applicable") (:end . 16)\n (:start . 6) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 27)\n (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "readthrough") (:form . "readthrough") (:end . 39)\n (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 45) (:start . 40)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "RB") (:stem . "rigorously") (:form . "rigorously") (:end . 60)\n (:start . 50) (:id . 50))\n ((:tag . "VBZ") (:stem . "exclude") (:form . "excludes") (:end . 69)\n (:start . 61) (:id . 51))\n ((:tag . "NNS") (:stem . "pseudogene") (:form . "pseudogenes") (:end . 81)\n (:start . 70) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n (:id . 53))\n ((:tag . "NN") (:stem . "sequencing") (:form . "sequencing") (:end . 96)\n (:start . 86) (:id . 54))\n ((:tag . "NNS") (:stem . "error") (:form . "errors") (:end . 103)\n (:start . 97) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s1.265) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100265@unknown@formal@none@1@S@Moreover, it does not assume the occurrence of non-readthrough homologs in the public databases.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 12) (:start . 10)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 17) (:start . 13)\n (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "VB") (:stem . "assume") (:form . "assume") (:end . 28)\n (:start . 22) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n (:id . 48))\n ((:tag . "NN") (:stem . "occurrence") (:form . "occurrence") (:end . 43)\n (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n (:id . 50))\n ((:tag . "JJ") (:stem . "non-readthrough") (:form . "non-readthrough")\n (:end . 62) (:start . 47) (:id . 51))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 71)\n (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n (:id . 54))\n ((:tag . "JJ") (:stem . "public") (:form . "public") (:end . 85)\n (:start . 79) (:id . 55))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 95)\n (:start . 86) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n (:id . 57)))@@@1@16@((:ncues ((:id . :x1.266.1) (:span 18 21)))\n (:nscopes ((:id . :x1.266.1) (:span 18 95)))\n (:identifiers (:sid . :s1.266) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100266@unknown@formal@none@1@S@It will help in identification of novel readthrough genes from the rapidly expanding collection of complete microbial genomes.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VB") (:stem . "help") (:form . "help") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n (:end . 30) (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n (:id . 47))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 39) (:start . 34)\n (:id . 48))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 51)\n (:start . 40) (:id . 49))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 57) (:start . 52)\n (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 62) (:start . 58)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n (:id . 52))\n ((:tag . "RB") (:stem . "rapidly") (:form . "rapidly") (:end . 74)\n (:start . 67) (:id . 53))\n ((:tag . "VBG") (:stem . "expand") (:form . "expanding") (:end . 84)\n (:start . 75) (:id . 54))\n ((:tag . "NN") (:stem . "collection") (:form . "collection") (:end . 95)\n (:start . 85) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n (:id . 56))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 107)\n (:start . 99) (:id . 57))\n ((:tag . "JJ") (:stem . "microbial") (:form . "microbial") (:end . 117)\n (:start . 108) (:id . 58))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 125)\n (:start . 118) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.267) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100267@unknown@formal@none@1@S@Methods@(((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 7)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s1.268) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Title|)))@oe@9-2-2011 5100268@unknown@formal@none@1@S@Enumeration of iORFs from prokaryotic genomes@(((:tag . "NNP") (:stem . "Enumeration") (:form . "Enumeration") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 43))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 20) (:start . 15)\n (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 25) (:start . 21)\n (:id . 45))\n ((:tag . "JJ") (:stem . "prokaryotic") (:form . "prokaryotic") (:end . 37)\n (:start . 26) (:id . 46))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 45)\n (:start . 38) (:id . 47)))@@@1@6@((:identifiers (:sid . :s1.269) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100270@unknown@formal@none@1@S@From them, 191 representative organisms were selected by excluding close relatives.@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 44))\n ((:tag . "CD") (:stem . "191") (:form . "191") (:end . 14) (:start . 11)\n (:id . 45))\n ((:tag . "JJ") (:stem . "representative") (:form . "representative")\n (:end . 29) (:start . 15) (:id . 46))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 39)\n (:start . 30) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 44) (:start . 40)\n (:id . 48))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 53)\n (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 56) (:start . 54)\n (:id . 50))\n ((:tag . "VBG") (:stem . "exclude") (:form . "excluding") (:end . 66)\n (:start . 57) (:id . 51))\n ((:tag . "JJ") (:stem . "close") (:form . "close") (:end . 72) (:start . 67)\n (:id . 52))\n ((:tag . "NNS") (:stem . "relative") (:form . "relatives") (:end . 82)\n (:start . 73) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s1.271) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100271@unknown@formal@none@1@S@The threshold was set to average sequence identity 90% of two house-keeping genes, DNA polymerase III α subunit and alanyl-tRNA synthetase.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 21) (:start . 18)\n (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 24) (:start . 22)\n (:id . 46))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 32)\n (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "sequence") (:form . 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"CD") (:stem . "iii") (:form . "III") (:end . 101) (:start . 98)\n (:id . 59))\n ((:tag . "NNP") (:stem . "α") (:form . "α") (:end . 103) (:start . 102)\n (:id . 60))\n ((:tag . "NN") (:stem . "subunit") (:form . "subunit") (:end . 111)\n (:start . 104) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n (:id . 62))\n ((:tag . "NN") (:stem . "alanyl-trna") (:form . "alanyl-tRNA") (:end . 127)\n (:start . 116) (:id . 63))\n ((:tag . "NN") (:stem . "synthetase") (:form . "synthetase") (:end . 138)\n (:start . 128) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s1.272) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100272@unknown@formal@none@1@S@From these 191 genomes, iORFs longer than 80 codons were enumerated using inhouse software, which is available from the author's web site 26.@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "CD") (:stem . "191") (:form . "191") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 22)\n (:start . 15) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n (:id . 46))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 29) (:start . 24)\n (:id . 47))\n ((:tag . "JJR") (:stem . "long") (:form . "longer") (:end . 36) (:start . 30)\n (:id . 48))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 41) (:start . 37)\n (:id . 49))\n ((:tag . "CD") (:stem . "80") (:form . "80") (:end . 44) (:start . 42)\n (:id . 50))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 51)\n (:start . 45) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 56) (:start . 52)\n (:id . 52))\n ((:tag . "VBN") (:stem . "enumerate") (:form . "enumerated") (:end . 67)\n (:start . 57) (:id . 53))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 73) (:start . 68)\n (:id . 54))\n ((:tag . "NN") (:stem . "inhouse") (:form . "inhouse") (:end . 81)\n (:start . 74) (:id . 55))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 90)\n (:start . 82) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n (:id . 57))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 97) (:start . 92)\n (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 100) (:start . 98)\n (:id . 59))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 110)\n (:start . 101) (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 115) (:start . 111)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n (:id . 62))\n ((:tag . "NN") (:stem . "author") (:form . "author") (:end . 126)\n (:start . 120) (:id . 63))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 128) (:start . 126)\n (:id . 64))\n ((:tag . "NN") (:stem . "web") (:form . "web") (:end . 132) (:start . 129)\n (:id . 65))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 137) (:start . 133)\n (:id . 66))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 140) (:start . 138)\n (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.273) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100273@unknown@formal@none@1@S@Both upstream and downstream regions of its inframe stop codon were required to be longer than 10 codons.@(((:tag . "CC") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "JJ") (:stem . "downstream") (:form . "downstream") (:end . 28)\n (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 36)\n (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n (:id . 47))\n ((:tag . "PRP$") (:stem . "its") (:form . 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"codon") (:form . "codons") (:end . 104)\n (:start . 98) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.274) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100274@unknown@formal@none@1@S@Two stop codons of an iORF (i.e. the inframe and C-terminal stops) can be any combination of canonical stop codons (TAA, TAG, TGA).@(((:tag . "CD") (:stem . "two") (:form . "Two") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 15) (:start . 9)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 21) (:start . 19)\n (:id . 46))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 26) (:start . 22)\n (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 28) (:start . 27)\n (:id . 48))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 32) (:start . 28)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n (:id . 50))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 44)\n (:start . 37) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n (:id . 52))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 59)\n (:start . 49) (:id . 53))\n ((:tag . "NNS") (:stem . "stop") (:form . "stops") (:end . 65) (:start . 60)\n (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 66) (:start . 65)\n (:id . 55))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 70) (:start . 67)\n (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 73) (:start . 71)\n (:id . 57))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 77) (:start . 74)\n (:id . 58))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 89)\n (:start . 78) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n (:id . 60))\n ((:tag . "JJ") (:stem . "canonical") (:form . "canonical") (:end . 102)\n (:start . 93) (:id . 61))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 107) (:start . 103)\n (:id . 62))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 114)\n (:start . 108) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 116) (:start . 115)\n (:id . 64))\n ((:tag . "NNP") (:stem . "TAA") (:form . "TAA") (:end . 119) (:start . 116)\n (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n (:id . 66))\n ((:tag . "NNP") (:stem . "TAG") (:form . "TAG") (:end . 124) (:start . 121)\n (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n (:id . 68))\n ((:tag . "NNP") (:stem . "TGA") (:form . "TGA") (:end . 129) (:start . 126)\n (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 130) (:start . 129)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s1.275) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100275@unknown@formal@none@1@S@However, for Mycoplasma, only TAA and TAG were used.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Mycoplasma") (:form . "Mycoplasma") (:end . 23)\n (:start . 13) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n (:id . 46))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 29) (:start . 25)\n (:id . 47))\n ((:tag . "NNP") (:stem . "TAA") (:form . "TAA") (:end . 33) (:start . 30)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n (:id . 49))\n ((:tag . "NNP") (:stem . "TAG") (:form . "TAG") (:end . 41) (:start . 38)\n (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 46) (:start . 42)\n (:id . 51))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 51) (:start . 47)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 52) (:start . 51)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s1.276) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100276@unknown@formal@none@1@S@Three codons ATG, TTG and GTG were allowed to be start signals.@(((:tag . "CD") (:stem . "three") (:form . "Three") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 12) (:start . 6)\n (:id . 43))\n ((:tag . "NNP") (:stem . "ATG") (:form . "ATG") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "NNP") (:stem . "TTG") (:form . "TTG") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 25) (:start . 22)\n (:id . 47))\n ((:tag . "NNP") (:stem . "GTG") (:form . "GTG") (:end . 29) (:start . 26)\n (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 34) (:start . 30)\n (:id . 49))\n ((:tag . "VBN") (:stem . "allow") (:form . "allowed") (:end . 42)\n (:start . 35) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 45) (:start . 43)\n (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 48) (:start . 46)\n (:id . 52))\n ((:tag . "JJ") (:stem . "start") (:form . "start") (:end . 54) (:start . 49)\n (:id . 53))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 62)\n (:start . 55) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s1.277) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100277@unknown@formal@none@1@S@The iORFs of each organism were compared with protein-coding genes of the organism using BLASTX.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n (:id . 44))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 17) (:start . 13)\n (:id . 45))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 26)\n (:start . 18) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 31) (:start . 27)\n (:id . 47))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 40)\n (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 45) (:start . 41)\n (:id . 49))\n ((:tag . "JJ") (:stem . "protein-coding") (:form . "protein-coding")\n (:end . 60) (:start . 46) (:id . 50))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 66) (:start . 61)\n (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n (:id . 53))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 82)\n (:start . 74) (:id . 54))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 88) (:start . 83)\n (:id . 55))\n ((:tag . "NNP") (:stem . "BLASTX") (:form . "BLASTX") (:end . 95)\n (:start . 89) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.278) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100278@unknown@formal@none@1@S@If an iORF matched any protein-coding genes (E-value < 10-3) and their reading frames did not coincide, the iORF was discarded.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 10) (:start . 6)\n (:id . 44))\n ((:tag . "VBD") (:stem . "match") (:form . "matched") (:end . 18)\n (:start . 11) (:id . 45))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 22) (:start . 19)\n (:id . 46))\n ((:tag . "JJ") (:stem . "protein-coding") (:form . "protein-coding")\n (:end . 37) (:start . 23) (:id . 47))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 43) (:start . 38)\n (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n (:id . 49))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-value") (:end . 52)\n (:start . 45) (:id . 50))\n ((:tag . "SYM") (:stem . "<") (:form . "<") (:end . 54) (:start . 53)\n (:id . 51))\n ((:tag . "CD") (:stem . "10-3") (:form . "10-3") (:end . 59) (:start . 55)\n (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 60) (:start . 59)\n (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 64) (:start . 61)\n (:id . 54))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 70)\n (:start . 65) (:id . 55))\n ((:tag . "NN") (:stem . "reading") (:form . "reading") (:end . 78)\n (:start . 71) (:id . 56))\n ((:tag . "NNS") (:stem . "frame") (:form . "frames") (:end . 85)\n (:start . 79) (:id . 57))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 89) (:start . 86)\n (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 93) (:start . 90)\n (:id . 59))\n ((:tag . "VB") (:stem . "coincide") (:form . "coincide") (:end . 102)\n (:start . 94) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n (:id . 62))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 112) (:start . 108)\n (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 116) (:start . 113)\n (:id . 64))\n ((:tag . "VBN") (:stem . "discard") (:form . "discarded") (:end . 126)\n (:start . 117) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n (:id . 66)))@@@1@25@((:ncues ((:id . :x1.279.1) (:span 90 93)))\n (:nscopes ((:id . :x1.279.1) (:span 90 102)))\n (:identifiers (:sid . :s1.279) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100280@unknown@formal@none@1@S@Remaining iORFs were translated into amino acid sequences.@(((:tag . "VBG") (:stem . "remain") (:form . "Remaining") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 15) (:start . 10)\n (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 20) (:start . 16)\n (:id . 44))\n ((:tag . "VBN") (:stem . "translate") (:form . "translated") (:end . 31)\n (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 36) (:start . 32)\n (:id . 46))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 42) (:start . 37)\n (:id . 47))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 47) (:start . 43)\n (:id . 48))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 57)\n (:start . 48) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 58) (:start . 57)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s1.281) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100281@unknown@formal@none@1@S@We translated all three types of nonsense codons into the one-letter code U, so as to simplify visual inspection of sequence alignments.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "translate") (:form . "translated") (:end . 13)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 23) (:start . 18)\n (:id . 45))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 29) (:start . 24)\n (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n (:id . 47))\n ((:tag . "JJ") (:stem . "nonsense") (:form . "nonsense") (:end . 41)\n (:start . 33) (:id . 48))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 48)\n (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 53) (:start . 49)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n (:id . 51))\n ((:tag . "JJ") (:stem . "one-letter") (:form . "one-letter") (:end . 68)\n (:start . 58) (:id . 52))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 73) (:start . 69)\n (:id . 53))\n ((:tag . "NNP") (:stem . "U") (:form . "U") (:end . 75) (:start . 74)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n (:id . 55))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 79) (:start . 77)\n (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 82) (:start . 80)\n (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 85) (:start . 83)\n (:id . 58))\n ((:tag . "VB") (:stem . "simplify") (:form . "simplify") (:end . 94)\n (:start . 86) (:id . 59))\n ((:tag . "JJ") (:stem . "visual") (:form . "visual") (:end . 101)\n (:start . 95) (:id . 60))\n ((:tag . "NN") (:stem . "inspection") (:form . "inspection") (:end . 112)\n (:start . 102) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n (:id . 62))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 124)\n (:start . 116) (:id . 63))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 135)\n (:start . 125) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s1.282) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100282@unknown@formal@none@1@S@Although the code U is usually for selenocysteine, it will be harmless because U is automatically converted into × inside the BLAST programs.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 43))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 17) (:start . 13)\n (:id . 44))\n ((:tag . "NNP") (:stem . "U") (:form . "U") (:end . 19) (:start . 18)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 22) (:start . 20)\n (:id . 46))\n ((:tag . "RB") (:stem . "usually") (:form . "usually") (:end . 30)\n (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 34) (:start . 31)\n (:id . 48))\n ((:tag . "NN") (:stem . "selenocysteine") (:form . "selenocysteine")\n (:end . 49) (:start . 35) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n (:id . 50))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 53) (:start . 51)\n (:id . 51))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 58) (:start . 54)\n (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 61) (:start . 59)\n (:id . 53))\n ((:tag . "JJ") (:stem . "harmless") (:form . "harmless") (:end . 70)\n (:start . 62) (:id . 54))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 78)\n (:start . 71) (:id . 55))\n ((:tag . "NNP") (:stem . "U") (:form . "U") (:end . 80) (:start . 79)\n (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 83) (:start . 81)\n (:id . 57))\n ((:tag . "RB") (:stem . "automatically") (:form . "automatically")\n (:end . 97) (:start . 84) (:id . 58))\n ((:tag . "VBN") (:stem . "convert") (:form . "converted") (:end . 107)\n (:start . 98) (:id . 59))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 112) (:start . 108)\n (:id . 60))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 114) (:start . 113)\n (:id . 61))\n ((:tag . "IN") (:stem . "inside") (:form . "inside") (:end . 121)\n (:start . 115) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n (:id . 63))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 131)\n (:start . 126) (:id . 64))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 140)\n (:start . 132) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s1.283) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100283@unknown@formal@none@1@S@Construction of clusters of conserved iORFs@(((:tag . "NN") (:stem . "construction") (:form . "Construction") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 43))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 24)\n (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n (:id . 45))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 37)\n (:start . 28) (:id . 46))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 43) (:start . 38)\n (:id . 47)))@@@1@6@((:identifiers (:sid . :s1.284) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100284@unknown@formal@none@1@S@To examine evolutionary conservation of the iORFs, a window of 101 residues around the inframe stop codon was extracted and subjected to TBLASTN searches against the above 191 genome sequences.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "examine") (:form . "examine") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 23)\n (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 36)\n (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n (:id . 47))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 49) (:start . 44)\n (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n (:id . 50))\n ((:tag . "NN") (:stem . "window") (:form . "window") (:end . 59)\n (:start . 53) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n (:id . 52))\n ((:tag . "CD") (:stem . "101") (:form . "101") (:end . 66) (:start . 63)\n (:id . 53))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 75)\n (:start . 67) (:id . 54))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 82)\n (:start . 76) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n (:id . 56))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 94)\n (:start . 87) (:id . 57))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 99) (:start . 95)\n (:id . 58))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 105)\n (:start . 100) (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 109) (:start . 106)\n (:id . 60))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 119)\n (:start . 110) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n (:id . 62))\n ((:tag . "VBN") (:stem . "subject") (:form . "subjected") (:end . 133)\n (:start . 124) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 136) (:start . 134)\n (:id . 64))\n ((:tag . "NN") (:stem . "tblastn") (:form . "TBLASTN") (:end . 144)\n (:start . 137) (:id . 65))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 153)\n (:start . 145) (:id . 66))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 161)\n (:start . 154) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n (:id . 68))\n ((:tag . "JJ") (:stem . "above") (:form . "above") (:end . 171)\n (:start . 166) (:id . 69))\n ((:tag . "CD") (:stem . "191") (:form . "191") (:end . 175) (:start . 172)\n (:id . 70))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 182)\n (:start . 176) (:id . 71))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 192)\n (:start . 183) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s1.285) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100285@unknown@formal@none@1@S@If there were any hits (E-value < 0.01) in other organisms, and if the hit includes 10 upstream and 10 downstream residues of the inframe stop codon, then the iORF was retained.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 17) (:start . 14)\n (:id . 45))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 22) (:start . 18)\n (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 24) (:start . 23)\n (:id . 47))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-value") (:end . 31)\n (:start . 24) (:id . 48))\n ((:tag . "SYM") (:stem . "<") (:form . "<") (:end . 33) (:start . 32)\n (:id . 49))\n ((:tag . "CD") (:stem . "0.01") (:form . "0.01") (:end . 38) (:start . 34)\n (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 39) (:start . 38)\n (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n (:id . 52))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 48) (:start . 43)\n (:id . 53))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 58)\n (:start . 49) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n (:id . 56))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 66) (:start . 64)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n (:id . 58))\n ((:tag . "NN") (:stem . "hit") (:form . "hit") (:end . 74) (:start . 71)\n (:id . 59))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 83)\n (:start . 75) (:id . 60))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 86) (:start . 84)\n (:id . 61))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 95)\n (:start . 87) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n (:id . 63))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 102) (:start . 100)\n (:id . 64))\n ((:tag . "JJ") (:stem . "downstream") (:form . "downstream") (:end . 113)\n (:start . 103) (:id . 65))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 122)\n (:start . 114) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 125) (:start . 123)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n (:id . 68))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 137)\n (:start . 130) (:id . 69))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 142) (:start . 138)\n (:id . 70))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 148)\n (:start . 143) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n (:id . 72))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 154) (:start . 150)\n (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 158) (:start . 155)\n (:id . 74))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 163) (:start . 159)\n (:id . 75))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 167) (:start . 164)\n (:id . 76))\n ((:tag . "VBN") (:stem . "retain") (:form . "retained") (:end . 176)\n (:start . 168) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n (:id . 78)))@@@1@37@((:identifiers (:sid . :s1.286) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100286@unknown@formal@none@1@S@However, if there were any hits (E-value < 10-5) that did not cover the inframe stop codon, the iORF was discarded.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 17) (:start . 12)\n (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 22) (:start . 18)\n (:id . 46))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 26) (:start . 23)\n (:id . 47))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 31) (:start . 27)\n (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 33) (:start . 32)\n (:id . 49))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-value") (:end . 40)\n (:start . 33) (:id . 50))\n ((:tag . "SYM") (:stem . "<") (:form . "<") (:end . 42) (:start . 41)\n (:id . 51))\n ((:tag . "CD") (:stem . "10-5") (:form . "10-5") (:end . 47) (:start . 43)\n (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 48) (:start . 47)\n (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 53) (:start . 49)\n (:id . 54))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 57) (:start . 54)\n (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 61) (:start . 58)\n (:id . 56))\n ((:tag . "VB") (:stem . "cover") (:form . "cover") (:end . 67) (:start . 62)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n (:id . 58))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 79)\n (:start . 72) (:id . 59))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 84) (:start . 80)\n (:id . 60))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 90) (:start . 85)\n (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n (:id . 63))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 100) (:start . 96)\n (:id . 64))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 104) (:start . 101)\n (:id . 65))\n ((:tag . "VBN") (:stem . "discard") (:form . "discarded") (:end . 114)\n (:start . 105) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n (:id . 67)))@@@1@26@((:ncues ((:id . :x1.287.1) (:span 58 61)))\n (:nscopes ((:id . :x1.287.1) (:span 58 90)))\n (:identifiers (:sid . :s1.287) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100287@unknown@formal@none@1@S@Eligible iORFs were then clustered using BLASTCLUST with score density 0.5 and minimum length coverage 0.6.@(((:tag . "JJ") (:stem . "eligible") (:form . "Eligible") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 14) (:start . 9)\n (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 24) (:start . 20)\n (:id . 45))\n ((:tag . "VBN") (:stem . "cluster") (:form . "clustered") (:end . 34)\n (:start . 25) (:id . 46))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 40) (:start . 35)\n (:id . 47))\n ((:tag . "NN") (:stem . "blastclust") (:form . "BLASTCLUST") (:end . 51)\n (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 56) (:start . 52)\n (:id . 49))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 62) (:start . 57)\n (:id . 50))\n ((:tag . "NN") (:stem . "density") (:form . "density") (:end . 70)\n (:start . 63) (:id . 51))\n ((:tag . "CD") (:stem . "0.5") (:form . "0.5") (:end . 74) (:start . 71)\n (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n (:id . 53))\n ((:tag . "JJ") (:stem . "minimum") (:form . "minimum") (:end . 86)\n (:start . 79) (:id . 54))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 93)\n (:start . 87) (:id . 55))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 102)\n (:start . 94) (:id . 56))\n ((:tag . "CD") (:stem . "0.6") (:form . "0.6") (:end . 106) (:start . 103)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.288) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100288@unknown@formal@none@1@S@After removing singleton clusters, multiple sequence alignments of the remaining clusters were computed using MAFFT 27 with the L-INS-i option.@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBG") (:stem . "remove") (:form . "removing") (:end . 14)\n (:start . 6) (:id . 43))\n ((:tag . "JJ") (:stem . "singleton") (:form . "singleton") (:end . 24)\n (:start . 15) (:id . 44))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 33)\n (:start . 25) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n (:id . 46))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 43)\n (:start . 35) (:id . 47))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 52)\n (:start . 44) (:id . 48))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 63)\n (:start . 53) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n (:id . 51))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 80)\n (:start . 71) (:id . 52))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 89)\n (:start . 81) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 94) (:start . 90)\n (:id . 54))\n ((:tag . "VBN") (:stem . "compute") (:form . "computed") (:end . 103)\n (:start . 95) (:id . 55))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 109) (:start . 104)\n (:id . 56))\n ((:tag . "NNP") (:stem . "MAFFT") (:form . "MAFFT") (:end . 115)\n (:start . 110) (:id . 57))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 118) (:start . 116)\n (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 123) (:start . 119)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n (:id . 60))\n ((:tag . "NNP") (:stem . "L-INS-i") (:form . "L-INS-i") (:end . 135)\n (:start . 128) (:id . 61))\n ((:tag . "NN") (:stem . "option") (:form . "option") (:end . 142)\n (:start . 136) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.289) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100290@unknown@formal@none@1@S@If the location or type of stop codons was not identical, the cluster was discarded.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "location") (:form . "location") (:end . 15)\n (:start . 7) (:id . 44))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 18) (:start . 16)\n (:id . 45))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 31) (:start . 27)\n (:id . 48))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 38)\n (:start . 32) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 42) (:start . 39)\n (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 46) (:start . 43)\n (:id . 51))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 56)\n (:start . 47) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n (:id . 54))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 69)\n (:start . 62) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 73) (:start . 70)\n (:id . 56))\n ((:tag . "VBN") (:stem . "discard") (:form . "discarded") (:end . 83)\n (:start . 74) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n (:id . 58)))@@@1@17@((:ncues ((:id . :x1.291.1) (:span 43 46)))\n (:nscopes ((:id . :x1.291.1) (:span 43 56)))\n (:identifiers (:sid . :s1.291) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100291@unknown@formal@none@1@S@Three-step filtering of the candidate clusters@(((:tag . "JJ") (:stem . "three-step") (:form . "Three-step") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "filtering") (:form . "filtering") (:end . 20)\n (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n (:id . 45))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 37)\n (:start . 28) (:id . 46))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 46)\n (:start . 38) (:id . 47)))@@@1@6@((:identifiers (:sid . :s1.292) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100292@unknown@formal@none@1@S@The first filter examines protein-likeliness of the iORFs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 16)\n (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "examine") (:form . "examines") (:end . 25)\n (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "protein-likeliness") (:form . "protein-likeliness")\n (:end . 44) (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n (:id . 48))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 57) (:start . 52)\n (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 58) (:start . 57)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s1.293) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100293@unknown@formal@none@1@S@This filter is mainly designed to remove conserved non-coding sequences (CNS) immediately downstream of non-readthrough genes.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "RB") (:stem . "mainly") (:form . "mainly") (:end . 21)\n (:start . 15) (:id . 45))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 30)\n (:start . 22) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 33) (:start . 31)\n (:id . 47))\n ((:tag . "VB") (:stem . "remove") (:form . "remove") (:end . 40)\n (:start . 34) (:id . 48))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 50)\n (:start . 41) (:id . 49))\n ((:tag . "JJ") (:stem . "non-coding") (:form . "non-coding") (:end . 61)\n (:start . 51) (:id . 50))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 71)\n (:start . 62) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n (:id . 52))\n ((:tag . "NNS") (:stem . "cns") (:form . "CNS") (:end . 76) (:start . 73)\n (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n (:id . 54))\n ((:tag . "RB") (:stem . "immediately") (:form . "immediately") (:end . 89)\n (:start . 78) (:id . 55))\n ((:tag . "JJ") (:stem . "downstream") (:form . "downstream") (:end . 100)\n (:start . 90) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n (:id . 57))\n ((:tag . "JJ") (:stem . "non-readthrough") (:form . "non-readthrough")\n (:end . 119) (:start . 104) (:id . 58))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 125)\n (:start . 120) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.294) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100294@unknown@formal@none@1@S@If we measure purifying selection for amino acid sequences by the ratio of nonsynonymous to synonymous substitution rates (dN/dS), a protein with a stop-codon-encoded amino acid will indicate the sign of selection, while CNS will not.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "VBP") (:stem . "measure") (:form . "measure") (:end . 13)\n (:start . 6) (:id . 44))\n ((:tag . "VBG") (:stem . "purify") (:form . "purifying") (:end . 23)\n (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 33)\n (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 37) (:start . 34)\n (:id . 47))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 43) (:start . 38)\n (:id . 48))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 48) (:start . 44)\n (:id . 49))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 58)\n (:start . 49) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 61) (:start . 59)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n (:id . 52))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 71) (:start . 66)\n (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n (:id . 54))\n ((:tag . "JJ") (:stem . "nonsynonymous") (:form . "nonsynonymous")\n (:end . 88) (:start . 75) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n (:id . 56))\n ((:tag . "JJ") (:stem . "synonymous") (:form . "synonymous") (:end . 102)\n (:start . 92) (:id . 57))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 115)\n (:start . 103) (:id . 58))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 121)\n (:start . 116) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 123) (:start . 122)\n (:id . 60))\n ((:tag . "NN") (:stem . "dn/ds") (:form . "dN/dS") (:end . 128)\n (:start . 123) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 132) (:start . 131)\n (:id . 64))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 140)\n (:start . 133) (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 145) (:start . 141)\n (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 147) (:start . 146)\n (:id . 67))\n ((:tag . "JJ") (:stem . "stop-codon-encoded") (:form . "stop-codon-encoded")\n (:end . 166) (:start . 148) (:id . 68))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 172)\n (:start . 167) (:id . 69))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 177) (:start . 173)\n (:id . 70))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 182) (:start . 178)\n (:id . 71))\n ((:tag . "VB") (:stem . "indicate") (:form . "indicate") (:end . 191)\n (:start . 183) (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 195) (:start . 192)\n (:id . 73))\n ((:tag . "NN") (:stem . "sign") (:form . "sign") (:end . 200) (:start . 196)\n (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 203) (:start . 201)\n (:id . 75))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 213)\n (:start . 204) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 214) (:start . 213)\n (:id . 77))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 220)\n (:start . 215) (:id . 78))\n ((:tag . "NN") (:stem . "cns") (:form . "CNS") (:end . 224) (:start . 221)\n (:id . 79))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 229) (:start . 225)\n (:id . 80))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 233) (:start . 230)\n (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n (:id . 82)))@@@1@41@((:ncues ((:id . :x1.295.1) (:span 230 233)))\n (:nscopes ((:id . :x1.295.1) (:span 230 233)))\n (:identifiers (:sid . :s1.295) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100295@unknown@formal@none@1@S@The dN/dS was calculated for each of the two parts flanking the inframe stop codon in an iORF using codeml program in the PAML package 28.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "dn/ds") (:form . "dN/dS") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 24)\n (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n (:id . 49))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 44) (:start . 41)\n (:id . 50))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 50) (:start . 45)\n (:id . 51))\n ((:tag . "VBG") (:stem . "flank") (:form . "flanking") (:end . 59)\n (:start . 51) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n (:id . 53))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 71)\n (:start . 64) (:id . 54))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 76) (:start . 72)\n (:id . 55))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 82) (:start . 77)\n (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 85) (:start . 83)\n (:id . 57))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 88) (:start . 86)\n (:id . 58))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 93) (:start . 89)\n (:id . 59))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 99) (:start . 94)\n (:id . 60))\n ((:tag . "NN") (:stem . "codeml") (:form . "codeml") (:end . 106)\n (:start . 100) (:id . 61))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 114)\n (:start . 107) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 117) (:start . 115)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n (:id . 64))\n ((:tag . "NNP") (:stem . "PAML") (:form . "PAML") (:end . 126) (:start . 122)\n (:id . 65))\n ((:tag . "NN") (:stem . "package") (:form . "package") (:end . 134)\n (:start . 127) (:id . 66))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 137) (:start . 135)\n (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.296) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100296@unknown@formal@none@1@S@Statistical significance was estimated by likelihood ratio test 29.@(((:tag . "JJ") (:stem . "statistical") (:form . "Statistical") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 24)\n (:start . 12) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 28) (:start . 25)\n (:id . 44))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 38)\n (:start . 29) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 41) (:start . 39)\n (:id . 46))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 52)\n (:start . 42) (:id . 47))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 58) (:start . 53)\n (:id . 48))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 63) (:start . 59)\n (:id . 49))\n ((:tag . "CD") (:stem . "29") (:form . "29") (:end . 66) (:start . 64)\n (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s1.297) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100297@unknown@formal@none@1@S@The observed alignment was fitted to two distinct substitution models, one of which estimates dN/dS from the data, and the other fixes it to 1.0.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 22)\n (:start . 13) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 26) (:start . 23)\n (:id . 45))\n ((:tag . "VBN") (:stem . "fit") (:form . "fitted") (:end . 33) (:start . 27)\n (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 36) (:start . 34)\n (:id . 47))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 40) (:start . 37)\n (:id . 48))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 49)\n (:start . 41) (:id . 49))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 62)\n (:start . 50) (:id . 50))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 69)\n (:start . 63) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n (:id . 52))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 74) (:start . 71)\n (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n (:id . 54))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 83) (:start . 78)\n (:id . 55))\n ((:tag . "VBZ") (:stem . "estimate") (:form . "estimates") (:end . 93)\n (:start . 84) (:id . 56))\n ((:tag . "NN") (:stem . "dn/ds") (:form . "dN/dS") (:end . 99) (:start . 94)\n (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 104) (:start . 100)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n (:id . 59))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 113)\n (:start . 109) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n (:id . 63))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 128)\n (:start . 123) (:id . 64))\n ((:tag . "NNS") (:stem . "fix") (:form . "fixes") (:end . 134) (:start . 129)\n (:id . 65))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 137) (:start . 135)\n (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 140) (:start . 138)\n (:id . 67))\n ((:tag . "CD") (:stem . "1.0") (:form . "1.0") (:end . 144) (:start . 141)\n (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.298) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100298@unknown@formal@none@1@S@Let lfree and lfix denote log likelihood of these models.@(((:tag . "VB") (:stem . "let") (:form . "Let") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "lfree") (:form . "lfree") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "NN") (:stem . "lfix") (:form . "lfix") (:end . 18) (:start . 14)\n (:id . 45))\n ((:tag . "VBP") (:stem . "denote") (:form . "denote") (:end . 25)\n (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "log") (:form . "log") (:end . 29) (:start . 26)\n (:id . 47))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 40)\n (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n (:id . 49))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 49) (:start . 44)\n (:id . 50))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 56)\n (:start . 50) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 57) (:start . 56)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s1.299) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100300@unknown@formal@none@1@S@If dN/dS was less than 1.0, and the statistics 2Δl was larger than a threshold, we regard it as a sign of purifying selection.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "dn/ds") (:form . "dN/dS") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 17) (:start . 13)\n (:id . 45))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 22) (:start . 18)\n (:id . 46))\n ((:tag . "CD") (:stem . "1.0") (:form . "1.0") (:end . 26) (:start . 23)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 31) (:start . 28)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n (:id . 50))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 46)\n (:start . 36) (:id . 51))\n ((:tag . "NN") (:stem . "2δl") (:form . "2Δl") (:end . 50) (:start . 47)\n (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 54) (:start . 51)\n (:id . 53))\n ((:tag . "JJR") (:stem . "large") (:form . "larger") (:end . 61)\n (:start . 55) (:id . 54))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 66) (:start . 62)\n (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 68) (:start . 67)\n (:id . 56))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 78)\n (:start . 69) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n (:id . 58))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 82) (:start . 80)\n (:id . 59))\n ((:tag . "VBP") (:stem . "regard") (:form . "regard") (:end . 89)\n (:start . 83) (:id . 60))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 92) (:start . 90)\n (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 95) (:start . 93)\n (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 97) (:start . 96)\n (:id . 63))\n ((:tag . "NN") (:stem . "sign") (:form . "sign") (:end . 102) (:start . 98)\n (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n (:id . 65))\n ((:tag . "VBG") (:stem . "purify") (:form . "purifying") (:end . 115)\n (:start . 106) (:id . 66))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 125)\n (:start . 116) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.301) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100301@unknown@formal@none@1@S@In this study, the threshold was set to 5.0 (corresponds to P < 0.025) so that the known readthrough proteins score higher than the threshold.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 46))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 28)\n (:start . 19) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 32) (:start . 29)\n (:id . 48))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 36) (:start . 33)\n (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n (:id . 50))\n ((:tag . "CD") (:stem . "5.0") (:form . "5.0") (:end . 43) (:start . 40)\n (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n (:id . 52))\n ((:tag . "VBZ") (:stem . "correspond") (:form . "corresponds") (:end . 56)\n (:start . 45) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n (:id . 54))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 61) (:start . 60)\n (:id . 55))\n ((:tag . "JJR") (:stem . "<") (:form . "<") (:end . 63) (:start . 62)\n (:id . 56))\n ((:tag . "CD") (:stem . "0.025") (:form . "0.025") (:end . 69) (:start . 64)\n (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n (:id . 58))\n ((:tag . "IN") (:stem . "so") (:form . "so") (:end . 73) (:start . 71)\n (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 78) (:start . 74)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n (:id . 61))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 88) (:start . 83)\n (:id . 62))\n ((:tag . "NN") (:stem . "readthrough") (:form . "readthrough") (:end . 100)\n (:start . 89) (:id . 63))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 109)\n (:start . 101) (:id . 64))\n ((:tag . "VBP") (:stem . "score") (:form . "score") (:end . 115)\n (:start . 110) (:id . 65))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 122)\n (:start . 116) (:id . 66))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 127) (:start . 123)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n (:id . 68))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 141)\n (:start . 132) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s1.302) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100302@unknown@formal@none@1@S@For each of the above clusters, an all-against-all comparison of cluster members was performed.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n (:id . 45))\n ((:tag . "JJ") (:stem . "above") (:form . "above") (:end . 21) (:start . 16)\n (:id . 46))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 30)\n (:start . 22) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 34) (:start . 32)\n (:id . 49))\n ((:tag . "JJ") (:stem . "all-against-all") (:form . "all-against-all")\n (:end . 50) (:start . 35) (:id . 50))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 61)\n (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n (:id . 52))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 72)\n (:start . 65) (:id . 53))\n ((:tag . "NNS") (:stem . "member") (:form . "members") (:end . 80)\n (:start . 73) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 84) (:start . 81)\n (:id . 55))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 94)\n (:start . 85) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.303) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100303@unknown@formal@none@1@S@If any pair exhibits such signals in both the N- and C-terminal parts, the cluster was retained.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "exhibit") (:form . "exhibits") (:end . 20)\n (:start . 12) (:id . 45))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 25) (:start . 21)\n (:id . 46))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 33)\n (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n (:id . 48))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 41) (:start . 37)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n (:id . 50))\n ((:tag . "NNP") (:stem . "N-") (:form . "N-") (:end . 48) (:start . 46)\n (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n (:id . 52))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 63)\n (:start . 53) (:id . 53))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 69) (:start . 64)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n (:id . 56))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 82)\n (:start . 75) (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 86) (:start . 83)\n (:id . 58))\n ((:tag . "VBN") (:stem . "retain") (:form . "retained") (:end . 95)\n (:start . 87) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.304) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100304@unknown@formal@none@1@S@Even if both the upstream and downstream regions of the inframe stop codon code proteins, they may be two adjacent genes instead of a readthrough protein.@(((:tag . "RB") (:stem . "even") (:form . "Even") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 25)\n (:start . 17) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 29) (:start . 26)\n (:id . 47))\n ((:tag . "JJ") (:stem . "downstream") (:form . "downstream") (:end . 40)\n (:start . 30) (:id . 48))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 48)\n (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n (:id . 51))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 63)\n (:start . 56) (:id . 52))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 68) (:start . 64)\n (:id . 53))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 74) (:start . 69)\n (:id . 54))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 79) (:start . 75)\n (:id . 55))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 88)\n (:start . 80) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n (:id . 57))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 94) (:start . 90)\n (:id . 58))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 98) (:start . 95)\n (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 101) (:start . 99)\n (:id . 60))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 105) (:start . 102)\n (:id . 61))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 114)\n (:start . 106) (:id . 62))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 120)\n (:start . 115) (:id . 63))\n ((:tag . "RB") (:stem . "instead") (:form . "instead") (:end . 128)\n (:start . 121) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 133) (:start . 132)\n (:id . 66))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 145)\n (:start . 134) (:id . 67))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 153)\n (:start . 146) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n (:id . 69)))@@@1@28@((:hcues ((:id . :x1.305.2) (:span 95 98)))\n (:ncues ((:id . :x1.305.1) (:span 121 131)))\n (:hscopes ((:id . :x1.305.2) (:span 95 153)))\n (:nscopes ((:id . :x1.305.1) (:span 121 153)))\n (:identifiers (:sid . :s1.305) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100305@unknown@formal@none@1@S@The second and third filtering processes remove such genes based on BLAST alignment patterns.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "filtering") (:form . "filtering") (:end . 30)\n (:start . 21) (:id . 46))\n ((:tag . "NNS") (:stem . "process") (:form . "processes") (:end . 40)\n (:start . 31) (:id . 47))\n ((:tag . "VBP") (:stem . "remove") (:form . "remove") (:end . 47)\n (:start . 41) (:id . 48))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 52) (:start . 48)\n (:id . 49))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 58) (:start . 53)\n (:id . 50))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 64) (:start . 59)\n (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 67) (:start . 65)\n (:id . 52))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 73) (:start . 68)\n (:id . 53))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 83)\n (:start . 74) (:id . 54))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 92)\n (:start . 84) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s1.306) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100306@unknown@formal@none@1@S@Although the boundary analysis applied previously has the same goal (Figure 1b), some gene pairs escaped elimination.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 43))\n ((:tag . "JJ") (:stem . "boundary") (:form . "boundary") (:end . 21)\n (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 30)\n (:start . 22) (:id . 45))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 38)\n (:start . 31) (:id . 46))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 49)\n (:start . 39) (:id . 47))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 53) (:start . 50)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n (:id . 49))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 62) (:start . 58)\n (:id . 50))\n ((:tag . "NN") (:stem . "goal") (:form . "goal") (:end . 67) (:start . 63)\n (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n (:id . 52))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 75)\n (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "1b") (:form . "1b") (:end . 78) (:start . 76)\n (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 79) (:start . 78)\n (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n (:id . 56))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 85) (:start . 81)\n (:id . 57))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 90) (:start . 86)\n (:id . 58))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 96) (:start . 91)\n (:id . 59))\n ((:tag . "VBD") (:stem . "escape") (:form . "escaped") (:end . 104)\n (:start . 97) (:id . 60))\n ((:tag . "NN") (:stem . "elimination") (:form . "elimination") (:end . 116)\n (:start . 105) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s1.307) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100307@unknown@formal@none@1@S@To enhance sensitivity of the filters, the whole length of an iORF was used as a BLAST query instead of the partial sequence, and the size of the BLAST database was increased from the 191 nonredundant genomes to the 328 complete genomes in GenomeNet and 246 draft genome sequences downloaded from GenBank in May 2006.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "enhance") (:form . "enhance") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 22)\n (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n (:id . 46))\n ((:tag . "NNS") (:stem . "filter") (:form . "filters") (:end . 37)\n (:start . 30) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n (:id . 49))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 48) (:start . 43)\n (:id . 50))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 55)\n (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 61) (:start . 59)\n (:id . 53))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 66) (:start . 62)\n (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 70) (:start . 67)\n (:id . 55))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 75) (:start . 71)\n (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 78) (:start . 76)\n (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 80) (:start . 79)\n (:id . 58))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 86) (:start . 81)\n (:id . 59))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 92) (:start . 87)\n (:id . 60))\n ((:tag . "RB") (:stem . "instead") (:form . "instead") (:end . 100)\n (:start . 93) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n (:id . 63))\n ((:tag . "JJ") (:stem . "partial") (:form . "partial") (:end . 115)\n (:start . 108) (:id . 64))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 124)\n (:start . 116) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n (:id . 68))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 138) (:start . 134)\n (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 141) (:start . 139)\n (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n (:id . 71))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 151)\n (:start . 146) (:id . 72))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 160)\n (:start . 152) (:id . 73))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 164) (:start . 161)\n (:id . 74))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 174)\n (:start . 165) (:id . 75))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 179) (:start . 175)\n (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 183) (:start . 180)\n (:id . 77))\n ((:tag . "CD") (:stem . "191") (:form . "191") (:end . 187) (:start . 184)\n (:id . 78))\n ((:tag . "JJ") (:stem . "nonredundant") (:form . "nonredundant") (:end . 200)\n (:start . 188) (:id . 79))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 208)\n (:start . 201) (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 211) (:start . 209)\n (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 215) (:start . 212)\n (:id . 82))\n ((:tag . "CD") (:stem . "328") (:form . "328") (:end . 219) (:start . 216)\n (:id . 83))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 228)\n (:start . 220) (:id . 84))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 236)\n (:start . 229) (:id . 85))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 239) (:start . 237)\n (:id . 86))\n ((:tag . "NNP") (:stem . "GenomeNet") (:form . "GenomeNet") (:end . 249)\n (:start . 240) (:id . 87))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 253) (:start . 250)\n (:id . 88))\n ((:tag . "CD") (:stem . "246") (:form . "246") (:end . 257) (:start . 254)\n (:id . 89))\n ((:tag . "NN") (:stem . "draft") (:form . "draft") (:end . 263)\n (:start . 258) (:id . 90))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 270)\n (:start . 264) (:id . 91))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 280)\n (:start . 271) (:id . 92))\n ((:tag . "VBD") (:stem . "downloade") (:form . "downloaded") (:end . 291)\n (:start . 281) (:id . 93))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 296) (:start . 292)\n (:id . 94))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 304)\n (:start . 297) (:id . 95))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 307) (:start . 305)\n (:id . 96))\n ((:tag . "NNP") (:stem . "May") (:form . "May") (:end . 311) (:start . 308)\n (:id . 97))\n ((:tag . "CD") (:stem . "2006") (:form . "2006") (:end . 316) (:start . 312)\n (:id . 98))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 317) (:start . 316)\n (:id . 99)))@@@1@58@((:ncues ((:id . :x1.308.1) (:span 93 103)))\n (:nscopes ((:id . :x1.308.1) (:span 93 124)))\n (:identifiers (:sid . :s1.308) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100308@unknown@formal@none@1@S@The second filter inspects synteny of iORFs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 17)\n (:start . 11) (:id . 44))\n ((:tag . "VBZ") (:stem . "inspect") (:form . "inspects") (:end . 26)\n (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "synteny") (:form . "synteny") (:end . 34)\n (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n (:id . 47))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 43) (:start . 38)\n (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 44) (:start . 43)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s1.309) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100310@unknown@formal@none@1@S@Translated sequences of iORFs in the pre-filtering clusters were subjected to TBLASTN searches against the genome database.@(((:tag . "VBN") (:stem . "translate") (:form . "Translated") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 20)\n (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 44))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 29) (:start . 24)\n (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n (:id . 47))\n ((:tag . "JJ") (:stem . "pre-filtering") (:form . "pre-filtering")\n (:end . 50) (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 59)\n (:start . 51) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 64) (:start . 60)\n (:id . 50))\n ((:tag . "VBN") (:stem . "subject") (:form . "subjected") (:end . 74)\n (:start . 65) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 77) (:start . 75)\n (:id . 52))\n ((:tag . "NN") (:stem . "tblastn") (:form . "TBLASTN") (:end . 85)\n (:start . 78) (:id . 53))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 94)\n (:start . 86) (:id . 54))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 102)\n (:start . 95) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n (:id . 56))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 113)\n (:start . 107) (:id . 57))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 122)\n (:start . 114) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s1.311) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100311@unknown@formal@none@1@S@If both the best hits of the N- and C-terminal parts are statistically significant (E-value < 10-5), and distance between them is less than 1 kbp, we call these hits 'syntenic hits'.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n (:id . 44))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 16) (:start . 12)\n (:id . 45))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 21) (:start . 17)\n (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n (:id . 48))\n ((:tag . "NNP") (:stem . "N-") (:form . "N-") (:end . 31) (:start . 29)\n (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n (:id . 50))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 46)\n (:start . 36) (:id . 51))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 52) (:start . 47)\n (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 56) (:start . 53)\n (:id . 53))\n ((:tag . "RB") (:stem . "statistically") (:form . "statistically")\n (:end . 70) (:start . 57) (:id . 54))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 82)\n (:start . 71) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n (:id . 56))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-value") (:end . 91)\n (:start . 84) (:id . 57))\n ((:tag . "SYM") (:stem . "<") (:form . "<") (:end . 93) (:start . 92)\n (:id . 58))\n ((:tag . "CD") (:stem . "10-5") (:form . "10-5") (:end . 98) (:start . 94)\n (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 104) (:start . 101)\n (:id . 62))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 113)\n (:start . 105) (:id . 63))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 121)\n (:start . 114) (:id . 64))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 126) (:start . 122)\n (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 129) (:start . 127)\n (:id . 66))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 134) (:start . 130)\n (:id . 67))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 139) (:start . 135)\n (:id . 68))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 141) (:start . 140)\n (:id . 69))\n ((:tag . "NN") (:stem . "kbp") (:form . "kbp") (:end . 145) (:start . 142)\n (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n (:id . 71))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 149) (:start . 147)\n (:id . 72))\n ((:tag . "VBP") (:stem . "call") (:form . "call") (:end . 154) (:start . 150)\n (:id . 73))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 160)\n (:start . 155) (:id . 74))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 165) (:start . 161)\n (:id . 75))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 167) (:start . 166)\n (:id . 76))\n ((:tag . "JJ") (:stem . "syntenic") (:form . "syntenic") (:end . 175)\n (:start . 167) (:id . 77))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 180) (:start . 176)\n (:id . 78))\n ((:tag . "POS") (:stem . "'") (:form . "’") (:end . 181) (:start . 180)\n (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n (:id . 80)))@@@1@39@((:identifiers (:sid . :s1.312) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100312@unknown@formal@none@1@S@If any syntenic hits with non-coinciding reading frames were found, the cluster was removed.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "syntenic") (:form . "syntenic") (:end . 15)\n (:start . 7) (:id . 44))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 25) (:start . 21)\n (:id . 46))\n ((:tag . "JJ") (:stem . "non-coinciding") (:form . "non-coinciding")\n (:end . 40) (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . "reading") (:form . "reading") (:end . 48)\n (:start . 41) (:id . 48))\n ((:tag . "NNS") (:stem . "frame") (:form . "frames") (:end . 55)\n (:start . 49) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 60) (:start . 56)\n (:id . 50))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 66) (:start . 61)\n (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n (:id . 53))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 79)\n (:start . 72) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 83) (:start . 80)\n (:id . 55))\n ((:tag . "VBN") (:stem . "remove") (:form . "removed") (:end . 91)\n (:start . 84) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.313) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100313@unknown@formal@none@1@S@The third filter uses co-occurrence of residues around the inframe stop codon as another source of information for screening stop codon readthrough.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 16)\n (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "use") (:form . "uses") (:end . 21) (:start . 17)\n (:id . 45))\n ((:tag . "NN") (:stem . "co-occurrence") (:form . "co-occurrence")\n (:end . 35) (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n (:id . 47))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 47)\n (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 54)\n (:start . 48) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n (:id . 50))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 66)\n (:start . 59) (:id . 51))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 71) (:start . 67)\n (:id . 52))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 77) (:start . 72)\n (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 80) (:start . 78)\n (:id . 54))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 88)\n (:start . 81) (:id . 55))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 95)\n (:start . 89) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n (:id . 57))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 110)\n (:start . 99) (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 114) (:start . 111)\n (:id . 59))\n ((:tag . "VBG") (:stem . "screen") (:form . "screening") (:end . 124)\n (:start . 115) (:id . 60))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 129) (:start . 125)\n (:id . 61))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 135)\n (:start . 130) (:id . 62))\n ((:tag . "NN") (:stem . "readthrough") (:form . "readthrough") (:end . 147)\n (:start . 136) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s1.314) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100314@unknown@formal@none@1@S@Suppose a window of 21 residues centered at the inframe stop codon.@(((:tag . "VB") (:stem . "suppose") (:form . "Suppose") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 9) (:start . 8)\n (:id . 43))\n ((:tag . "NN") (:stem . "window") (:form . "window") (:end . 16)\n (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 22) (:start . 20)\n (:id . 46))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 31)\n (:start . 23) (:id . 47))\n ((:tag . "VBN") (:stem . "center") (:form . "centered") (:end . 40)\n (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 43) (:start . 41)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n (:id . 50))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 55)\n (:start . 48) (:id . 51))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 60) (:start . 56)\n (:id . 52))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 66) (:start . 61)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s1.315) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100315@unknown@formal@none@1@S@In prokaryotes, most stop-codon-encoded amino acids are located inside a domain, the unit of evolutionary sequence conservation.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "prokaryote") (:form . "prokaryotes") (:end . 14)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n (:id . 44))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "JJ") (:stem . "stop-codon-encoded") (:form . "stop-codon-encoded")\n (:end . 39) (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 45) (:start . 40)\n (:id . 47))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 51) (:start . 46)\n (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 55) (:start . 52)\n (:id . 49))\n ((:tag . "JJ") (:stem . "located") (:form . "located") (:end . 63)\n (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "inside") (:form . "inside") (:end . 70)\n (:start . 64) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 72) (:start . 71)\n (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 79)\n (:start . 73) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n (:id . 55))\n ((:tag . "NN") (:stem . "unit") (:form . "unit") (:end . 89) (:start . 85)\n (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n (:id . 57))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 105)\n (:start . 93) (:id . 58))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 114)\n (:start . 106) (:id . 59))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 127)\n (:start . 115) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.316) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100316@unknown@formal@none@1@S@Therefore, in an ideal situation the presence or absence of the 21 residues in alignments will be synchronized.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "JJ") (:stem . "ideal") (:form . "ideal") (:end . 22) (:start . 17)\n (:id . 46))\n ((:tag . "NN") (:stem . "situation") (:form . "situation") (:end . 32)\n (:start . 23) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n (:id . 48))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 45)\n (:start . 37) (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 48) (:start . 46)\n (:id . 50))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 56)\n (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n (:id . 53))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 66) (:start . 64)\n (:id . 54))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 75)\n (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n (:id . 56))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 89)\n (:start . 79) (:id . 57))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 94) (:start . 90)\n (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 97) (:start . 95)\n (:id . 59))\n ((:tag . "VBN") (:stem . "synchronize") (:form . "synchronized") (:end . 110)\n (:start . 98) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n (:id . 61)))@@@1@20@((:ncues ((:id . :x1.317.1) (:span 49 56)))\n (:nscopes ((:id . :x1.317.1) (:span 49 89)))\n (:identifiers (:sid . :s1.317) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100317@unknown@formal@none@1@S@In contrast, if the iORF is actually two adjacent genes, then upstream and downstream residues of the stop codon will appear separately in many alignments.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 46))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 24) (:start . 20)\n (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n (:id . 48))\n ((:tag . "RB") (:stem . "actually") (:form . "actually") (:end . 36)\n (:start . 28) (:id . 49))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 40) (:start . 37)\n (:id . 50))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 49)\n (:start . 41) (:id . 51))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 55) (:start . 50)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n (:id . 53))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 61) (:start . 57)\n (:id . 54))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 70)\n (:start . 62) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n (:id . 56))\n ((:tag . "JJ") (:stem . "downstream") (:form . "downstream") (:end . 85)\n (:start . 75) (:id . 57))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 94)\n (:start . 86) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n (:id . 60))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 106) (:start . 102)\n (:id . 61))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 112)\n (:start . 107) (:id . 62))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 117) (:start . 113)\n (:id . 63))\n ((:tag . "VB") (:stem . "appear") (:form . "appear") (:end . 124)\n (:start . 118) (:id . 64))\n ((:tag . "RB") (:stem . "separately") (:form . "separately") (:end . 135)\n (:start . 125) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 138) (:start . 136)\n (:id . 66))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 143) (:start . 139)\n (:id . 67))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 154)\n (:start . 144) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.318) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100318@unknown@formal@none@1@S@We defined a co-occurrence matrix as a 21 × 21 matrix whose (i,j)-th element represents how often residue i and j appeared simultaneously in N alignments.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "define") (:form . "defined") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "co-occurrence") (:form . "co-occurrence")\n (:end . 26) (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 33)\n (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 36) (:start . 34)\n (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n (:id . 48))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 41) (:start . 39)\n (:id . 49))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 43) (:start . 42)\n (:id . 50))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 46) (:start . 44)\n (:id . 51))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 53)\n (:start . 47) (:id . 52))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 59) (:start . 54)\n (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 61) (:start . 60)\n (:id . 54))\n ((:tag . "JJ") (:stem . "i,j)-th") (:form . "i,j)-th") (:end . 68)\n (:start . 61) (:id . 55))\n ((:tag . "NN") (:stem . "element") (:form . "element") (:end . 76)\n (:start . 69) (:id . 56))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 87)\n (:start . 77) (:id . 57))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 91) (:start . 88)\n (:id . 58))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 97) (:start . 92)\n (:id . 59))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 105)\n (:start . 98) (:id . 60))\n ((:tag . "NN") (:stem . "i") (:form . "i") (:end . 107) (:start . 106)\n (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n (:id . 62))\n ((:tag . "NN") (:stem . "j") (:form . "j") (:end . 113) (:start . 112)\n (:id . 63))\n ((:tag . "VBD") (:stem . "appear") (:form . "appeared") (:end . 122)\n (:start . 114) (:id . 64))\n ((:tag . "RB") (:stem . "simultaneously") (:form . "simultaneously")\n (:end . 137) (:start . 123) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 140) (:start . 138)\n (:id . 66))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 142) (:start . 141)\n (:id . 67))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 153)\n (:start . 143) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.319) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100320@unknown@formal@none@1@S@By definition, the more often the upstream and downstream residues of the inframe stop codon co-occur in the alignments, the higher the density in the upper right quarter of the matrix.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "definition") (:form . "definition") (:end . 13)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 29) (:start . 24)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 48))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 42)\n (:start . 34) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n (:id . 50))\n ((:tag . "JJ") (:stem . "downstream") (:form . "downstream") (:end . 57)\n (:start . 47) (:id . 51))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 66)\n (:start . 58) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n (:id . 54))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 81)\n (:start . 74) (:id . 55))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 86) (:start . 82)\n (:id . 56))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 92) (:start . 87)\n (:id . 57))\n ((:tag . "VBP") (:stem . "co-occur") (:form . "co-occur") (:end . 101)\n (:start . 93) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 104) (:start . 102)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n (:id . 60))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 119)\n (:start . 109) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n (:id . 63))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 131)\n (:start . 125) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 135) (:start . 132)\n (:id . 65))\n ((:tag . "NN") (:stem . "density") (:form . "density") (:end . 143)\n (:start . 136) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 146) (:start . 144)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 150) (:start . 147)\n (:id . 68))\n ((:tag . "JJ") (:stem . "upper") (:form . "upper") (:end . 156)\n (:start . 151) (:id . 69))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 162)\n (:start . 157) (:id . 70))\n ((:tag . "NN") (:stem . "quarter") (:form . "quarter") (:end . 170)\n (:start . 163) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 173) (:start . 171)\n (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 177) (:start . 174)\n (:id . 73))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 184)\n (:start . 178) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s1.321) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100321@unknown@formal@none@1@S@If average density in the quarter was lower than 0.85, the cluster was filtered out.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "density") (:form . "density") (:end . 18)\n (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 46))\n ((:tag . "NN") (:stem . "quarter") (:form . "quarter") (:end . 33)\n (:start . 26) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 37) (:start . 34)\n (:id . 48))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 43) (:start . 38)\n (:id . 49))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 48) (:start . 44)\n (:id . 50))\n ((:tag . "CD") (:stem . "0.85") (:form . "0.85") (:end . 53) (:start . 49)\n (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n (:id . 53))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 66)\n (:start . 59) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 70) (:start . 67)\n (:id . 55))\n ((:tag . "VBN") (:stem . "filter") (:form . "filtered") (:end . 79)\n (:start . 71) (:id . 56))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 83) (:start . 80)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.322) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100322@unknown@formal@none@1@S@Stop codon usage@(((:tag . "NNP") (:stem . "Stop") (:form . "Stop") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "usage") (:form . "usage") (:end . 16) (:start . 11)\n (:id . 44)))@@@1@3@((:identifiers (:sid . :s1.323) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100323@unknown@formal@none@1@S@For each organism, its iORFs were extracted from the pre-filtering clusters, and codon usage at the inframe stop positions was counted.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 17)\n (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n (:id . 45))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 22) (:start . 19)\n (:id . 46))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 28) (:start . 23)\n (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 33) (:start . 29)\n (:id . 48))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 43)\n (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 48) (:start . 44)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n (:id . 51))\n ((:tag . "JJ") (:stem . "pre-filtering") (:form . "pre-filtering")\n (:end . 66) (:start . 53) (:id . 52))\n ((:tag . "NNS") (:stem . "cluster") (:form . 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(:end . 82) (:start . 81)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.326) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100326@unknown@formal@none@1@S@The p-value was corrected for multiple testing using the Bonferroni correction because there were 127 organisms in the pre-filtering clusters.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "p-value") (:form . "p-value") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "VBN") (:stem . "correct") (:form . "corrected") (:end . 25)\n (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 29) (:start . 26)\n (:id . 46))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 38)\n (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "testing") (:form . 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"JJ") (:stem . "transitive") (:form . "Transitive") (:end . 161)\n (:start . 151) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 163) (:start . 162)\n (:id . 79))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 164) (:start . 163)\n (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 165) (:start . 164)\n (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n (:id . 82)))@@@1@41@((:identifiers (:sid . :s2.67) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100394@unknown@formal@none@1@S@Figure 1 illustrates the training scheme and architecture of the method.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 8) (:start . 7)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "illustrate") (:form . "illustrates") (:end . 20)\n (:start . 9) (:id . 44))\n ((:tag . 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(:end . 72) (:start . 71)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.68) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100395@unknown@formal@none@1@S@The Expression, Orthology, Combined and Disorder modules can calculate likelihood ratios (LR) of interaction independently and are referred to as the Group A modules (Figure 1A).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Expression") (:form . "Expression") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Orthology") (:form . "Orthology") (:end . 25)\n (:start . 16) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Combined") (:form . "Combined") (:end . 35)\n (:start . 27) (:id . 47))\n ((:tag . "CC") (:stem . 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"predictor") (:end . 29)\n (:start . 20) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n (:id . 46))\n ((:tag . "NNS") (:stem . "likelihood") (:form . "likelihoods") (:end . 45)\n (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n (:id . 49))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 60)\n (:start . 53) (:id . 50)))@@@1@9@((:identifiers (:sid . :s2.75) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5100402@unknown@formal@none@1@S@Architecture of the predictor and likelihoods of the modules.@(((:tag . "NNP") (:stem . "Architecture") (:form . "Architecture") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 43))\n ((:tag . "DT") (:stem . 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(:end . 61) (:start . 60)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s2.76) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100403@unknown@formal@none@1@S@The predictor consists of two different parts (A and B) which are trained consecutively.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 22)\n (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n (:id . 45))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 29) (:start . 26)\n (:id . 46))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 39)\n (:start . 30) (:id . 47))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 45) (:start . 40)\n (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 47) (:start . 46)\n (:id . 49))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 48) (:start . 47)\n (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n (:id . 51))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 54) (:start . 53)\n (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 61) (:start . 56)\n (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 65) (:start . 62)\n (:id . 55))\n ((:tag . "VBN") (:stem . "train") (:form . "trained") (:end . 73)\n (:start . 66) (:id . 56))\n ((:tag . "RB") (:stem . "consecutively") (:form . "consecutively")\n (:end . 87) (:start . 74) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.77) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100404@unknown@formal@none@1@S@The Group A modules (shown in panel A) are trained in parallel.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Group") (:form . "Group") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 11) (:start . 10)\n (:id . 44))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 19)\n (:start . 12) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 21) (:start . 20)\n (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 26) (:start . 21)\n (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n (:id . 48))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 35) (:start . 30)\n (:id . 49))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 37) (:start . 36)\n (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 38) (:start . 37)\n (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 42) (:start . 39)\n (:id . 52))\n ((:tag . "VBN") (:stem . "train") (:form . "trained") (:end . 50)\n (:start . 43) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n (:id . 54))\n ((:tag . "NN") (:stem . "parallel") (:form . "parallel") (:end . 62)\n (:start . 54) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.78) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100405@unknown@formal@none@1@S@The likelihood ratios (LR) for most of their states are shown in panel A (their complete likelihood ratios are available in Additional File 4).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 21)\n (:start . 15) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 23) (:start . 22)\n (:id . 45))\n ((:tag . "NNP") (:stem . "LR") (:form . "LR") (:end . 25) (:start . 23)\n (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 26) (:start . 25)\n (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 30) (:start . 27)\n (:id . 48))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 35) (:start . 31)\n (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n (:id . 50))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 44)\n (:start . 39) (:id . 51))\n ((:tag . "NNS") (:stem . "state") (:form . "states") (:end . 51)\n (:start . 45) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 55) (:start . 52)\n (:id . 53))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 61) (:start . 56)\n (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n (:id . 55))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 70) (:start . 65)\n (:id . 56))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 72) (:start . 71)\n (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 74) (:start . 73)\n (:id . 58))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 79)\n (:start . 74) (:id . 59))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 88)\n (:start . 80) (:id . 60))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 99)\n (:start . 89) (:id . 61))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 106)\n (:start . 100) (:id . 62))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 110) (:start . 107)\n (:id . 63))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 120)\n (:start . 111) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 123) (:start . 121)\n (:id . 65))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 134)\n (:start . 124) (:id . 66))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 139) (:start . 135)\n (:id . 67))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 141) (:start . 140)\n (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s2.79) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100406@unknown@formal@none@1@S@The product of the likelihood ratios of all Group A modules considered in a given prediction is referred to as the preliminary score (PS) and can be calculated for all human protein pairs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "product") (:form . "product") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 29)\n (:start . 19) (:id . 46))\n ((:tag . 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"and") (:form . "and") (:end . 141) (:start . 138)\n (:id . 68))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 145) (:start . 142)\n (:id . 69))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 148) (:start . 146)\n (:id . 70))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 159)\n (:start . 149) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 163) (:start . 160)\n (:id . 72))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 167) (:start . 164)\n (:id . 73))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 173)\n (:start . 168) (:id . 74))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 181)\n (:start . 174) (:id . 75))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 187)\n (:start . 182) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s2.80) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100407@unknown@formal@none@1@S@If the Transitive module is not considered, the final likelihood ratios assigned to all protein pairs is the preliminary score (PS).@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 17)\n (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 24)\n (:start . 18) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 31) (:start . 28)\n (:id . 47))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 42)\n (:start . 32) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n (:id . 50))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 53) (:start . 48)\n (:id . 51))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 64)\n (:start . 54) (:id . 52))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 71)\n (:start . 65) (:id . 53))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 80)\n (:start . 72) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 83) (:start . 81)\n (:id . 55))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 87) (:start . 84)\n (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 95)\n (:start . 88) (:id . 57))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 101) (:start . 96)\n (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 104) (:start . 102)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n (:id . 60))\n ((:tag . "JJ") (:stem . "preliminary") (:form . "preliminary") (:end . 120)\n (:start . 109) (:id . 61))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 126)\n (:start . 121) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 128) (:start . 127)\n (:id . 63))\n ((:tag . "NNP") (:stem . "PS") (:form . "PS") (:end . 130) (:start . 128)\n (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 131) (:start . 130)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n (:id . 66)))@@@1@25@((:ncues ((:id . :x2.81.1) (:span 28 31)))\n (:nscopes ((:id . :x2.81.1) (:span 3 42)))\n (:identifiers (:sid . :s2.81) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100408@unknown@formal@none@1@S@If the Transitive module is considered, the local topology of the network determined by the assignment of preliminary scores to all protein pairs considered in the training set is used to calculate the likelihood ratios for the transitive module (shown in panel B) for every protein pair in the training set.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 17)\n (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "module") (:form . 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"interologs") (:end . 333)\n (:start . 323) (:id . 121))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 336) (:start . 334)\n (:id . 122))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 341) (:start . 337)\n (:id . 123))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 346) (:start . 342)\n (:id . 124))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 350) (:start . 347)\n (:id . 125))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 359)\n (:start . 351) (:id . 126))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 360) (:start . 359)\n (:id . 127)))@@@1@86@((:identifiers (:sid . :s2.84) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100411@unknown@formal@none@1@S@For the Combined module, –— refers to the lowest scoring bin (for the domain (Dom), post-translational modification (PTM) and subcellular localization (Loc) features), – refers to the second lowest scoring bin and +, ++, +++ refer respectively to the third highest, second highest and highest scoring bins.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "VBN") (:stem . "combine") (:form . "Combined") (:end . 16)\n (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 23)\n (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . 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",") (:form . ",") (:end . 220) (:start . 219)\n (:id . 89))\n ((:tag . "SYM") (:stem . "+++") (:form . "+++") (:end . 224) (:start . 221)\n (:id . 90))\n ((:tag . "VBP") (:stem . "refer") (:form . "refer") (:end . 230)\n (:start . 225) (:id . 91))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 243)\n (:start . 231) (:id . 92))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 246) (:start . 244)\n (:id . 93))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 250) (:start . 247)\n (:id . 94))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 256)\n (:start . 251) (:id . 95))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 264)\n (:start . 257) (:id . 96))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 265) (:start . 264)\n (:id . 97))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 272)\n (:start . 266) (:id . 98))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 280)\n (:start . 273) (:id . 99))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 284) (:start . 281)\n (:id . 100))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 292)\n (:start . 285) (:id . 101))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 300)\n (:start . 293) (:id . 102))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 305) (:start . 301)\n (:id . 103))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 306) (:start . 305)\n (:id . 104)))@@@1@63@((:identifiers (:sid . :s2.85) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100412@unknown@formal@none@1@S@The likelihood ratios of interaction are evaluated for each module by considering the relative proportions of positive and negative training examples that have a specific state (i.e. that fall in a particular bin of a module).@(((:tag . "DT") (:stem . "the") (:form . 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(:end . 68) (:start . 67)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.97) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100424@unknown@formal@none@1@S@Likelihood ratios of the modules@(((:tag . "NN") (:stem . "likelihood") (:form . "Likelihood") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 17)\n (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n (:id . 45))\n ((:tag . "NNS") (:stem . "module") (:form . 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"IN") (:stem . "for") (:form . "for") (:end . 54) (:start . 51)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n (:id . 50))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 63) (:start . 59)\n (:id . 51))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 71)\n (:start . 64) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.99) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100426@unknown@formal@none@1@S@The different modules differ in the range of likelihood ratio values achieved by their different states.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "module") (:form . 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(:end . 162) (:start . 161)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x2.108.1) (:span 48 62)))\n (:ncues ((:id . :x2.108.2) (:span 8 11)))\n (:hscopes ((:id . :x2.108.1) (:span 48 156)))\n (:nscopes ((:id . :x2.108.2) (:span 8 22)))\n (:identifiers (:sid . :s2.108) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100435@unknown@formal@none@1@S@In contrast, the consideration of human interactions paralogous to the human protein pairs under investigation results in likelihood ratios of 431 and 1034 (depending on how close the paralogs are as described in Methods) which is much higher than those obtained for any single model organism.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . 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(:end . 134) (:start . 133)\n (:id . 61)))@@@1@20@((:hcues ((:id . :x2.110.1) (:span 38 47)))\n (:hscopes ((:id . :x2.110.1) (:span 38 130)))\n (:identifiers (:sid . :s2.110) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100437@unknown@formal@none@1@S@The Combined module uses domain co-occurrence, post-translational modification (PTM) co-occurrence and subcellular localization information to predict interaction.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "combine") (:form . "Combined") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 19)\n (:start . 13) (:id . 44))\n ((:tag . "VBZ") (:stem . "use") (:form . "uses") (:end . 24) (:start . 20)\n (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 31)\n (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . 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(:end . 163) (:start . 162)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.111) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100438@unknown@formal@none@1@S@These features were originally investigated separately, as shown in Figure 3, but their combination into one module that considers all dependencies between them achieves higher accuracy (data not shown) and higher likelihood ratios (as can be seen by comparing to Figure 1) while still being computationally feasible.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 14)\n (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "RB") (:stem . "originally") (:form . "originally") (:end . 30)\n (:start . 20) (:id . 45))\n ((:tag . "VBN") (:stem . "investigate") (:form . 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"CD") (:stem . "1") (:form . "1") (:end . 272) (:start . 271)\n (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 273) (:start . 272)\n (:id . 89))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 279)\n (:start . 274) (:id . 90))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 285)\n (:start . 280) (:id . 91))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 291) (:start . 286)\n (:id . 92))\n ((:tag . "RB") (:stem . "computationally") (:form . "computationally")\n (:end . 307) (:start . 292) (:id . 93))\n ((:tag . "JJ") (:stem . "feasible") (:form . "feasible") (:end . 316)\n (:start . 308) (:id . 94))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 317) (:start . 316)\n (:id . 95)))@@@1@54@((:ncues ((:id . :x2.112.1) (:span 192 195)))\n (:nscopes ((:id . :x2.112.1) (:span 186 202)))\n (:identifiers (:sid . :s2.112) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100440@unknown@formal@none@1@S@Likelihood ratios of the features that form the Combined module, considered separately@(((:tag . "NN") (:stem . "likelihood") (:form . "Likelihood") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 17)\n (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n (:id . 45))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 33)\n (:start . 25) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 38) (:start . 34)\n (:id . 47))\n ((:tag . "VBP") (:stem . "form") (:form . "form") (:end . 43) (:start . 39)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n (:id . 49))\n ((:tag . "VBN") (:stem . "combine") (:form . "Combined") (:end . 56)\n (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 63)\n (:start . 57) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n (:id . 52))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 75)\n (:start . 65) (:id . 53))\n ((:tag . "RB") (:stem . "separately") (:form . "separately") (:end . 86)\n (:start . 76) (:id . 54)))@@@1@13@((:identifiers (:sid . :s2.114) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|FigureLegend|)))@oe@9-2-2011 5100441@unknown@formal@none@1@S@Likelihood ratios of the features that form the Combined module, considered separately.@(((:tag . "NN") (:stem . "likelihood") (:form . "Likelihood") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 17)\n (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n (:id . 45))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 33)\n (:start . 25) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 38) (:start . 34)\n (:id . 47))\n ((:tag . "VBP") (:stem . "form") (:form . "form") (:end . 43) (:start . 39)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n (:id . 49))\n ((:tag . "VBN") (:stem . "combine") (:form . "Combined") (:end . 56)\n (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 63)\n (:start . 57) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n (:id . 52))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 75)\n (:start . 65) (:id . 53))\n ((:tag . "RB") (:stem . "separately") (:form . "separately") (:end . 86)\n (:start . 76) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.115) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100442@unknown@formal@none@1@S@The Combined module considers simultaneously three distinct features: the co-occurrence of both domains and PTMs as well as the subcellular co-localization of proteins.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "combine") (:form . "Combined") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 19)\n (:start . 13) (:id . 44))\n ((:tag . "VBZ") (:stem . "consider") (:form . "considers") (:end . 29)\n (:start . 20) (:id . 45))\n ((:tag . "RB") (:stem . "simultaneously") (:form . "simultaneously")\n (:end . 44) (:start . 30) (:id . 46))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 50) (:start . 45)\n (:id . 47))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 59)\n (:start . 51) (:id . 48))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 68)\n (:start . 60) (:id . 49))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 69) (:start . 68)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n (:id . 51))\n ((:tag . "NN") (:stem . "co-occurrence") (:form . "co-occurrence")\n (:end . 87) (:start . 74) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n (:id . 53))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 95) (:start . 91)\n (:id . 54))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 103)\n (:start . 96) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n (:id . 56))\n ((:tag . "NNS") (:stem . "ptm") (:form . "PTMs") (:end . 112) (:start . 108)\n (:id . 57))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 115) (:start . 113)\n (:id . 58))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 120) (:start . 116)\n (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 123) (:start . 121)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n (:id . 61))\n ((:tag . "JJ") (:stem . "subcellular") (:form . "subcellular") (:end . 139)\n (:start . 128) (:id . 62))\n ((:tag . "NN") (:stem . "co-localization") (:form . "co-localization")\n (:end . 155) (:start . 140) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 158) (:start . 156)\n (:id . 64))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 167)\n (:start . 159) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s2.116) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100443@unknown@formal@none@1@S@Here the likelihood ratios of these features considered separately are shown.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 19)\n (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 26)\n (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 35) (:start . 30)\n (:id . 47))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 44)\n (:start . 36) (:id . 48))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 55)\n (:start . 45) (:id . 49))\n ((:tag . "RB") (:stem . "separately") (:form . "separately") (:end . 66)\n (:start . 56) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 70) (:start . 67)\n (:id . 51))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 76) (:start . 71)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.117) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100444@unknown@formal@none@1@S@In panel A, all domain pairs considered were given scores and likelihood ratios were estimated for different values of these scores.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 10) (:start . 9)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 45))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 15) (:start . 12)\n (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 22)\n (:start . 16) (:id . 47))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 28) (:start . 23)\n (:id . 48))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 39)\n (:start . 29) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 44) (:start . 40)\n (:id . 50))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 50) (:start . 45)\n (:id . 51))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 57)\n (:start . 51) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n (:id . 53))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 72)\n (:start . 62) (:id . 54))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 79)\n (:start . 73) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 84) (:start . 80)\n (:id . 56))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 94)\n (:start . 85) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 98) (:start . 95)\n (:id . 58))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 108)\n (:start . 99) (:id . 59))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 115)\n (:start . 109) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 118) (:start . 116)\n (:id . 61))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 124)\n (:start . 119) (:id . 62))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 131)\n (:start . 125) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.118) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100445@unknown@formal@none@1@S@Similarly, shown in panel B are the likelihood ratios for different values of PTM co-occurrence scores.@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 16) (:start . 11)\n (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 25) (:start . 20)\n (:id . 46))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 27) (:start . 26)\n (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 31) (:start . 28)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n (:id . 49))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 46)\n (:start . 36) (:id . 50))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 53)\n (:start . 47) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 57) (:start . 54)\n (:id . 52))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 67)\n (:start . 58) (:id . 53))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 74)\n (:start . 68) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n (:id . 55))\n ((:tag . "NNP") (:stem . "PTM") (:form . "PTM") (:end . 81) (:start . 78)\n (:id . 56))\n ((:tag . "NN") (:stem . "co-occurrence") (:form . "co-occurrence")\n (:end . 95) (:start . 82) (:id . 57))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 102)\n (:start . 96) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s2.119) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100446@unknown@formal@none@1@S@Panel C shows the likelihood ratios for protein pairs localized to different sets of cellular compartments.@(((:tag . "NN") (:stem . "panel") (:form . "Panel") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 7) (:start . 6)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 45))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 28)\n (:start . 18) (:id . 46))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 35)\n (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 47)\n (:start . 40) (:id . 49))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 53) (:start . 48)\n (:id . 50))\n ((:tag . "VBD") (:stem . "localize") (:form . "localized") (:end . 63)\n (:start . 54) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n (:id . 52))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 76)\n (:start . 67) (:id . 53))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 81) (:start . 77)\n (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n (:id . 55))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 93)\n (:start . 85) (:id . 56))\n ((:tag . "NNS") (:stem . "compartment") (:form . "compartments") (:end . 106)\n (:start . 94) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.120) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100447@unknown@formal@none@1@S@Previous methods have investigated the use of co-occurring domains to predict interaction (see for example 2346).@(((:tag . "JJ") (:stem . "previous") (:form . "Previous") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 16)\n (:start . 9) (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 21) (:start . 17)\n (:id . 44))\n ((:tag . "VBN") (:stem . "investigate") (:form . "investigated") (:end . 34)\n (:start . 22) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n (:id . 46))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 42) (:start . 39)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n (:id . 48))\n ((:tag . "VBG") (:stem . "co-occurre") (:form . "co-occurring") (:end . 58)\n (:start . 46) (:id . 49))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 66)\n (:start . 59) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 69) (:start . 67)\n (:id . 51))\n ((:tag . "VB") (:stem . "predict") (:form . "predict") (:end . 77)\n (:start . 70) (:id . 52))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 89)\n (:start . 78) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n (:id . 54))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 94) (:start . 91)\n (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 98) (:start . 95)\n (:id . 56))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 106)\n (:start . 99) (:id . 57))\n ((:tag . "CD") (:stem . "2346") (:form . "2346") (:end . 111) (:start . 107)\n (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s2.121) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100448@unknown@formal@none@1@S@Many pairs of domains co-occur in proteins known to interact.@(((:tag . "JJ") (:stem . "many") (:form . "Many") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 21)\n (:start . 14) (:id . 45))\n ((:tag . "VBP") (:stem . "co-occur") (:form . "co-occur") (:end . 30)\n (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 42)\n (:start . 34) (:id . 48))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 48) (:start . 43)\n (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n (:id . 50))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 60)\n (:start . 52) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 61) (:start . 60)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s2.122) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100450@unknown@formal@none@1@S@Similarly, the co-occurrence of PTMs is also predictive of interaction, with its highest scoring bin obtaining a likelihood ratio of 6 as shown in Figure 3B.@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . 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"than") (:end . 268) (:start . 264)\n (:id . 86))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 275)\n (:start . 269) (:id . 87))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 283)\n (:start . 276) (:id . 88))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 289)\n (:start . 284) (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 290) (:start . 289)\n (:id . 90)))@@@1@49@((:identifiers (:sid . :s2.129) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100456@unknown@formal@none@1@S@Individual localization features achieve low interaction likelihood ratios.@(((:tag . "JJ") (:stem . "individual") (:form . "Individual") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "localization") (:form . "localization") (:end . 23)\n (:start . 11) (:id . 43))\n ((:tag . "NNS") (:stem . "feature") (:form . 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(:end . 75) (:start . 74)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s2.130) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100457@unknown@formal@none@1@S@However, when integrated into the Combined module, domain, PTM and localization information together achieve likelihood ratios that are high enough to predict interaction on their own (i.e. above 400).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "VBN") (:stem . "integrate") (:form . "integrated") (:end . 24)\n (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 29) (:start . 25)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 47))\n ((:tag . "VBN") (:stem . "combine") (:form . "Combined") (:end . 42)\n (:start . 34) (:id . 48))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 49)\n (:start . 43) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 57)\n (:start . 51) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n (:id . 52))\n ((:tag . "NNP") (:stem . "PTM") (:form . "PTM") (:end . 62) (:start . 59)\n (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n (:id . 54))\n ((:tag . "NN") (:stem . "localization") (:form . "localization") (:end . 79)\n (:start . 67) (:id . 55))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 91)\n (:start . 80) (:id . 56))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 100)\n (:start . 92) (:id . 57))\n ((:tag . "VBP") (:stem . "achieve") (:form . "achieve") (:end . 108)\n (:start . 101) (:id . 58))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 119)\n (:start . 109) (:id . 59))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 126)\n (:start . 120) (:id . 60))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 131) (:start . 127)\n (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 135) (:start . 132)\n (:id . 62))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 140) (:start . 136)\n (:id . 63))\n ((:tag . "RB") (:stem . "enough") (:form . "enough") (:end . 147)\n (:start . 141) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 150) (:start . 148)\n (:id . 65))\n ((:tag . "VB") (:stem . "predict") (:form . "predict") (:end . 158)\n (:start . 151) (:id . 66))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 170)\n (:start . 159) (:id . 67))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 173) (:start . 171)\n (:id . 68))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 179)\n (:start . 174) (:id . 69))\n ((:tag . "JJ") (:stem . "own") (:form . "own") (:end . 183) (:start . 180)\n (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 185) (:start . 184)\n (:id . 71))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 189) (:start . 185)\n (:id . 72))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 195)\n (:start . 190) (:id . 73))\n ((:tag . "CD") (:stem . "400") (:form . "400") (:end . 199) (:start . 196)\n (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 200) (:start . 199)\n (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s2.131) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100458@unknown@formal@none@1@S@As expected, the highest likelihood ratio bins for the Combined module are those representing the highest combinations of the three features separately.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 24)\n (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 35)\n (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 41) (:start . 36)\n (:id . 48))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 46) (:start . 42)\n (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 50) (:start . 47)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n (:id . 51))\n ((:tag . "VBN") (:stem . "combine") (:form . "Combined") (:end . 63)\n (:start . 55) (:id . 52))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 70)\n (:start . 64) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 74) (:start . 71)\n (:id . 54))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 80) (:start . 75)\n (:id . 55))\n ((:tag . "VBG") (:stem . "represent") (:form . "representing") (:end . 93)\n (:start . 81) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n (:id . 57))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 105)\n (:start . 98) (:id . 58))\n ((:tag . "NNS") (:stem . "combination") (:form . "combinations") (:end . 118)\n (:start . 106) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n (:id . 61))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 131)\n (:start . 126) (:id . 62))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 140)\n (:start . 132) (:id . 63))\n ((:tag . "RB") (:stem . "separately") (:form . "separately") (:end . 151)\n (:start . 141) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.132) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100460@unknown@formal@none@1@S@The likelihood ratios for different values of the neighborhood topology score are shown in Figure 1B.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 21)\n (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 35)\n (:start . 26) (:id . 46))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 42)\n (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "NN") (:stem . "neighborhood") (:form . "neighborhood") (:end . 62)\n (:start . 50) (:id . 50))\n ((:tag . "NN") (:stem . "topology") (:form . "topology") (:end . 71)\n (:start . 63) (:id . 51))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 77) (:start . 72)\n (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 81) (:start . 78)\n (:id . 53))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 87) (:start . 82)\n (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 97)\n (:start . 91) (:id . 56))\n ((:tag . "NN") (:stem . "1b") (:form . "1B") (:end . 100) (:start . 98)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.134) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100461@unknown@formal@none@1@S@The Transitive module is highly predictive of interaction and achieves likelihood ratios as high as 229.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 21)\n (:start . 15) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 24) (:start . 22)\n (:id . 45))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 31)\n (:start . 25) (:id . 46))\n ((:tag . "JJ") (:stem . "predictive") (:form . "predictive") (:end . 42)\n (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n (:id . 48))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 57)\n (:start . 46) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "achieve") (:form . "achieves") (:end . 70)\n (:start . 62) (:id . 51))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 81)\n (:start . 71) (:id . 52))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 88)\n (:start . 82) (:id . 53))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 91) (:start . 89)\n (:id . 54))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 96) (:start . 92)\n (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 99) (:start . 97)\n (:id . 56))\n ((:tag . "CD") (:stem . "229") (:form . "229") (:end . 103) (:start . 100)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.135) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100462@unknown@formal@none@1@S@This module cannot be used alone as it requires as input the output of at least one group A module.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "cannot") (:form . "cannot") (:end . 18)\n (:start . 12) (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 26) (:start . 22)\n (:id . 46))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 32) (:start . 27)\n (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 35) (:start . 33)\n (:id . 48))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 38) (:start . 36)\n (:id . 49))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 47)\n (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 50) (:start . 48)\n (:id . 51))\n ((:tag . "NN") (:stem . "input") (:form . "input") (:end . 56) (:start . 51)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n (:id . 53))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 67)\n (:start . 61) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 73) (:start . 71)\n (:id . 56))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 79) (:start . 74)\n (:id . 57))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 83) (:start . 80)\n (:id . 58))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 89) (:start . 84)\n (:id . 59))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 91) (:start . 90)\n (:id . 60))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 98)\n (:start . 92) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 62)))@@@1@21@((:ncues ((:id . :x2.136.1) (:span 12 18)))\n (:nscopes ((:id . :x2.136.1) (:span 0 32)))\n (:identifiers (:sid . :s2.136) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100463@unknown@formal@none@1@S@However, it can predict interacting protein pairs with a posterior odds ratio above 1.0 when used in combination with any single module in group A (as the product of the highest likelihood ratios of the transitive module and any group A module is greater than 400 as can be seen from Figure 1).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 15) (:start . 12)\n (:id . 45))\n ((:tag . "VB") (:stem . "predict") (:form . "predict") (:end . 23)\n (:start . 16) (:id . 46))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 35)\n (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 43)\n (:start . 36) (:id . 48))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 49) (:start . 44)\n (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 54) (:start . 50)\n (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 56) (:start . 55)\n (:id . 51))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 66)\n (:start . 57) (:id . 52))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 71) (:start . 67)\n (:id . 53))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 77) (:start . 72)\n (:id . 54))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 83) (:start . 78)\n (:id . 55))\n ((:tag . "CD") (:stem . "1.0") (:form . "1.0") (:end . 87) (:start . 84)\n (:id . 56))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 92) (:start . 88)\n (:id . 57))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 97) (:start . 93)\n (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 100) (:start . 98)\n (:id . 59))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 112)\n (:start . 101) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 117) (:start . 113)\n (:id . 61))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 121) (:start . 118)\n (:id . 62))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 128)\n (:start . 122) (:id . 63))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 135)\n (:start . 129) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 138) (:start . 136)\n (:id . 65))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 144)\n (:start . 139) (:id . 66))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 146) (:start . 145)\n (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n (:id . 68))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 150) (:start . 148)\n (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n (:id . 70))\n ((:tag . "NN") (:stem . "product") (:form . "product") (:end . 162)\n (:start . 155) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 165) (:start . 163)\n (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 169) (:start . 166)\n (:id . 73))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 177)\n (:start . 170) (:id . 74))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 188)\n (:start . 178) (:id . 75))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 195)\n (:start . 189) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 198) (:start . 196)\n (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 202) (:start . 199)\n (:id . 78))\n ((:tag . "JJ") (:stem . "transitive") (:form . "transitive") (:end . 213)\n (:start . 203) (:id . 79))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 220)\n (:start . 214) (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 224) (:start . 221)\n (:id . 81))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 228) (:start . 225)\n (:id . 82))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 234)\n (:start . 229) (:id . 83))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 236) (:start . 235)\n (:id . 84))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 243)\n (:start . 237) (:id . 85))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 246) (:start . 244)\n (:id . 86))\n ((:tag . "JJR") (:stem . "great") (:form . 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(:form . ".") (:end . 294) (:start . 293)\n (:id . 98)))@@@1@57@((:hcues ((:id . :x2.137.1) (:span 16 23)))\n (:hscopes ((:id . :x2.137.1) (:span 16 146)))\n (:identifiers (:sid . :s2.137) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100464@unknown@formal@none@1@S@Independence of the modules@(((:tag . "NN") (:stem . "independence") (:form . "Independence") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 44))\n ((:tag . "NNS") (:stem . "module") (:form . 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"modules") (:end . 44)\n (:start . 37) (:id . 47)))@@@1@6@((:identifiers (:sid . :s2.145) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|TableLegend|)))@oe@9-2-2011 5100472@unknown@formal@none@1@S@Accuracy of the predictors@(((:tag . "NN") (:stem . "accuracy") (:form . "Accuracy") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "NNS") (:stem . "predictor") (:form . "predictors") (:end . 26)\n (:start . 16) (:id . 45)))@@@1@4@((:identifiers (:sid . :s2.146) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100473@unknown@formal@none@1@S@All combinations of modules were examined to determine which of the resulting predictors achieved the highest prediction accuracy.@(((:tag . 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(:end . 130) (:start . 129)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s2.147) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100474@unknown@formal@none@1@S@In order to analyze the predictions, five-fold cross validation experiments were performed and the area under partial ROC (receiver operator characteristic) curves (partial AUCs) measured.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "VB") (:stem . "analyze") (:form . "analyze") (:end . 19)\n (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n (:id . 46))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 35)\n (:start . 24) (:id . 47))\n ((:tag . 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"partial") (:end . 172)\n (:start . 165) (:id . 68))\n ((:tag . "NNS") (:stem . "auc") (:form . "AUCs") (:end . 177) (:start . 173)\n (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 178) (:start . 177)\n (:id . 70))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 187)\n (:start . 179) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n (:id . 72)))@@@1@31@((:identifiers (:sid . :s2.148) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100475@unknown@formal@none@1@S@ROC50 and ROC100 curves were selected as they consider a large enough number of positives to include all protein pairs predicted to have a posterior odds ratio above 1.0 by all the predictors investigated.@(((:tag . "NNP") (:stem . "ROC50") (:form . "ROC50") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . 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"NN") (:stem . "number") (:form . "number") (:end . 76)\n (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n (:id . 55))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 89)\n (:start . 80) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 92) (:start . 90)\n (:id . 57))\n ((:tag . "VB") (:stem . "include") (:form . "include") (:end . 100)\n (:start . 93) (:id . 58))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 104) (:start . 101)\n (:id . 59))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 112)\n (:start . 105) (:id . 60))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 118)\n (:start . 113) (:id . 61))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 128)\n (:start . 119) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 131) (:start . 129)\n (:id . 63))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 136) (:start . 132)\n (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 138) (:start . 137)\n (:id . 65))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 148)\n (:start . 139) (:id . 66))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 153) (:start . 149)\n (:id . 67))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 159)\n (:start . 154) (:id . 68))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 165)\n (:start . 160) (:id . 69))\n ((:tag . "CD") (:stem . "1.0") (:form . "1.0") (:end . 169) (:start . 166)\n (:id . 70))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 172) (:start . 170)\n (:id . 71))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 176) (:start . 173)\n (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 180) (:start . 177)\n (:id . 73))\n ((:tag . "NNS") (:stem . "predictor") (:form . "predictors") (:end . 191)\n (:start . 181) (:id . 74))\n ((:tag . "VBN") (:stem . "investigate") (:form . "investigated") (:end . 204)\n (:start . 192) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n (:id . 76)))@@@1@35@((:hcues ((:id . :x2.149.1) (:span 119 128)))\n (:hscopes ((:id . :x2.149.1) (:span 101 204)))\n (:identifiers (:sid . :s2.149) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100476@unknown@formal@none@1@S@Protein pairs predicted to have a posterior odds ratio below 1.0 have an estimated true positive rate below 50% and thus are more likely not to interact than to interact.@(((:tag . "NN") (:stem . "protein") (:form . "Protein") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 13) (:start . 8)\n (:id . 43))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 23)\n (:start . 14) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 26) (:start . 24)\n (:id . 45))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 31) (:start . 27)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n (:id . 47))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 43)\n (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 48) (:start . 44)\n (:id . 49))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 54) (:start . 49)\n (:id . 50))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 60) (:start . 55)\n (:id . 51))\n ((:tag . "CD") (:stem . "1.0") (:form . "1.0") (:end . 64) (:start . 61)\n (:id . 52))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 69) (:start . 65)\n (:id . 53))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 72) (:start . 70)\n (:id . 54))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 82)\n (:start . 73) (:id . 55))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 87) (:start . 83)\n (:id . 56))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 96)\n (:start . 88) (:id . 57))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 101) (:start . 97)\n (:id . 58))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 107)\n (:start . 102) (:id . 59))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 110) (:start . 108)\n (:id . 60))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 111) (:start . 110)\n (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n (:id . 62))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 120) (:start . 116)\n (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 124) (:start . 121)\n (:id . 64))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 129) (:start . 125)\n (:id . 65))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 136)\n (:start . 130) (:id . 66))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 140) (:start . 137)\n (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 143) (:start . 141)\n (:id . 68))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 152)\n (:start . 144) (:id . 69))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 157) (:start . 153)\n (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 160) (:start . 158)\n (:id . 71))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 169)\n (:start . 161) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n (:id . 73)))@@@1@32@((:hcues ((:id . :x2.150.2) (:span 130 136)))\n (:ncues ((:id . :x2.150.1) (:span 137 140)))\n (:hscopes ((:id . :x2.150.2) (:span 121 169)))\n (:nscopes ((:id . :x2.150.1) (:span 137 152)))\n (:identifiers (:sid . :s2.150) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100477@unknown@formal@none@1@S@These protein pairs are therefore not of interest in this context.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 13)\n (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 19) (:start . 14)\n (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 33)\n (:start . 24) (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 37) (:start . 34)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n (:id . 48))\n ((:tag . "NN") (:stem . "interest") (:form . "interest") (:end . 49)\n (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n (:id . 50))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 57) (:start . 53)\n (:id . 51))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 65)\n (:start . 58) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n (:id . 53)))@@@1@12@((:ncues ((:id . :x2.151.1) (:span 34 37)))\n (:nscopes ((:id . :x2.151.1) (:span 34 65)))\n (:identifiers (:sid . :s2.151) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100478@unknown@formal@none@1@S@The area under all ROCn curves considered is relatively low because of the high proportion of negatives with respect to positives in the training and test sets (100:1).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "NNP") (:stem . "ROCn") (:form . "ROCn") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "NNS") (:stem . "curve") (:form . 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"NNS") (:stem . "negative") (:form . "negatives") (:end . 103)\n (:start . 94) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 108) (:start . 104)\n (:id . 59))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 116)\n (:start . 109) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 119) (:start . 117)\n (:id . 61))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 129)\n (:start . 120) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 132) (:start . 130)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n (:id . 64))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 145)\n (:start . 137) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 149) (:start . 146)\n (:id . 66))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 154) (:start . 150)\n (:id . 67))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 159) (:start . 155)\n (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 161) (:start . 160)\n (:id . 69))\n ((:tag . "CD") (:stem . "100:1") (:form . "100:1") (:end . 166)\n (:start . 161) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n (:id . 72)))@@@1@31@((:identifiers (:sid . :s2.152) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100480@unknown@formal@none@1@S@Individual modules do not achieve high scores for the areas under the ROC50 and ROC100.@(((:tag . "JJ") (:stem . "individual") (:form . "Individual") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 18)\n (:start . 11) (:id . 43))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 21) (:start . 19)\n (:id . 44))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "VB") (:stem . "achieve") (:form . "achieve") (:end . 33)\n (:start . 26) (:id . 46))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 38) (:start . 34)\n (:id . 47))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 45)\n (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n (:id . 50))\n ((:tag . "NNS") (:stem . "area") (:form . "areas") (:end . 59) (:start . 54)\n (:id . 51))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 65) (:start . 60)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n (:id . 53))\n ((:tag . "NNP") (:stem . "ROC50") (:form . "ROC50") (:end . 75) (:start . 70)\n (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 79) (:start . 76)\n (:id . 55))\n ((:tag . "NNP") (:stem . "ROC100") (:form . "ROC100") (:end . 86)\n (:start . 80) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n (:id . 57)))@@@1@16@((:ncues ((:id . :x2.154.1) (:span 22 25)))\n (:nscopes ((:id . :x2.154.1) (:span 22 86)))\n (:identifiers (:sid . :s2.154) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100481@unknown@formal@none@1@S@In fact, all ROC50 AUC values achieved by individual modules are below 0.025 and the Expression and Disorder modules do not predict any protein pairs (positive or negative) above a posterior odds ratio of 1, which is expected as the highest likelihood ratios they achieve are lower than 400 (see Figure 1A).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 12) (:start . 9)\n (:id . 45))\n ((:tag . "NNP") (:stem . "ROC50") (:form . "ROC50") (:end . 18) (:start . 13)\n (:id . 46))\n ((:tag . "NNP") (:stem . "AUC") (:form . "AUC") (:end . 22) (:start . 19)\n (:id . 47))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 29)\n (:start . 23) (:id . 48))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 38)\n (:start . 30) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 41) (:start . 39)\n (:id . 50))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 52)\n (:start . 42) (:id . 51))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 60)\n (:start . 53) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 64) (:start . 61)\n (:id . 53))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 70) (:start . 65)\n (:id . 54))\n ((:tag . 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(:end . 250) (:start . 249)\n (:id . 85)))@@@1@44@((:hcues ((:id . :x2.156.1) (:span 113 118)))\n (:hscopes ((:id . :x2.156.1) (:span 113 130)))\n (:identifiers (:sid . :s2.156) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100483@unknown@formal@none@1@S@For example, the predictor that considers both the Expression and Combined modules achieves a ROC50 AUC of 0.033 compared to 0.003 and 0.022 respectively for the individual modules.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 26)\n (:start . 17) (:id . 46))\n ((:tag . "WDT") (:stem . 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(:end . 185) (:start . 184)\n (:id . 75)))@@@1@34@((:ncues ((:id . :x2.158.1) (:span 174 177))\n ((:id . :x2.158.2) (:span 115 118)))\n (:nscopes ((:id . :x2.158.1) (:span 174 184))\n ((:id . :x2.158.2) (:span 115 184)))\n (:identifiers (:sid . :s2.158) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100485@unknown@formal@none@1@S@For example, both the Expression-Orthology predictor and the Expression-Orthology-Disorder predictor achieve a ROC50 AUC of 0.024.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 17) (:start . 13)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . 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(:end . 142) (:start . 141)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.160) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100487@unknown@formal@none@1@S@However, this appears to add more noise to the prediction without increasing the accuracy.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 21)\n (:start . 14) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 24) (:start . 22)\n (:id . 46))\n ((:tag . "VB") (:stem . "add") (:form . "add") (:end . 28) (:start . 25)\n (:id . 47))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 33) (:start . 29)\n (:id . 48))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 39) (:start . 34)\n (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 42) (:start . 40)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n (:id . 51))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 57)\n (:start . 47) (:id . 52))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 65)\n (:start . 58) (:id . 53))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 76)\n (:start . 66) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n (:id . 55))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 89)\n (:start . 81) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n (:id . 57)))@@@1@16@((:hcues ((:id . :x2.161.2) (:span 14 21)))\n (:ncues ((:id . :x2.161.1) (:span 58 65)))\n (:hscopes ((:id . :x2.161.2) (:span 9 89)))\n (:nscopes ((:id . :x2.161.1) (:span 58 89)))\n (:identifiers (:sid . :s2.161) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100488@unknown@formal@none@1@S@Prediction accuracy of different combinations of modules@(((:tag . "NN") (:stem . "prediction") (:form . "Prediction") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 19)\n (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n (:id . 44))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 32)\n (:start . 23) (:id . 45))\n ((:tag . "NNS") (:stem . "combination") (:form . "combinations") (:end . 45)\n (:start . 33) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n (:id . 47))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 56)\n (:start . 49) (:id . 48)))@@@1@7@((:identifiers (:sid . :s2.162) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|TableLegend|)))@oe@9-2-2011 5100490@unknown@formal@none@1@S@For example, the Expression-Orthology predictor achieves a ROC50 AUC of 0.024 and predicts 5670 interactions at a posterior odds ratio greater than 1 whereas the Expression-Orthology-Combined predictor achieves a ROC50 AUC of 0.044 and predicts over 15000 interactions at a posterior odds ratio above 1.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . 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"ratio") (:end . 294)\n (:start . 289) (:id . 85))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 300)\n (:start . 295) (:id . 86))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 302) (:start . 301)\n (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 303) (:start . 302)\n (:id . 88)))@@@1@47@((:identifiers (:sid . :s2.164) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100491@unknown@formal@none@1@S@The best combination of Group A modules is the predictor consisting of the Expression, Orthology and Combined modules.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 20)\n (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Group") (:form . "Group") (:end . 29) (:start . 24)\n (:id . 46))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 31) (:start . 30)\n (:id . 47))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 39)\n (:start . 32) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 42) (:start . 40)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n (:id . 50))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 56)\n (:start . 47) (:id . 51))\n ((:tag . "VBG") (:stem . "consist") (:form . "consisting") (:end . 67)\n (:start . 57) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n (:id . 54))\n ((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 85)\n (:start . 75) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n (:id . 56))\n ((:tag . "NNP") (:stem . "Orthology") (:form . "Orthology") (:end . 96)\n (:start . 87) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Combined") (:form . "Combined") (:end . 109)\n (:start . 101) (:id . 59))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 117)\n (:start . 110) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s2.165) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100492@unknown@formal@none@1@S@The Transitive module, which can only be used in combination with other modules, increases substantially the scores and number of interactions predicted.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . 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"of") (:end . 129) (:start . 127)\n (:id . 63))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 142)\n (:start . 130) (:id . 64))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 152)\n (:start . 143) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s2.166) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100493@unknown@formal@none@1@S@The right-hand portion of Table 3 shows the accuracy measures for the highest scoring subset of predictors that consider the Transitive module.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "right-hand") (:form . "right-hand") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 22)\n (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n (:id . 45))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 31) (:start . 26)\n (:id . 46))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 33) (:start . 32)\n (:id . 47))\n ((:tag . "NNS") (:stem . "show") (:form . "shows") (:end . 39) (:start . 34)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n (:id . 49))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 52)\n (:start . 44) (:id . 50))\n ((:tag . "NNS") (:stem . "measure") (:form . "measures") (:end . 61)\n (:start . 53) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 65) (:start . 62)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n (:id . 53))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 77)\n (:start . 70) (:id . 54))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 85)\n (:start . 78) (:id . 55))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 92)\n (:start . 86) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n (:id . 57))\n ((:tag . "NNS") (:stem . "predictor") (:form . "predictors") (:end . 106)\n (:start . 96) (:id . 58))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 111) (:start . 107)\n (:id . 59))\n ((:tag . "VBP") (:stem . "consider") (:form . "consider") (:end . 120)\n (:start . 112) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n (:id . 61))\n ((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 135)\n (:start . 125) (:id . 62))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 142)\n (:start . 136) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.167) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100494@unknown@formal@none@1@S@The Transitive module enhances the prediction by identifying among protein pairs with a relatively high preliminary score those that are most likely to interact, by considering the local topology of the network around them.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 21)\n (:start . 15) (:id . 44))\n ((:tag . "VBZ") (:stem . "enhance") (:form . "enhances") (:end . 30)\n (:start . 22) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 46))\n ((:tag . "NN") (:stem . "prediction") (:form . 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(:end . 223) (:start . 222)\n (:id . 77)))@@@1@36@((:hcues ((:id . :x2.168.1) (:span 142 148)))\n (:hscopes ((:id . :x2.168.1) (:span 128 160)))\n (:identifiers (:sid . :s2.168) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100495@unknown@formal@none@1@S@For example, the ROC50 AUC rises from 0.044 to 0.075 when the Transitive module is added to the Expression-Orthology-Combined predictor, and the number of predictions above a posterior odds ratio of 1 doubles from 15330 to 34780.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "NNP") (:stem . "ROC50") (:form . 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"VBZ") (:stem . "be") (:form . "is") (:end . 82) (:start . 80)\n (:id . 57))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 88) (:start . 83)\n (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n (:id . 60))\n ((:tag . "JJ") (:stem . "expression-orthology-combined")\n (:form . "Expression-Orthology-Combined") (:end . 125) (:start . 96)\n (:id . 61))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 135)\n (:start . 126) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n (:id . 65))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 151)\n (:start . 145) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 154) (:start . 152)\n (:id . 67))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 166)\n (:start . 155) (:id . 68))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 172)\n (:start . 167) (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 174) (:start . 173)\n (:id . 70))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 184)\n (:start . 175) (:id . 71))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 189) (:start . 185)\n (:id . 72))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 195)\n (:start . 190) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 198) (:start . 196)\n (:id . 74))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 200) (:start . 199)\n (:id . 75))\n ((:tag . "NNS") (:stem . "double") (:form . "doubles") (:end . 208)\n (:start . 201) (:id . 76))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 213) (:start . 209)\n (:id . 77))\n ((:tag . "CD") (:stem . "15330") (:form . "15330") (:end . 219)\n (:start . 214) (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 222) (:start . 220)\n (:id . 79))\n ((:tag . "CD") (:stem . "34780") (:form . "34780") (:end . 228)\n (:start . 223) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n (:id . 81)))@@@1@40@((:identifiers (:sid . :s2.169) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100496@unknown@formal@none@1@S@Once again, the Disorder module does not contribute positively to the prediction.@(((:tag . "RB") (:stem . "once") (:form . "Once") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "again") (:form . "again") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Disorder") (:form . "Disorder") (:end . 24)\n (:start . 16) (:id . 46))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 31)\n (:start . 25) (:id . 47))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 36) (:start . 32)\n (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 40) (:start . 37)\n (:id . 49))\n ((:tag . "VB") (:stem . "contribute") (:form . "contribute") (:end . 51)\n (:start . 41) (:id . 50))\n ((:tag . "RB") (:stem . "positively") (:form . "positively") (:end . 62)\n (:start . 52) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 65) (:start . 63)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n (:id . 53))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 80)\n (:start . 70) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n (:id . 55)))@@@1@14@((:ncues ((:id . :x2.170.1) (:span 37 40)))\n (:nscopes ((:id . :x2.170.1) (:span 37 80)))\n (:identifiers (:sid . :s2.170) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100497@unknown@formal@none@1@S@Its inclusion does not increase any of the measures of accuracy considered.@(((:tag . "PRP$") (:stem . "its") (:form . "Its") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "inclusion") (:form . "inclusion") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "VB") (:stem . "increase") (:form . "increase") (:end . 31)\n (:start . 23) (:id . 46))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 35) (:start . 32)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n (:id . 49))\n ((:tag . "NNS") (:stem . "measure") (:form . "measures") (:end . 51)\n (:start . 43) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n (:id . 51))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 63)\n (:start . 55) (:id . 52))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 74)\n (:start . 64) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n (:id . 54)))@@@1@13@((:ncues ((:id . :x2.171.1) (:span 19 22)))\n (:nscopes ((:id . :x2.171.1) (:span 19 74)))\n (:identifiers (:sid . :s2.171) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100498@unknown@formal@none@1@S@The predictor that considers the Expression, Orthology, Combined and Transitive modules is the one that achieves the highest accuracy overall.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "consider") (:form . "considers") (:end . 28)\n (:start . 19) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Expression") (:form . "Expression") (:end . 43)\n (:start . 33) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Orthology") (:form . "Orthology") (:end . 54)\n (:start . 45) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Combined") (:form . "Combined") (:end . 64)\n (:start . 56) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n (:id . 52))\n ((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 79)\n (:start . 69) (:id . 53))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 87)\n (:start . 80) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 90) (:start . 88)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n (:id . 56))\n ((:tag . "NN") (:stem . "one") (:form . "one") (:end . 98) (:start . 95)\n (:id . 57))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 103) (:start . 99)\n (:id . 58))\n ((:tag . "VBZ") (:stem . "achieve") (:form . "achieves") (:end . 112)\n (:start . 104) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n (:id . 60))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 124)\n (:start . 117) (:id . 61))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 133)\n (:start . 125) (:id . 62))\n ((:tag . "RB") (:stem . "overall") (:form . "overall") (:end . 141)\n (:start . 134) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.172) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100500@unknown@formal@none@1@S@Comparison to predictions generated using alternative training sets@(((:tag . "NN") (:stem . "comparison") (:form . "Comparison") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 13) (:start . 11)\n (:id . 43))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 25)\n (:start . 14) (:id . 44))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 35)\n (:start . 26) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 41) (:start . 36)\n (:id . 46))\n ((:tag . "JJ") (:stem . "alternative") (:form . "alternative") (:end . 53)\n (:start . 42) (:id . 47))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 62)\n (:start . 54) (:id . 48))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 67) (:start . 63)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s2.174) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100501@unknown@formal@none@1@S@In this work training sets were used that comprised 100 times more negatives than positives, with the negatives randomly selected and filtered to remove any known or suspected positives (see Methods).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 21)\n (:start . 13) (:id . 45))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 26) (:start . 22)\n (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 31) (:start . 27)\n (:id . 47))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 36) (:start . 32)\n (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 41) (:start . 37)\n (:id . 49))\n ((:tag . "VBD") (:stem . "comprise") (:form . "comprised") (:end . 51)\n (:start . 42) (:id . 50))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 55) (:start . 52)\n (:id . 51))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 61) (:start . 56)\n (:id . 52))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 66) (:start . 62)\n (:id . 53))\n ((:tag . "NNS") (:stem . "negative") (:form . "negatives") (:end . 76)\n (:start . 67) (:id . 54))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 81) (:start . 77)\n (:id . 55))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 91)\n (:start . 82) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 97) (:start . 93)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n (:id . 59))\n ((:tag . "NNS") (:stem . "negative") (:form . "negatives") (:end . 111)\n (:start . 102) (:id . 60))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 120)\n (:start . 112) (:id . 61))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 129)\n (:start . 121) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 133) (:start . 130)\n (:id . 63))\n ((:tag . "VBN") (:stem . "filter") (:form . "filtered") (:end . 142)\n (:start . 134) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 145) (:start . 143)\n (:id . 65))\n ((:tag . "VB") (:stem . "remove") (:form . "remove") (:end . 152)\n (:start . 146) (:id . 66))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 156) (:start . 153)\n (:id . 67))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 162)\n (:start . 157) (:id . 68))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 165) (:start . 163)\n (:id . 69))\n ((:tag . "VBN") (:stem . "suspect") (:form . "suspected") (:end . 175)\n (:start . 166) (:id . 70))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 185)\n (:start . 176) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 187) (:start . 186)\n (:id . 72))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 190) (:start . 187)\n (:id . 73))\n ((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 198)\n (:start . 191) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 199) (:start . 198)\n (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n (:id . 76)))@@@1@35@((:hcues ((:id . :x2.175.1) (:span 166 175)))\n (:hscopes ((:id . :x2.175.1) (:span 166 185)))\n (:identifiers (:sid . :s2.175) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100502@unknown@formal@none@1@S@Other groups have used negative:positive ratios ranging from 1 to more than 600 (see for example 374752).@(((:tag . "JJ") (:stem . "other") (:form . "Other") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 12) (:start . 6)\n (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 17) (:start . 13)\n (:id . 44))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 22) (:start . 18)\n (:id . 45))\n ((:tag . "JJ") (:stem . "negative:positive") (:form . "negative:positive")\n (:end . 40) (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 47)\n (:start . 41) (:id . 47))\n ((:tag . "VBG") (:stem . "range") (:form . "ranging") (:end . 55)\n (:start . 48) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 60) (:start . 56)\n (:id . 49))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 62) (:start . 61)\n (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 65) (:start . 63)\n (:id . 51))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 70) (:start . 66)\n (:id . 52))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 75) (:start . 71)\n (:id . 53))\n ((:tag . "CD") (:stem . "600") (:form . "600") (:end . 79) (:start . 76)\n (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 81) (:start . 80)\n (:id . 55))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 84) (:start . 81)\n (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 88) (:start . 85)\n (:id . 57))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 96)\n (:start . 89) (:id . 58))\n ((:tag . "CD") (:stem . "374752") (:form . "374752") (:end . 103)\n (:start . 97) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s2.176) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100503@unknown@formal@none@1@S@In addition, several groups use localization-derived negatives (i.e. protein pairs that are not annotated as being localized to the same cellular compartment) rather than randomly chosen negatives (see for example 374346).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . 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(:end . 253) (:start . 252)\n (:id . 82)))@@@1@41@((:hcues ((:id . :x2.179.1) (:span 43 46)))\n (:hscopes ((:id . :x2.179.1) (:span 43 67)))\n (:identifiers (:sid . :s2.179) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100506@unknown@formal@none@1@S@Table 4 compares the accuracy of predictors trained with negative:positive ratios of 1:100 and 1:1 and tested by five-fold cross validation.@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 7) (:start . 6)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "compare") (:form . "compares") (:end . 16)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 29)\n (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . 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"architecture") (:end . 139)\n (:start . 127) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n (:id . 64))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 156)\n (:start . 147) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n (:id . 66)))@@@1@25@((:ncues ((:id . :x2.181.1) (:span 29 32)))\n (:nscopes ((:id . :x2.181.1) (:span 0 43)))\n (:identifiers (:sid . :s2.181) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100508@unknown@formal@none@1@S@To perform such a comparison, the EOCT predictor (Expression, Orthology, Combined and Transitive modules) was trained on datasets consisting of either equal numbers of positives and negatives or 100 times more negatives than positives and then tested on both types of datasets.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "perform") (:form . "perform") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "PDT") (:stem . "such") (:form . "such") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "NN") (:stem . 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(:end . 146) (:start . 145)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x2.185.1) (:span 5 10)))\n (:hscopes ((:id . :x2.185.1) (:span 5 145)))\n (:identifiers (:sid . :s2.185) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100512@unknown@formal@none@1@S@When equal numbers of positives and negatives are used in training, the diversity that exists in the non-interacting protein pair space may not be captured, thus resulting in misleading likelihood ratios for the predictive modules.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 18)\n (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "NNS") (:stem . "positive") (:form . 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"Influence") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "negative:positive") (:form . "negative:positive")\n (:end . 34) (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 43)\n (:start . 35) (:id . 46))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 47) (:start . 44)\n (:id . 47))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 53) (:start . 48)\n (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 56) (:start . 54)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n (:id . 50))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 71)\n (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "accuracy") (:form . 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(:end . 172) (:start . 171)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s2.194) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100521@unknown@formal@none@1@S@Contamination is probably below 1%, which is likely lower than the contamination rate of the positive dataset as discussed in 47.@(((:tag . "NN") (:stem . "contamination") (:form . "Contamination")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n (:id . 43))\n ((:tag . "RB") (:stem . "probably") (:form . "probably") (:end . 25)\n (:start . 17) (:id . 44))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 31) (:start . 26)\n (:id . 45))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 33) (:start . 32)\n (:id . 46))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 34) (:start . 33)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . 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(:end . 207) (:start . 206)\n (:id . 76)))@@@1@35@((:hcues ((:id . :x2.196.1) (:span 51 57)))\n (:hscopes ((:id . :x2.196.1) (:span 51 82)))\n (:identifiers (:sid . :s2.196) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100523@unknown@formal@none@1@S@However, one can argue that localization-derived negatives might not be able to capture the full diversity of the non-interacting protein space since many proteins in the same cellular compartment do not interact.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "one") (:form . "one") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "VB") (:stem . "argue") (:form . "argue") (:end . 22) (:start . 17)\n (:id . 46))\n ((:tag . 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(:end . 213) (:start . 212)\n (:id . 75)))@@@1@34@((:hcues ((:id . :x2.197.3) (:span 59 64)))\n (:ncues ((:id . :x2.197.1) (:span 200 203))\n ((:id . :x2.197.2) (:span 65 68)))\n (:hscopes ((:id . :x2.197.3) (:span 59 143)))\n (:nscopes ((:id . :x2.197.1) (:span 200 212))\n ((:id . :x2.197.2) (:span 65 143)))\n (:identifiers (:sid . :s2.197) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100524@unknown@formal@none@1@S@In addition, proteins specific to a cellular compartment may have different characteristics to proteins in other compartments.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "NNS") (:stem . "protein") (:form . 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"to") (:end . 94) (:start . 92)\n (:id . 55))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 103)\n (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n (:id . 57))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 112)\n (:start . 107) (:id . 58))\n ((:tag . "NNS") (:stem . "compartment") (:form . "compartments") (:end . 125)\n (:start . 113) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n (:id . 60)))@@@1@19@((:hcues ((:id . :x2.198.1) (:span 57 60)))\n (:hscopes ((:id . :x2.198.1) (:span 57 125)))\n (:identifiers (:sid . :s2.198) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100525@unknown@formal@none@1@S@Such predictors may not generalize well when predicting on cell-wide protein pairs which consist not only of non-colocalized non-interacting pairs but also numerous protein pairs that do not interact but are present in the same cellular compartment.@(((:tag . "JJ") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "predictor") (:form . "predictors") (:end . 15)\n (:start . 5) (:id . 43))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 19) (:start . 16)\n (:id . 44))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "VB") (:stem . "generalize") (:form . 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"JJ") (:stem . "cellular") (:form . "cellular") (:end . 236)\n (:start . 228) (:id . 77))\n ((:tag . "NN") (:stem . "compartment") (:form . "compartment") (:end . 248)\n (:start . 237) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 249) (:start . 248)\n (:id . 79)))@@@1@38@((:hcues ((:id . :x2.199.3) (:span 16 19)))\n (:ncues ((:id . :x2.199.1) (:span 187 190))\n ((:id . :x2.199.2) (:span 20 23)))\n (:hscopes ((:id . :x2.199.3) (:span 16 39)))\n (:nscopes ((:id . :x2.199.1) (:span 187 199))\n ((:id . :x2.199.2) (:span 20 39)))\n (:identifiers (:sid . :s2.199) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100526@unknown@formal@none@1@S@These issues have been discussed previously 52.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "issue") (:form . "issues") (:end . 12) (:start . 6)\n (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 17) (:start . 13)\n (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 22) (:start . 18)\n (:id . 45))\n ((:tag . "VBN") (:stem . "discuss") (:form . "discussed") (:end . 32)\n (:start . 23) (:id . 46))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 43)\n (:start . 33) (:id . 47))\n ((:tag . "CD") (:stem . "52") (:form . "52") (:end . 46) (:start . 44)\n (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 47) (:start . 46)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s2.200) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100527@unknown@formal@none@1@S@In order to see if different types of negatives could influence the accuracy of the predictors developed here we generated negative training/test sets as in 46 by identifying all pairs of human proteins for which one protein is annotated as being nuclear and the other is annotated as being localized to the plasma membrane in the HPRD database 15.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 15) (:start . 12)\n (:id . 45))\n ((:tag . "IN") (:stem . "if") (:form . 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(:end . 69) (:start . 68)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.206) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100533@unknown@formal@none@1@S@Contribution of the modules@(((:tag . "NN") (:stem . "contribution") (:form . "Contribution") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 44))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 27)\n (:start . 20) (:id . 45)))@@@1@4@((:identifiers (:sid . :s2.207) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100534@unknown@formal@none@1@S@The relative contribution of the modules to the prediction of interaction was investigated in order to gain a better understanding of the predictive power and areas of highest usefulness of the different modules.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "contribution") (:form . "contribution") (:end . 25)\n (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n (:id . 46))\n ((:tag . "NNS") (:stem . "module") (:form . 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"dataset") (:form . "datasets") (:end . 153)\n (:start . 145) (:id . 69))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 161)\n (:start . 154) (:id . 70))\n ((:tag . "NN") (:stem . "cross-validation") (:form . "cross-validation")\n (:end . 178) (:start . 162) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n (:id . 72)))@@@1@31@((:ncues ((:id . :x2.209.1) (:span 154 161)))\n (:nscopes ((:id . :x2.209.1) (:span 154 178)))\n (:identifiers (:sid . :s2.209) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100536@unknown@formal@none@1@S@This set consists of 37606 distinct predicted interactions and is referred to as the LR400 dataset (all these interactions are listed and ranked in Additional File 3).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "set") (:form . 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"to") (:end . 77) (:start . 75)\n (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 80) (:start . 78)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n (:id . 55))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 90) (:start . 85)\n (:id . 56))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 98)\n (:start . 91) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n (:id . 58))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 103) (:start . 100)\n (:id . 59))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 109)\n (:start . 104) (:id . 60))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 122)\n (:start . 110) (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 126) (:start . 123)\n (:id . 62))\n ((:tag . "VBN") (:stem . "list") (:form . "listed") (:end . 133)\n (:start . 127) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n (:id . 64))\n ((:tag . "VBN") (:stem . "rank") (:form . "ranked") (:end . 144)\n (:start . 138) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 147) (:start . 145)\n (:id . 66))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 158)\n (:start . 148) (:id . 67))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 163) (:start . 159)\n (:id . 68))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 165) (:start . 164)\n (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 166) (:start . 165)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s2.210) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100537@unknown@formal@none@1@S@These protein pairs represent the most probable interactors with respect to the features considered, among all protein pairs examined by the predictor.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 13)\n (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 19) (:start . 14)\n (:id . 44))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 29)\n (:start . 20) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 46))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 38) (:start . 34)\n (:id . 47))\n ((:tag . "JJ") (:stem . "probable") (:form . "probable") (:end . 47)\n (:start . 39) (:id . 48))\n ((:tag . "NNS") (:stem . "interactor") (:form . "interactors") (:end . 59)\n (:start . 48) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 64) (:start . 60)\n (:id . 50))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 72)\n (:start . 65) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 75) (:start . 73)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n (:id . 53))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 88)\n (:start . 80) (:id . 54))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 99)\n (:start . 89) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n (:id . 56))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 106)\n (:start . 101) (:id . 57))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 110) (:start . 107)\n (:id . 58))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 118)\n (:start . 111) (:id . 59))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 124)\n (:start . 119) (:id . 60))\n ((:tag . "VBN") (:stem . "examine") (:form . "examined") (:end . 133)\n (:start . 125) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 136) (:start . 134)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n (:id . 63))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 150)\n (:start . 141) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n (:id . 65)))@@@1@24@((:hcues ((:id . :x2.211.1) (:span 39 47)))\n (:hscopes ((:id . :x2.211.1) (:span 39 59)))\n (:identifiers (:sid . :s2.211) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100538@unknown@formal@none@1@S@To investigate the individual contribution of each module, we looked at the number of interactions predicted out of all LR400 pairs as a function of the minimum likelihood ratio of each module.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "investigate") (:form . "investigate") (:end . 14)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 44))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 29)\n (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "contribution") (:form . "contribution") (:end . 42)\n (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n (:id . 47))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 50) (:start . 46)\n (:id . 48))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 57)\n (:start . 51) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 61) (:start . 59)\n (:id . 51))\n ((:tag . "VBD") (:stem . "look") (:form . "looked") (:end . 68) (:start . 62)\n (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 71) (:start . 69)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n (:id . 54))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 82)\n (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n (:id . 56))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 98)\n (:start . 86) (:id . 57))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 108)\n (:start . 99) (:id . 58))\n ((:tag . "IN") (:stem . "out") (:form . "out") (:end . 112) (:start . 109)\n (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n (:id . 60))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 119) (:start . 116)\n (:id . 61))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 125)\n (:start . 120) (:id . 62))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 131)\n (:start . 126) (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 134) (:start . 132)\n (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 136) (:start . 135)\n (:id . 65))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 145)\n (:start . 137) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 148) (:start . 146)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n (:id . 68))\n ((:tag . "JJ") (:stem . "minimum") (:form . "minimum") (:end . 160)\n (:start . 153) (:id . 69))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 171)\n (:start . 161) (:id . 70))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 177)\n (:start . 172) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 180) (:start . 178)\n (:id . 72))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 185) (:start . 181)\n (:id . 73))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 192)\n (:start . 186) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s2.212) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100540@unknown@formal@none@1@S@The Transitive module and to an even greater extent, the Combined module contribute positively to the prediction of a very high proportion of the LR400 protein pairs (73% and 91% of the LR400 interactions have likelihood ratios greater than 1 for the Transitive and Combined modules respectively).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 21)\n (:start . 15) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 31) (:start . 29)\n (:id . 47))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 36) (:start . 32)\n (:id . 48))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 44)\n (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 51)\n (:start . 45) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n (:id . 52))\n ((:tag . "JJ") (:stem . "combined") (:form . "Combined") (:end . 65)\n (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 72)\n (:start . 66) (:id . 54))\n ((:tag . "VBP") (:stem . "contribute") (:form . "contribute") (:end . 83)\n (:start . 73) (:id . 55))\n ((:tag . "RB") (:stem . "positively") (:form . "positively") (:end . 94)\n (:start . 84) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 97) (:start . 95)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n (:id . 58))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 112)\n (:start . 102) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 117) (:start . 116)\n (:id . 61))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 122) (:start . 118)\n (:id . 62))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 127) (:start . 123)\n (:id . 63))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 138)\n (:start . 128) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 141) (:start . 139)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n (:id . 66))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 151)\n (:start . 146) (:id . 67))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 159)\n (:start . 152) (:id . 68))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 165)\n (:start . 160) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n (:id . 70))\n ((:tag . "CD") (:stem . "73") (:form . "73") (:end . 169) (:start . 167)\n (:id . 71))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 170) (:start . 169)\n (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 174) (:start . 171)\n (:id . 73))\n ((:tag . "CD") (:stem . "91") (:form . "91") (:end . 177) (:start . 175)\n (:id . 74))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 178) (:start . 177)\n (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 181) (:start . 179)\n (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 185) (:start . 182)\n (:id . 77))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 191)\n (:start . 186) (:id . 78))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 204)\n (:start . 192) (:id . 79))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 209) (:start . 205)\n (:id . 80))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 220)\n (:start . 210) (:id . 81))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 227)\n (:start . 221) (:id . 82))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 235)\n (:start . 228) (:id . 83))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 240) (:start . 236)\n (:id . 84))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 242) (:start . 241)\n (:id . 85))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 246) (:start . 243)\n (:id . 86))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 250) (:start . 247)\n (:id . 87))\n ((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 261)\n (:start . 251) (:id . 88))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 265) (:start . 262)\n (:id . 89))\n ((:tag . "JJ") (:stem . "combined") (:form . "Combined") (:end . 274)\n (:start . 266) (:id . 90))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 282)\n (:start . 275) (:id . 91))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 295)\n (:start . 283) (:id . 92))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 296) (:start . 295)\n (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 297) (:start . 296)\n (:id . 94)))@@@1@53@((:identifiers (:sid . :s2.214) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100541@unknown@formal@none@1@S@The Transitive module provides a likelihood ratio of 91 for the prediction of over 70% of the LR400 interactions.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 21)\n (:start . 15) (:id . 44))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 30)\n (:start . 22) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n (:id . 46))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 43)\n (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 49) (:start . 44)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n (:id . 49))\n ((:tag . "CD") (:stem . "91") (:form . "91") (:end . 55) (:start . 53)\n (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 59) (:start . 56)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n (:id . 52))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 74)\n (:start . 64) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n (:id . 54))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 82) (:start . 78)\n (:id . 55))\n ((:tag . "CD") (:stem . "70") (:form . "70") (:end . 85) (:start . 83)\n (:id . 56))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 86) (:start . 85)\n (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n (:id . 59))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 99) (:start . 94)\n (:id . 60))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 112)\n (:start . 100) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.215) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100542@unknown@formal@none@1@S@The Combined module provides positive evidence for the highest number of interactions of the LR400 dataset.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "combine") (:form . "Combined") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 19)\n (:start . 13) (:id . 44))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 28)\n (:start . 20) (:id . 45))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 37)\n (:start . 29) (:id . 46))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 46)\n (:start . 38) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 50) (:start . 47)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n (:id . 49))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 62)\n (:start . 55) (:id . 50))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 69)\n (:start . 63) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n (:id . 52))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 85)\n (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n (:id . 55))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 98) (:start . 93)\n (:id . 56))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 106)\n (:start . 99) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.216) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100543@unknown@formal@none@1@S@However, the value of the likelihood ratio it contributes is below 20 for over 50% of protein pairs in the LR400 dataset (which means that for these protein pairs, the Combined module must be used in combination with other modules to achieve a total likelihood ratio above 400).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . 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"total") (:end . 249)\n (:start . 244) (:id . 89))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 260)\n (:start . 250) (:id . 90))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 266)\n (:start . 261) (:id . 91))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 272)\n (:start . 267) (:id . 92))\n ((:tag . "CD") (:stem . "400") (:form . "400") (:end . 276) (:start . 273)\n (:id . 93))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 277) (:start . 276)\n (:id . 94))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 278) (:start . 277)\n (:id . 95)))@@@1@54@((:identifiers (:sid . :s2.217) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100544@unknown@formal@none@1@S@The Combined module does, however, achieve likelihood ratios high enough to predict over two thousand interactions of the LR400 dataset on its own, less than 15% of which are present in the training set.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "combine") (:form . "Combined") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 19)\n (:start . 13) (:id . 44))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 24) (:start . 20)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n (:id . 46))\n ((:tag . "RB") (:stem . "however") (:form . 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"CD") (:stem . "thousand") (:form . "thousand") (:end . 101)\n (:start . 93) (:id . 58))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 114)\n (:start . 102) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 117) (:start . 115)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n (:id . 61))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 127)\n (:start . 122) (:id . 62))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 135)\n (:start . 128) (:id . 63))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 138) (:start . 136)\n (:id . 64))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 142) (:start . 139)\n (:id . 65))\n ((:tag . "JJ") (:stem . "own") (:form . "own") (:end . 146) (:start . 143)\n (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n (:id . 67))\n ((:tag . "JJR") (:stem . "less") (:form . 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"NN") (:stem . "set") (:form . "set") (:end . 202) (:start . 199)\n (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n (:id . 80)))@@@1@39@((:identifiers (:sid . :s2.218) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100545@unknown@formal@none@1@S@The Orthology module contributes to the prediction of only 8474 protein pairs in the LR400 dataset (23%).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Orthology") (:form . "Orthology") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 20)\n (:start . 14) (:id . 44))\n ((:tag . "VBZ") (:stem . "contribute") (:form . "contributes") (:end . 32)\n (:start . 21) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . 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"(") (:form . "(") (:end . 100) (:start . 99)\n (:id . 58))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 102) (:start . 100)\n (:id . 59))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 103) (:start . 102)\n (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.219) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100546@unknown@formal@none@1@S@However, a large majority (> 75%) of these 8474 predicted interactions achieve likelihood ratios above 200 from this module.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n (:id . 44))\n ((:tag . 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(:end . 124) (:start . 123)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.220) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100547@unknown@formal@none@1@S@In fact, almost 40% of these LR400 interactions achieve a likelihood ratio above 400 from the Orthology module.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 15) (:start . 9)\n (:id . 45))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 18) (:start . 16)\n (:id . 46))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 19) (:start . 18)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n (:id . 48))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 28) (:start . 23)\n (:id . 49))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 34) (:start . 29)\n (:id . 50))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 47)\n (:start . 35) (:id . 51))\n ((:tag . "VBP") (:stem . "achieve") (:form . "achieve") (:end . 55)\n (:start . 48) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n (:id . 53))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 68)\n (:start . 58) (:id . 54))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 74) (:start . 69)\n (:id . 55))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 80) (:start . 75)\n (:id . 56))\n ((:tag . "CD") (:stem . "400") (:form . "400") (:end . 84) (:start . 81)\n (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 89) (:start . 85)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n (:id . 59))\n ((:tag . "NNP") (:stem . "Orthology") (:form . "Orthology") (:end . 103)\n (:start . 94) (:id . 60))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 110)\n (:start . 104) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.221) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100548@unknown@formal@none@1@S@This indicates that most interactions predicted by the Orthology module (alone or in combination with other modules) are based on the highest scoring Orthology bins (see Figure 1A) which are the most conserved yeast interactions (whose bin achieves a likelihood ratio of 237), as well as human paralogous interactions and interactions found in more than one model organism (both of which achieve a likelihood well above 400).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 14)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 24) (:start . 20)\n (:id . 45))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 37)\n (:start . 25) (:id . 46))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 47)\n (:start . 38) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 50) (:start . 48)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n (:id . 49))\n ((:tag . "NNP") (:stem . "Orthology") (:form . "Orthology") (:end . 64)\n (:start . 55) (:id . 50))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 71)\n (:start . 65) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n (:id . 52))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 78) (:start . 73)\n (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 81) (:start . 79)\n (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n (:id . 55))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 96)\n (:start . 85) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 101) (:start . 97)\n (:id . 57))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 107)\n (:start . 102) (:id . 58))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 115)\n (:start . 108) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 120) (:start . 117)\n (:id . 61))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 126)\n (:start . 121) (:id . 62))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 129) (:start . 127)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n (:id . 64))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 141)\n (:start . 134) (:id . 65))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 149)\n (:start . 142) (:id . 66))\n ((:tag . "NNP") (:stem . "Orthology") (:form . "Orthology") (:end . 159)\n (:start . 150) (:id . 67))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 164) (:start . 160)\n (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 166) (:start . 165)\n (:id . 69))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 169) (:start . 166)\n (:id . 70))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 176)\n (:start . 170) (:id . 71))\n ((:tag . "NN") (:stem . "1a") (:form . "1A") (:end . 179) (:start . 177)\n (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n (:id . 73))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 186)\n (:start . 181) (:id . 74))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 190) (:start . 187)\n (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 194) (:start . 191)\n (:id . 76))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 199) (:start . 195)\n (:id . 77))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 209)\n (:start . 200) (:id . 78))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 215)\n (:start . 210) (:id . 79))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 228)\n (:start . 216) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 230) (:start . 229)\n (:id . 81))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 235)\n (:start . 230) (:id . 82))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 239) (:start . 236)\n (:id . 83))\n ((:tag . "VBZ") (:stem . "achieve") (:form . "achieves") (:end . 248)\n (:start . 240) (:id . 84))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 250) (:start . 249)\n (:id . 85))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 261)\n (:start . 251) (:id . 86))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 267)\n (:start . 262) (:id . 87))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 270) (:start . 268)\n (:id . 88))\n ((:tag . "CD") (:stem . "237") (:form . "237") (:end . 274) (:start . 271)\n (:id . 89))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 275) (:start . 274)\n (:id . 90))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 276) (:start . 275)\n (:id . 91))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 279) (:start . 277)\n (:id . 92))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 284) (:start . 280)\n (:id . 93))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 287) (:start . 285)\n (:id . 94))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 293)\n (:start . 288) (:id . 95))\n ((:tag . "JJ") (:stem . "paralogous") (:form . "paralogous") (:end . 304)\n (:start . 294) (:id . 96))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 317)\n (:start . 305) (:id . 97))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 321) (:start . 318)\n (:id . 98))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 334)\n (:start . 322) (:id . 99))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 340)\n (:start . 335) (:id . 100))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 343) (:start . 341)\n (:id . 101))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 348) (:start . 344)\n (:id . 102))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 353) (:start . 349)\n (:id . 103))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 357) (:start . 354)\n (:id . 104))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 363)\n (:start . 358) (:id . 105))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 372)\n (:start . 364) (:id . 106))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 374) (:start . 373)\n (:id . 107))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 378) (:start . 374)\n (:id . 108))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 381) (:start . 379)\n (:id . 109))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 387)\n (:start . 382) (:id . 110))\n ((:tag . "VBP") (:stem . "achieve") (:form . "achieve") (:end . 395)\n (:start . 388) (:id . 111))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 397) (:start . 396)\n (:id . 112))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 408)\n (:start . 398) (:id . 113))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 413) (:start . 409)\n (:id . 114))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 419)\n (:start . 414) (:id . 115))\n ((:tag . "CD") (:stem . "400") (:form . "400") (:end . 423) (:start . 420)\n (:id . 116))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 424) (:start . 423)\n (:id . 117))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 425) (:start . 424)\n (:id . 118)))@@@1@77@((:hcues ((:id . :x2.222.1) (:span 5 19)))\n (:hscopes ((:id . :x2.222.1) (:span 5 424)))\n (:identifiers (:sid . :s2.222) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100550@unknown@formal@none@1@S@The Expression module provides positive evidence for a little less than half the predictions in the LR400 dataset.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 21)\n (:start . 15) (:id . 44))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 30)\n (:start . 22) (:id . 45))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 39)\n (:start . 31) (:id . 46))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 48)\n (:start . 40) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 52) (:start . 49)\n (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n (:id . 49))\n ((:tag . "RB") (:stem . "little") (:form . "little") (:end . 61)\n (:start . 55) (:id . 50))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 66) (:start . 62)\n (:id . 51))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 71) (:start . 67)\n (:id . 52))\n ((:tag . "PDT") (:stem . "half") (:form . "half") (:end . 76) (:start . 72)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n (:id . 54))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 92)\n (:start . 81) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 95) (:start . 93)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n (:id . 57))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 105)\n (:start . 100) (:id . 58))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 113)\n (:start . 106) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s2.224) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100551@unknown@formal@none@1@S@However, as previously noted, the highest likelihood provided by this module is 33 and thus the Expression module cannot predict interaction on its own.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 22)\n (:start . 12) (:id . 45))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 28) (:start . 23)\n (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 48))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 41)\n (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 52)\n (:start . 42) (:id . 50))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 61)\n (:start . 53) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 64) (:start . 62)\n (:id . 52))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 69) (:start . 65)\n (:id . 53))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 76)\n (:start . 70) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 79) (:start . 77)\n (:id . 55))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 82) (:start . 80)\n (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n (:id . 57))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 91) (:start . 87)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n (:id . 59))\n ((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 106)\n (:start . 96) (:id . 60))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 113)\n (:start . 107) (:id . 61))\n ((:tag . "NN") (:stem . "cannot") (:form . "cannot") (:end . 120)\n (:start . 114) (:id . 62))\n ((:tag . "VB") (:stem . "predict") (:form . "predict") (:end . 128)\n (:start . 121) (:id . 63))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 140)\n (:start . 129) (:id . 64))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 143) (:start . 141)\n (:id . 65))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 147) (:start . 144)\n (:id . 66))\n ((:tag . "JJ") (:stem . "own") (:form . "own") (:end . 151) (:start . 148)\n (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n (:id . 68)))@@@1@27@((:ncues ((:id . :x2.225.1) (:span 114 120)))\n (:nscopes ((:id . :x2.225.1) (:span 114 151)))\n (:identifiers (:sid . :s2.225) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100552@unknown@formal@none@1@S@Contribution of the modules@(((:tag . "NN") (:stem . "contribution") (:form . "Contribution") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 44))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 27)\n (:start . 20) (:id . 45)))@@@1@4@((:identifiers (:sid . :s2.226) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|FigureLegend|)))@oe@9-2-2011 5100553@unknown@formal@none@1@S@Contribution of the modules.@(((:tag . "NN") (:stem . "contribution") (:form . "Contribution") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 44))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 27)\n (:start . 20) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 28) (:start . 27)\n (:id . 46)))@@@1@5@((:identifiers (:sid . :s2.227) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100554@unknown@formal@none@1@S@To examine the contribution of the different modules, we plotted the number of interactions predicted among all LR400 interactions (all interactions predicted using the full predictor that obtain a likelihood ratio of interaction greater than 400) as a function of the minimum likelihood ratio of individual modules (in panel A) or of combinations of modules (in panel B).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "examine") (:form . "examine") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "contribution") (:form . "contribution") (:end . 27)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 44)\n (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 52)\n (:start . 45) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 56) (:start . 54)\n (:id . 51))\n ((:tag . "VBD") (:stem . "plot") (:form . "plotted") (:end . 64)\n (:start . 57) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n (:id . 53))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 75)\n (:start . 69) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n (:id . 55))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 91)\n (:start . 79) (:id . 56))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 101)\n (:start . 92) (:id . 57))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 107)\n (:start . 102) (:id . 58))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 111) (:start . 108)\n (:id . 59))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 117)\n (:start . 112) (:id . 60))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 130)\n (:start . 118) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 132) (:start . 131)\n (:id . 62))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 135) (:start . 132)\n (:id . 63))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 148)\n (:start . 136) (:id . 64))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 158)\n (:start . 149) (:id . 65))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 164) (:start . 159)\n (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n (:id . 67))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 173) (:start . 169)\n (:id . 68))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 183)\n (:start . 174) (:id . 69))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 188) (:start . 184)\n (:id . 70))\n ((:tag . "VBP") (:stem . "obtain") (:form . "obtain") (:end . 195)\n (:start . 189) (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 197) (:start . 196)\n (:id . 72))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 208)\n (:start . 198) (:id . 73))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 214)\n (:start . 209) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 217) (:start . 215)\n (:id . 75))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 229)\n (:start . 218) (:id . 76))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 237)\n (:start . 230) (:id . 77))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 242) (:start . 238)\n (:id . 78))\n ((:tag . "CD") (:stem . "400") (:form . "400") (:end . 246) (:start . 243)\n (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 247) (:start . 246)\n (:id . 80))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 250) (:start . 248)\n (:id . 81))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 252) (:start . 251)\n (:id . 82))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 261)\n (:start . 253) (:id . 83))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 264) (:start . 262)\n (:id . 84))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 268) (:start . 265)\n (:id . 85))\n ((:tag . "JJ") (:stem . "minimum") (:form . "minimum") (:end . 276)\n (:start . 269) (:id . 86))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 287)\n (:start . 277) (:id . 87))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 293)\n (:start . 288) (:id . 88))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 296) (:start . 294)\n (:id . 89))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 307)\n (:start . 297) (:id . 90))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 315)\n (:start . 308) (:id . 91))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 317) (:start . 316)\n (:id . 92))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 319) (:start . 317)\n (:id . 93))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 325)\n (:start . 320) (:id . 94))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 327) (:start . 326)\n (:id . 95))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 328) (:start . 327)\n (:id . 96))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 331) (:start . 329)\n (:id . 97))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 334) (:start . 332)\n (:id . 98))\n ((:tag . "NNS") (:stem . "combination") (:form . "combinations") (:end . 347)\n (:start . 335) (:id . 99))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 350) (:start . 348)\n (:id . 100))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 358)\n (:start . 351) (:id . 101))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 360) (:start . 359)\n (:id . 102))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 362) (:start . 360)\n (:id . 103))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 368)\n (:start . 363) (:id . 104))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 370) (:start . 369)\n (:id . 105))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 371) (:start . 370)\n (:id . 106))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 372) (:start . 371)\n (:id . 107)))@@@1@66@((:identifiers (:sid . :s2.228) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100555@unknown@formal@none@1@S@In the case of combinations of modules (panel B), the minimum likelihood ratio is the product of the likelihood ratios of the modules considered.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 45))\n ((:tag . "NNS") (:stem . "combination") (:form . "combinations") (:end . 27)\n (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 47))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 38)\n (:start . 31) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n (:id . 49))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 45) (:start . 40)\n (:id . 50))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 47) (:start . 46)\n (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 48) (:start . 47)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n (:id . 54))\n ((:tag . "JJ") (:stem . "minimum") (:form . "minimum") (:end . 61)\n (:start . 54) (:id . 55))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 72)\n (:start . 62) (:id . 56))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 78) (:start . 73)\n (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 81) (:start . 79)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n (:id . 59))\n ((:tag . "NN") (:stem . "product") (:form . "product") (:end . 93)\n (:start . 86) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n (:id . 62))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 111)\n (:start . 101) (:id . 63))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 118)\n (:start . 112) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n (:id . 66))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 133)\n (:start . 126) (:id . 67))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 144)\n (:start . 134) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s2.229) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100556@unknown@formal@none@1@S@Thus for example, the product of the expression and orthology ratios is greater than 1 for almost 20000 LR400 interactions and greater than 10 for approximately 10000 LR400 interactions (dark blue diamonds in panel B).@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 16)\n (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "NN") (:stem . "product") (:form . "product") (:end . 29)\n (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 47)\n (:start . 37) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n (:id . 51))\n ((:tag . "JJ") (:stem . "orthology") (:form . "orthology") (:end . 61)\n (:start . 52) (:id . 52))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 68)\n (:start . 62) (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 71) (:start . 69)\n (:id . 54))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 79)\n (:start . 72) (:id . 55))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 84) (:start . 80)\n (:id . 56))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 86) (:start . 85)\n (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 90) (:start . 87)\n (:id . 58))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 97)\n (:start . 91) (:id . 59))\n ((:tag . "CD") (:stem . "20000") (:form . "20000") (:end . 103) (:start . 98)\n (:id . 60))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 109)\n (:start . 104) (:id . 61))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 122)\n (:start . 110) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n (:id . 63))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 134)\n (:start . 127) (:id . 64))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 139) (:start . 135)\n (:id . 65))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 142) (:start . 140)\n (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 146) (:start . 143)\n (:id . 67))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 160) (:start . 147) (:id . 68))\n ((:tag . "CD") (:stem . "10000") (:form . "10000") (:end . 166)\n (:start . 161) (:id . 69))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 172)\n (:start . 167) (:id . 70))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 185)\n (:start . 173) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 187) (:start . 186)\n (:id . 72))\n ((:tag . "JJ") (:stem . "dark") (:form . "dark") (:end . 191) (:start . 187)\n (:id . 73))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 196) (:start . 192)\n (:id . 74))\n ((:tag . "NNS") (:stem . "diamond") (:form . "diamonds") (:end . 205)\n (:start . 197) (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 208) (:start . 206)\n (:id . 76))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 214)\n (:start . 209) (:id . 77))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 216) (:start . 215)\n (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 217) (:start . 216)\n (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n (:id . 80)))@@@1@39@((:identifiers (:sid . :s2.230) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100557@unknown@formal@none@1@S@E: Expression module, O: Orthology module, C: Combined module, T: Transitive module.@(((:tag . "NN") (:stem . "e") (:form . "E") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 2) (:start . 1) (:id . 43))\n ((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 13)\n (:start . 3) (:id . 44))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 20)\n (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n (:id . 46))\n ((:tag . "NNP") (:stem . "O") (:form . "O") (:end . 23) (:start . 22)\n (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 24) (:start . 23)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Orthology") (:form . "Orthology") (:end . 34)\n (:start . 25) (:id . 49))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 41)\n (:start . 35) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n (:id . 51))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 44) (:start . 43)\n (:id . 52))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 45) (:start . 44)\n (:id . 53))\n ((:tag . "VBN") (:stem . "combine") (:form . "Combined") (:end . 54)\n (:start . 46) (:id . 54))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 61)\n (:start . 55) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n (:id . 56))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 64) (:start . 63)\n (:id . 57))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 65) (:start . 64)\n (:id . 58))\n ((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 76)\n (:start . 66) (:id . 59))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 83)\n (:start . 77) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s2.231) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100558@unknown@formal@none@1@S@Figure 4B summarizes the contributions of different combinations of modules.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "4b") (:form . "4B") (:end . 9) (:start . 7)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "summarize") (:form . "summarizes") (:end . 20)\n (:start . 10) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n (:id . 45))\n ((:tag . "NNS") (:stem . "contribution") (:form . "contributions")\n (:end . 38) (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n (:id . 47))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 51)\n (:start . 42) (:id . 48))\n ((:tag . "NNS") (:stem . "combination") (:form . "combinations") (:end . 64)\n (:start . 52) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n (:id . 50))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 75)\n (:start . 68) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s2.232) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100560@unknown@formal@none@1@S@They alone can predict approximately 27000 of the 37606 interactions of the LR400 dataset.@(((:tag . "PRP") (:stem . "they") (:form . "They") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "VB") (:stem . "predict") (:form . "predict") (:end . 22)\n (:start . 15) (:id . 45))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 36) (:start . 23) (:id . 46))\n ((:tag . "CD") (:stem . "27000") (:form . "27000") (:end . 42) (:start . 37)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "CD") (:stem . "37606") (:form . "37606") (:end . 55) (:start . 50)\n (:id . 50))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 68)\n (:start . 56) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n (:id . 53))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 81) (:start . 76)\n (:id . 54))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 89)\n (:start . 82) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.234) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100561@unknown@formal@none@1@S@When they are both present, regardless of which other modules are also present, they predict over 70% of the LR400 interactions.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 18) (:start . 14)\n (:id . 45))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 26)\n (:start . 19) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n (:id . 47))\n ((:tag . "RB") (:stem . "regardless") (:form . "regardless") (:end . 38)\n (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n (:id . 49))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 47) (:start . 42)\n (:id . 50))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 53) (:start . 48)\n (:id . 51))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 61)\n (:start . 54) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 65) (:start . 62)\n (:id . 53))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 70) (:start . 66)\n (:id . 54))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 78)\n (:start . 71) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n (:id . 56))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 84) (:start . 80)\n (:id . 57))\n ((:tag . "VBP") (:stem . "predict") (:form . "predict") (:end . 92)\n (:start . 85) (:id . 58))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 97) (:start . 93)\n (:id . 59))\n ((:tag . "CD") (:stem . "70") (:form . "70") (:end . 100) (:start . 98)\n (:id . 60))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 101) (:start . 100)\n (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n (:id . 63))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 114)\n (:start . 109) (:id . 64))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 127)\n (:start . 115) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s2.235) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100562@unknown@formal@none@1@S@When either of these two modules is absent, fewer than 12500 interactions are predicted.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "either") (:form . "either") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 24) (:start . 21)\n (:id . 46))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 32)\n (:start . 25) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 35) (:start . 33)\n (:id . 48))\n ((:tag . "JJ") (:stem . "absent") (:form . "absent") (:end . 42)\n (:start . 36) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n (:id . 50))\n ((:tag . "JJR") (:stem . "few") (:form . "fewer") (:end . 49) (:start . 44)\n (:id . 51))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 54) (:start . 50)\n (:id . 52))\n ((:tag . "CD") (:stem . "12500") (:form . "12500") (:end . 60) (:start . 55)\n (:id . 53))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 73)\n (:start . 61) (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 77) (:start . 74)\n (:id . 55))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 87)\n (:start . 78) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n (:id . 57)))@@@1@16@((:ncues ((:id . :x2.236.1) (:span 36 42)))\n (:nscopes ((:id . :x2.236.1) (:span 5 42)))\n (:identifiers (:sid . :s2.236) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100563@unknown@formal@none@1@S@In contrast, the two remaining modules (Expression and Orthology) can predict approximately 5000 interactions together.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 20) (:start . 17)\n (:id . 46))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 30)\n (:start . 21) (:id . 47))\n ((:tag . 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"interactions") (:end . 109)\n (:start . 97) (:id . 58))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 118)\n (:start . 110) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s2.237) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100564@unknown@formal@none@1@S@This is interesting as many of the publicly available predicted interaction datasets mentioned in the Background section use mainly orthology transfer from model organisms to identify interactions.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "JJ") (:stem . "interesting") (:form . "interesting") (:end . 19)\n (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . 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"in") (:end . 97) (:start . 95)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n (:id . 56))\n ((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 112)\n (:start . 102) (:id . 57))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 120)\n (:start . 113) (:id . 58))\n ((:tag . "VBP") (:stem . "use") (:form . "use") (:end . 124) (:start . 121)\n (:id . 59))\n ((:tag . "RB") (:stem . "mainly") (:form . "mainly") (:end . 131)\n (:start . 125) (:id . 60))\n ((:tag . "JJ") (:stem . "orthology") (:form . "orthology") (:end . 141)\n (:start . 132) (:id . 61))\n ((:tag . "NN") (:stem . "transfer") (:form . "transfer") (:end . 150)\n (:start . 142) (:id . 62))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 155) (:start . 151)\n (:id . 63))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 161)\n (:start . 156) (:id . 64))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 171)\n (:start . 162) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 174) (:start . 172)\n (:id . 66))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 183)\n (:start . 175) (:id . 67))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 196)\n (:start . 184) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s2.238) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100565@unknown@formal@none@1@S@As the majority of the LR400 interactions are derived from the Combined and Transitive modules, it is possible that the method is identifying a large subset of interactions that are not common to previous human protein interaction datasets.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . 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"common") (:end . 192)\n (:start . 186) (:id . 74))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 195) (:start . 193)\n (:id . 75))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 204)\n (:start . 196) (:id . 76))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 210)\n (:start . 205) (:id . 77))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 218)\n (:start . 211) (:id . 78))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 230)\n (:start . 219) (:id . 79))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 239)\n (:start . 231) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 240) (:start . 239)\n (:id . 81)))@@@1@40@((:hcues ((:id . :x2.239.2) (:span 102 110)))\n (:ncues ((:id . :x2.239.1) (:span 182 185)))\n (:hscopes ((:id . :x2.239.2) (:span 102 239)))\n (:nscopes ((:id . :x2.239.1) (:span 182 239)))\n (:identifiers (:sid . :s2.239) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100566@unknown@formal@none@1@S@This is discussed further in the next section.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "VBN") (:stem . "discuss") (:form . "discussed") (:end . 17)\n (:start . 8) (:id . 44))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 25)\n (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n (:id . 47))\n ((:tag . "JJ") (:stem . "next") (:form . "next") (:end . 37) (:start . 33)\n (:id . 48))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 45)\n (:start . 38) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 46) (:start . 45)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s2.240) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100567@unknown@formal@none@1@S@The curve representing the full predictor (consisting of the Expression, Orthology, Combined and Transitive modules) is also represented in Figure 4B (the dark green squares).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "curve") (:form . "curve") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "VBG") (:stem . "represent") (:form . "representing") (:end . 22)\n (:start . 10) (:id . 44))\n ((:tag . "DT") (:stem . 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"4B") (:end . 149) (:start . 147)\n (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 151) (:start . 150)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n (:id . 68))\n ((:tag . "JJ") (:stem . "dark") (:form . "dark") (:end . 159) (:start . 155)\n (:id . 69))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 165)\n (:start . 160) (:id . 70))\n ((:tag . "NNS") (:stem . "square") (:form . "squares") (:end . 173)\n (:start . 166) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 174) (:start . 173)\n (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s2.241) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100568@unknown@formal@none@1@S@By definition, it predicts all proteins in the LR400 dataset at likelihood ratios equal to or above 400 (this is how the LR400 dataset was generated).@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "definition") (:form . "definition") (:end . 13)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 44))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 17) (:start . 15)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "predict") (:form . "predicts") (:end . 26)\n (:start . 18) (:id . 46))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 30) (:start . 27)\n (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . 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"DT") (:stem . "an") (:form . "an") (:end . 146) (:start . 144)\n (:id . 67))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 156)\n (:start . 147) (:id . 68))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 166)\n (:start . 157) (:id . 69))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 171) (:start . 167)\n (:id . 70))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 177)\n (:start . 172) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 180) (:start . 178)\n (:id . 72))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 182) (:start . 181)\n (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 183) (:start . 182)\n (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s2.244) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100571@unknown@formal@none@1@S@At a likelihood ratio of 4000, approximately 11000 interactions are predicted and at a likelihood ratio of 8000, approximately 6500 interactions are predicted.@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 15)\n (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 21) (:start . 16)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n (:id . 46))\n ((:tag . "CD") (:stem . "4000") (:form . "4000") (:end . 29) (:start . 25)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . 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(:end . 159) (:start . 158)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.245) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100572@unknown@formal@none@1@S@We verified that the increasing estimated posterior odds ratios translated into better predictive value.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "verify") (:form . "verified") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 31)\n (:start . 21) (:id . 46))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 41)\n (:start . 32) (:id . 47))\n ((:tag . "JJ") (:stem . "posterior") (:form . 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(:end . 104) (:start . 103)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.246) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100573@unknown@formal@none@1@S@Figure 5 shows the true positive rate versus false positive rate for different posterior odds ratios as measured by five-fold cross validation.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 8) (:start . 7)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 32)\n (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "rate") (:form . 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(:end . 143) (:start . 142)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.247) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100574@unknown@formal@none@1@S@As the posterior odds ratio increases, the false positive rate decreases and the relative proportion of true positives increases when compared to the proportion of false positives.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 16)\n (:start . 7) (:id . 44))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 21) (:start . 17)\n (:id . 45))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 27) (:start . 22)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "increase") (:form . "increases") (:end . 37)\n (:start . 28) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n (:id . 49))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 48) (:start . 43)\n (:id . 50))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 57)\n (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 62) (:start . 58)\n (:id . 52))\n ((:tag . "NNS") (:stem . "decrease") (:form . "decreases") (:end . 72)\n (:start . 63) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n (:id . 55))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 89)\n (:start . 81) (:id . 56))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 100)\n (:start . 90) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . 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"false") (:end . 169)\n (:start . 164) (:id . 68))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 179)\n (:start . 170) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s2.248) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100575@unknown@formal@none@1@S@Accordingly, subsets of very high quality predictions may be generated by choosing a suitably high posterior odds ratio threshold.@(((:tag . "RB") (:stem . "accordingly") (:form . "Accordingly") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 43))\n ((:tag . "NNS") (:stem . "subset") (:form . "subsets") (:end . 20)\n (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 45))\n ((:tag . "RB") (:stem . "very") (:form . 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"JJ") (:stem . "high") (:form . "high") (:end . 98) (:start . 94)\n (:id . 57))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 108)\n (:start . 99) (:id . 58))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 113) (:start . 109)\n (:id . 59))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 119)\n (:start . 114) (:id . 60))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 129)\n (:start . 120) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n (:id . 62)))@@@1@21@((:hcues ((:id . :x2.249.1) (:span 54 57)))\n (:hscopes ((:id . :x2.249.1) (:span 13 129)))\n (:identifiers (:sid . :s2.249) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100576@unknown@formal@none@1@S@True positive rate versus false positive rate for different estimated posterior odds ratios@(((:tag . "JJ") (:stem . "true") (:form . "True") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "IN") (:stem . "versus") (:form . "versus") (:end . 25)\n (:start . 19) (:id . 45))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 31) (:start . 26)\n (:id . 46))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 40)\n (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 45) (:start . 41)\n (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 59)\n (:start . 50) (:id . 50))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 69)\n (:start . 60) (:id . 51))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 79)\n (:start . 70) (:id . 52))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 84) (:start . 80)\n (:id . 53))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 91)\n (:start . 85) (:id . 54)))@@@1@13@((:identifiers (:sid . :s2.250) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|FigureLegend|)))@oe@9-2-2011 5100577@unknown@formal@none@1@S@True positive rate versus false positive rate for different estimated posterior odds ratios.@(((:tag . "JJ") (:stem . "true") (:form . "True") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "IN") (:stem . "versus") (:form . "versus") (:end . 25)\n (:start . 19) (:id . 45))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 31) (:start . 26)\n (:id . 46))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 40)\n (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 45) (:start . 41)\n (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 59)\n (:start . 50) (:id . 50))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 69)\n (:start . 60) (:id . 51))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 79)\n (:start . 70) (:id . 52))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 84) (:start . 80)\n (:id . 53))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 91)\n (:start . 85) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.251) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100578@unknown@formal@none@1@S@The true positive rate (TPR) versus false positive rate (FPR) is plotted for different values of the posterior odds ratio estimated for the dataset by five-fold cross-validation.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 17)\n (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 22) (:start . 18)\n (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 24) (:start . 23)\n (:id . 46))\n ((:tag . "NNP") (:stem . "TPR") (:form . "TPR") (:end . 27) (:start . 24)\n (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 28) (:start . 27)\n (:id . 48))\n ((:tag . "IN") (:stem . "versus") (:form . "versus") (:end . 35)\n (:start . 29) (:id . 49))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 41) (:start . 36)\n (:id . 50))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 50)\n (:start . 42) (:id . 51))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 55) (:start . 51)\n (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n (:id . 53))\n ((:tag . "NNP") (:stem . "FPR") (:form . "FPR") (:end . 60) (:start . 57)\n (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 61) (:start . 60)\n (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 64) (:start . 62)\n (:id . 56))\n ((:tag . "VBN") (:stem . "plot") (:form . "plotted") (:end . 72)\n (:start . 65) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 76) (:start . 73)\n (:id . 58))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 86)\n (:start . 77) (:id . 59))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 93)\n (:start . 87) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n (:id . 62))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 110)\n (:start . 101) (:id . 63))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 115) (:start . 111)\n (:id . 64))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 121)\n (:start . 116) (:id . 65))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 131)\n (:start . 122) (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 135) (:start . 132)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n (:id . 68))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 147)\n (:start . 140) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 150) (:start . 148)\n (:id . 70))\n ((:tag . "JJ") (:stem . "five-fold") (:form . "five-fold") (:end . 160)\n (:start . 151) (:id . 71))\n ((:tag . "NN") (:stem . "cross-validation") (:form . "cross-validation")\n (:end . 177) (:start . 161) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s2.252) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100580@unknown@formal@none@1@S@Thus, higher quality datasets can be generated by requiring higher posterior odds ratios.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 12) (:start . 6)\n (:id . 44))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 20)\n (:start . 13) (:id . 45))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 29)\n (:start . 21) (:id . 46))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 33) (:start . 30)\n (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 36) (:start . 34)\n (:id . 48))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 46)\n (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 49) (:start . 47)\n (:id . 50))\n ((:tag . "VBG") (:stem . "require") (:form . "requiring") (:end . 59)\n (:start . 50) (:id . 51))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 66) (:start . 60)\n (:id . 52))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 76)\n (:start . 67) (:id . 53))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 81) (:start . 77)\n (:id . 54))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 88)\n (:start . 82) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.254) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100581@unknown@formal@none@1@S@The TPR is calculated as the number of true positives predicted divided by the total number of positives in the test set.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "tpr") (:form . "TPR") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 10) (:start . 8)\n (:id . 44))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 21)\n (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 24) (:start . 22)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n (:id . 47))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 35)\n (:start . 29) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n (:id . 49))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 43) (:start . 39)\n (:id . 50))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 53)\n (:start . 44) (:id . 51))\n ((:tag . "VBD") (:stem . "predict") (:form . "predicted") (:end . 63)\n (:start . 54) (:id . 52))\n ((:tag . "VBN") (:stem . "divide") (:form . "divided") (:end . 71)\n (:start . 64) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 74) (:start . 72)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n (:id . 55))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 84) (:start . 79)\n (:id . 56))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 91)\n (:start . 85) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n (:id . 58))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 104)\n (:start . 95) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n (:id . 61))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 116) (:start . 112)\n (:id . 62))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 120) (:start . 117)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.255) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100582@unknown@formal@none@1@S@The FPR is calculated as the number of false positives predicted divided by the total number of negatives in the test set.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "fpr") (:form . "FPR") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 10) (:start . 8)\n (:id . 44))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 21)\n (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 24) (:start . 22)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n (:id . 47))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 35)\n (:start . 29) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n (:id . 49))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 44) (:start . 39)\n (:id . 50))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 54)\n (:start . 45) (:id . 51))\n ((:tag . "VBD") (:stem . "predict") (:form . "predicted") (:end . 64)\n (:start . 55) (:id . 52))\n ((:tag . "VBN") (:stem . "divide") (:form . "divided") (:end . 72)\n (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 75) (:start . 73)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n (:id . 55))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 85) (:start . 80)\n (:id . 56))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 92)\n (:start . 86) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n (:id . 58))\n ((:tag . "NNS") (:stem . "negative") (:form . "negatives") (:end . 105)\n (:start . 96) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n (:id . 61))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 117) (:start . 113)\n (:id . 62))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 121) (:start . 118)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.256) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100583@unknown@formal@none@1@S@Comparison to other interaction datasets@(((:tag . "NN") (:stem . "comparison") (:form . "Comparison") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 13) (:start . 11)\n (:id . 43))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 19) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 31)\n (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 40)\n (:start . 32) (:id . 46)))@@@1@5@((:identifiers (:sid . :s2.257) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100584@unknown@formal@none@1@S@The false positive rate (FPR) of our predictor was estimated by the method of D'Haeseleer and Church 1855 and used to compare it to other prediction datasets.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 18)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 23) (:start . 19)\n (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n (:id . 46))\n ((:tag . "NNP") (:stem . "FPR") (:form . "FPR") (:end . 28) (:start . 25)\n (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 29) (:start . 28)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n (:id . 49))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 36) (:start . 33)\n (:id . 50))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 46)\n (:start . 37) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 50) (:start . 47)\n (:id . 52))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 60)\n (:start . 51) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 63) (:start . 61)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n (:id . 55))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 74)\n (:start . 68) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n (:id . 57))\n ((:tag . "NNP") (:stem . "D'Haeseleer") (:form . "D’Haeseleer") (:end . 89)\n (:start . 78) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n (:id . 59))\n ((:tag . "NNP") (:stem . "Church") (:form . "Church") (:end . 100)\n (:start . 94) (:id . 60))\n ((:tag . "CD") (:stem . "1855") (:form . "1855") (:end . 105) (:start . 101)\n (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n (:id . 62))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 114) (:start . 110)\n (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 117) (:start . 115)\n (:id . 64))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 125)\n (:start . 118) (:id . 65))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 128) (:start . 126)\n (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 131) (:start . 129)\n (:id . 67))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 137)\n (:start . 132) (:id . 68))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 148)\n (:start . 138) (:id . 69))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 157)\n (:start . 149) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s2.258) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100585@unknown@formal@none@1@S@The Ramani interaction dataset that was automatically extracted from the literature 16 as well as all new interactions present in the October 2006 version of the manually curated HPRD database 15 (but none of the interactions also present in earlier versions of the HPRD which were used to train our predictor) were taken as reference datasets.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Ramani") (:form . "Ramani") (:end . 10)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 22)\n (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 30)\n (:start . 23) (:id . 45))\n ((:tag . "WDT") (:stem . 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"which") (:end . 276)\n (:start . 271) (:id . 87))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 281) (:start . 277)\n (:id . 88))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 286) (:start . 282)\n (:id . 89))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 289) (:start . 287)\n (:id . 90))\n ((:tag . "VB") (:stem . "train") (:form . "train") (:end . 295)\n (:start . 290) (:id . 91))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 299) (:start . 296)\n (:id . 92))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 309)\n (:start . 300) (:id . 93))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 310) (:start . 309)\n (:id . 94))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 315) (:start . 311)\n (:id . 95))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 321)\n (:start . 316) (:id . 96))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 324) (:start . 322)\n (:id . 97))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 334)\n (:start . 325) (:id . 98))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 343)\n (:start . 335) (:id . 99))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 344) (:start . 343)\n (:id . 100)))@@@1@59@((:ncues ((:id . :x2.259.1) (:span 201 205)))\n (:nscopes ((:id . :x2.259.1) (:span 201 343)))\n (:identifiers (:sid . :s2.259) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100586@unknown@formal@none@1@S@The D'Haeseleer and Church method compares two experimental datasets to a reference set and assumes that all intersections between the three datasets contain true positives.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "D'Haeseleer") (:form . "D’Haeseleer") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . 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"contain") (:end . 157)\n (:start . 150) (:id . 64))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 162) (:start . 158)\n (:id . 65))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 172)\n (:start . 163) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n (:id . 67)))@@@1@26@((:hcues ((:id . :x2.260.1) (:span 92 99)))\n (:hscopes ((:id . :x2.260.1) (:span 92 172)))\n (:identifiers (:sid . :s2.260) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100587@unknown@formal@none@1@S@It is thus possible to estimate the number of true positives predicted by an experimental dataset by comparing the number of interactions present in the different intersections of the two experimental methods and the reference dataset (for details, see 1855).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . 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"methods") (:end . 208)\n (:start . 201) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 212) (:start . 209)\n (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 216) (:start . 213)\n (:id . 75))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 226)\n (:start . 217) (:id . 76))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 234)\n (:start . 227) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 236) (:start . 235)\n (:id . 78))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 239) (:start . 236)\n (:id . 79))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 247)\n (:start . 240) (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 248) (:start . 247)\n (:id . 81))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 252) (:start . 249)\n (:id . 82))\n ((:tag . "CD") (:stem . "1855") (:form . "1855") (:end . 257) (:start . 253)\n (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 258) (:start . 257)\n (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 259) (:start . 258)\n (:id . 85)))@@@1@44@((:hcues ((:id . :x2.261.1) (:span 11 19)))\n (:hscopes ((:id . :x2.261.1) (:span 11 234)))\n (:identifiers (:sid . :s2.261) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100588@unknown@formal@none@1@S@Here, we compare three human interaction prediction datasets: the Rhodes probabilistic dataset 46, the Lehner orthology-derived dataset 36 and the most accurate of our predictors (the LR400 subset of the predictor considering the Expression, Orthology, Combined and Transitive modules).@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . 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"average") (:end . 224)\n (:start . 217) (:id . 86))\n ((:tag . "JJ") (:stem . "false-positive") (:form . "false-positive")\n (:end . 239) (:start . 225) (:id . 87))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 244) (:start . 240)\n (:id . 88))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 247) (:start . 245)\n (:id . 89))\n ((:tag . "CD") (:stem . "90") (:form . "90") (:end . 250) (:start . 248)\n (:id . 90))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 251) (:start . 250)\n (:id . 91))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 261)\n (:start . 252) (:id . 92))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 265) (:start . 262)\n (:id . 93))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 270) (:start . 266)\n (:id . 94))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 280)\n (:start . 271) (:id . 95))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 286)\n (:start . 281) (:id . 96))\n ((:tag . "JJ") (:stem . "high-throughput") (:form . "high-throughput")\n (:end . 302) (:start . 287) (:id . 97))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 315)\n (:start . 303) (:id . 98))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 319) (:start . 316)\n (:id . 99))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 330)\n (:start . 320) (:id . 100))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 342)\n (:start . 331) (:id . 101))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 351)\n (:start . 343) (:id . 102))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 354) (:start . 352)\n (:id . 103))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 355) (:start . 354)\n (:id . 104)))@@@1@63@((:identifiers (:sid . :s2.265) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100592@unknown@formal@none@1@S@It should be noted that the Rhodes, Lehner and Ramani datasets annotate interactions as a relationship between human genes and not their protein products directly.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 12) (:start . 10)\n (:id . 44))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Rhodes") (:form . "Rhodes") (:end . 34)\n (:start . 28) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n (:id . 49))\n ((:tag . "NNP") (:stem . "Lehner") (:form . "Lehner") (:end . 42)\n (:start . 36) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n (:id . 51))\n ((:tag . "NNP") (:stem . "Ramani") (:form . "Ramani") (:end . 53)\n (:start . 47) (:id . 52))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 62)\n (:start . 54) (:id . 53))\n ((:tag . "VBP") (:stem . "annotate") (:form . "annotate") (:end . 71)\n (:start . 63) (:id . 54))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 84)\n (:start . 72) (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 87) (:start . 85)\n (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 89) (:start . 88)\n (:id . 57))\n ((:tag . "NN") (:stem . "relationship") (:form . "relationship") (:end . 102)\n (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 110)\n (:start . 103) (:id . 59))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 116)\n (:start . 111) (:id . 60))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 122)\n (:start . 117) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n (:id . 62))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 130) (:start . 127)\n (:id . 63))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 136)\n (:start . 131) (:id . 64))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 144)\n (:start . 137) (:id . 65))\n ((:tag . "NNS") (:stem . "product") (:form . "products") (:end . 153)\n (:start . 145) (:id . 66))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 162)\n (:start . 154) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n (:id . 68)))@@@1@27@((:ncues ((:id . :x2.266.1) (:span 127 130)))\n (:nscopes ((:id . :x2.266.1) (:span 127 162)))\n (:identifiers (:sid . :s2.266) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100593@unknown@formal@none@1@S@However, not all proteins encoded by a single gene will necessarily interact with all protein products encoded by a second gene, even if one such protein pair does.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 25)\n (:start . 17) (:id . 46))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 33)\n (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 36) (:start . 34)\n (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n (:id . 49))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 45)\n (:start . 39) (:id . 50))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 50) (:start . 46)\n (:id . 51))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 55) (:start . 51)\n (:id . 52))\n ((:tag . "RB") (:stem . "necessarily") (:form . "necessarily") (:end . 67)\n (:start . 56) (:id . 53))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 76)\n (:start . 68) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 81) (:start . 77)\n (:id . 55))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 85) (:start . 82)\n (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 93)\n (:start . 86) (:id . 57))\n ((:tag . "NNS") (:stem . "product") (:form . "products") (:end . 102)\n (:start . 94) (:id . 58))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 110)\n (:start . 103) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 113) (:start . 111)\n (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 115) (:start . 114)\n (:id . 61))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 122)\n (:start . 116) (:id . 62))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 127) (:start . 123)\n (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n (:id . 64))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 133) (:start . 129)\n (:id . 65))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 136) (:start . 134)\n (:id . 66))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 140) (:start . 137)\n (:id . 67))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 145) (:start . 141)\n (:id . 68))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 153)\n (:start . 146) (:id . 69))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 158) (:start . 154)\n (:id . 70))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 163) (:start . 159)\n (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n (:id . 72)))@@@1@31@((:identifiers (:sid . :s2.267) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100594@unknown@formal@none@1@S@This is why we describe interactions as a relationship between two proteins, allowing for a more precise description of the interaction.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "WRB") (:stem . "why") (:form . "why") (:end . 11) (:start . 8)\n (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 14) (:start . 12)\n (:id . 45))\n ((:tag . "VBP") (:stem . "describe") (:form . "describe") (:end . 23)\n (:start . 15) (:id . 46))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 36)\n (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 39) (:start . 37)\n (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 41) (:start . 40)\n (:id . 49))\n ((:tag . "NN") (:stem . "relationship") (:form . "relationship") (:end . 54)\n (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 62)\n (:start . 55) (:id . 51))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 66) (:start . 63)\n (:id . 52))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 75)\n (:start . 67) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n (:id . 54))\n ((:tag . "VBG") (:stem . "allow") (:form . "allowing") (:end . 85)\n (:start . 77) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 89) (:start . 86)\n (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 91) (:start . 90)\n (:id . 57))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 96) (:start . 92)\n (:id . 58))\n ((:tag . "JJ") (:stem . "precise") (:form . "precise") (:end . 104)\n (:start . 97) (:id . 59))\n ((:tag . "NN") (:stem . "description") (:form . "description") (:end . 116)\n (:start . 105) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n (:id . 62))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 135)\n (:start . 124) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.268) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100595@unknown@formal@none@1@S@To compare our predictions to these datasets, we consider that two genes interact if at least one of their respective protein products interact.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 26)\n (:start . 15) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 35) (:start . 30)\n (:id . 47))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 44)\n (:start . 36) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n (:id . 49))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 48) (:start . 46)\n (:id . 50))\n ((:tag . "VBP") (:stem . "consider") (:form . "consider") (:end . 57)\n (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 62) (:start . 58)\n (:id . 52))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 66) (:start . 63)\n (:id . 53))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 72) (:start . 67)\n (:id . 54))\n ((:tag . "VBP") (:stem . "interact") (:form . "interact") (:end . 81)\n (:start . 73) (:id . 55))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 84) (:start . 82)\n (:id . 56))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 87) (:start . 85)\n (:id . 57))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 93) (:start . 88)\n (:id . 58))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 97) (:start . 94)\n (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n (:id . 60))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 106)\n (:start . 101) (:id . 61))\n ((:tag . "JJ") (:stem . "respective") (:form . "respective") (:end . 117)\n (:start . 107) (:id . 62))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 125)\n (:start . 118) (:id . 63))\n ((:tag . "NNS") (:stem . "product") (:form . "products") (:end . 134)\n (:start . 126) (:id . 64))\n ((:tag . "VBP") (:stem . "interact") (:form . "interact") (:end . 143)\n (:start . 135) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x2.269.1) (:span 49 57)))\n (:hscopes ((:id . :x2.269.1) (:span 49 143)))\n (:identifiers (:sid . :s2.269) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100596@unknown@formal@none@1@S@Comparison to other interaction datasets@(((:tag . "NN") (:stem . "comparison") (:form . "Comparison") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 13) (:start . 11)\n (:id . 43))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 19) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 31)\n (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 40)\n (:start . 32) (:id . 46)))@@@1@5@((:identifiers (:sid . :s2.270) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|FigureLegend|)))@oe@9-2-2011 5100597@unknown@formal@none@1@S@Comparison to other interaction datasets.@(((:tag . "NN") (:stem . "comparison") (:form . "Comparison") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 13) (:start . 11)\n (:id . 43))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 19) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 31)\n (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 40)\n (:start . 32) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 41) (:start . 40)\n (:id . 47)))@@@1@6@((:identifiers (:sid . :s2.271) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100598@unknown@formal@none@1@S@The false positive rates shown in panel A were estimated for the LR400 dataset as well as the Rhodes [46] and Lehner [36] predictions using the method described in [18, 55] by comparing them two-by-two to a reference dataset.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 18)\n (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 24) (:start . 19)\n (:id . 45))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 30) (:start . 25)\n (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n (:id . 47))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 39) (:start . 34)\n (:id . 48))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 41) (:start . 40)\n (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 46) (:start . 42)\n (:id . 50))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 56)\n (:start . 47) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 60) (:start . 57)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n (:id . 53))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 70) (:start . 65)\n (:id . 54))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 78)\n (:start . 71) (:id . 55))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n (:id . 56))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 86) (:start . 82)\n (:id . 57))\n ((:tag . "IN") (:stem . 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"which") (:end . 196)\n (:start . 191) (:id . 77))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 200) (:start . 197)\n (:id . 78))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 205) (:start . 201)\n (:id . 79))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 208) (:start . 206)\n (:id . 80))\n ((:tag . "VB") (:stem . "train") (:form . "train") (:end . 214)\n (:start . 209) (:id . 81))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 218) (:start . 215)\n (:id . 82))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 228)\n (:start . 219) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n (:id . 84)))@@@1@43@((:identifiers (:sid . :s2.274) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100601@unknown@formal@none@1@S@The Rhodes dataset was trained using an earlier version of the HPRD.@(((:tag . "DT") (:stem . 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(:end . 136) (:start . 135)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.276) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100603@unknown@formal@none@1@S@Both the Rhodes dataset and our LR400 dataset predict interactions involving many proteins that are not even present in their positive training set (the HPRD).@(((:tag . "CC") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Rhodes") (:form . "Rhodes") (:end . 15)\n (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 23)\n (:start . 16) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 27) (:start . 24)\n (:id . 46))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 31) (:start . 28)\n (:id . 47))\n ((:tag . "NN") (:stem . "lr400") (:form . 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"determine") (:end . 143)\n (:start . 134) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 147) (:start . 144)\n (:id . 68))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 152) (:start . 148)\n (:id . 69))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 159)\n (:start . 153) (:id . 70))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 165)\n (:start . 160) (:id . 71))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 178)\n (:start . 166) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n (:id . 73)))@@@1@32@((:hcues ((:id . :x2.279.1) (:span 153 159)) ((:id . :x2.279.2) (:span 71 79))\n ((:id . :x2.279.3) (:span 3 12)))\n (:hscopes ((:id . :x2.279.1) (:span 153 178))\n ((:id . :x2.279.2) (:span 71 178)) ((:id . :x2.279.3) (:span 3 178)))\n (:identifiers (:sid . :s2.279) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100606@unknown@formal@none@1@S@Another human interaction dataset has recently become available: the IntNetDB 56.@(((:tag . "DT") (:stem . "another") (:form . "Another") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 13) (:start . 8)\n (:id . 43))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 25)\n (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 33)\n (:start . 26) (:id . 45))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 37) (:start . 34)\n (:id . 46))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 46)\n (:start . 38) (:id . 47))\n ((:tag . "VBN") (:stem . "become") (:form . "become") (:end . 53)\n (:start . 47) (:id . 48))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 63)\n (:start . 54) (:id . 49))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 64) (:start . 63)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n (:id . 51))\n ((:tag . "NNP") (:stem . "IntNetDB") (:form . "IntNetDB") (:end . 77)\n (:start . 69) (:id . 52))\n ((:tag . "CD") (:stem . "56") (:form . "56") (:end . 80) (:start . 78)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s2.280) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100607@unknown@formal@none@1@S@It was generated by integrating seven different features (four of which involve transferring interactions or characteristics of protein pairs from model organisms to human) in a probabilistic framework.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 16)\n (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . "VBG") (:stem . "integrate") (:form . "integrating") (:end . 31)\n (:start . 20) (:id . 46))\n ((:tag . "CD") (:stem . "seven") (:form . "seven") (:end . 37) (:start . 32)\n (:id . 47))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 47)\n (:start . 38) (:id . 48))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 56)\n (:start . 48) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n (:id . 50))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 62) (:start . 58)\n (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 71) (:start . 66)\n (:id . 53))\n ((:tag . "VBP") (:stem . "involve") (:form . "involve") (:end . 79)\n (:start . 72) (:id . 54))\n ((:tag . "VBG") (:stem . "transfer") (:form . "transferring") (:end . 92)\n (:start . 80) (:id . 55))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 105)\n (:start . 93) (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . 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")") (:end . 172) (:start . 171)\n (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 175) (:start . 173)\n (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 177) (:start . 176)\n (:id . 69))\n ((:tag . "JJ") (:stem . "probabilistic") (:form . "probabilistic")\n (:end . 191) (:start . 178) (:id . 70))\n ((:tag . "NN") (:stem . "framework") (:form . "framework") (:end . 201)\n (:start . 192) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n (:id . 72)))@@@1@31@((:identifiers (:sid . :s2.281) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100608@unknown@formal@none@1@S@Interactions were predicted above a TP/FP ratio (number of true positives divided by the number of false positives in the test set) of 1.@(((:tag . "NNS") (:stem . "interaction") (:form . "Interactions") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n (:id . 43))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 27)\n (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 33) (:start . 28)\n (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 35) (:start . 34)\n (:id . 46))\n ((:tag . "NNP") (:stem . "TP/FP") (:form . "TP/FP") (:end . 41) (:start . 36)\n (:id . 47))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 47) (:start . 42)\n (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 49) (:start . 48)\n (:id . 49))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 55)\n (:start . 49) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n (:id . 51))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 63) (:start . 59)\n (:id . 52))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 73)\n (:start . 64) (:id . 53))\n ((:tag . "VBN") (:stem . "divide") (:form . "divided") (:end . 81)\n (:start . 74) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 84) (:start . 82)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n (:id . 56))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 95)\n (:start . 89) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n (:id . 58))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 104) (:start . 99)\n (:id . 59))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 114)\n (:start . 105) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 117) (:start . 115)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n (:id . 62))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 126) (:start . 122)\n (:id . 63))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 130) (:start . 127)\n (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 131) (:start . 130)\n (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 134) (:start . 132)\n (:id . 66))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 136) (:start . 135)\n (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s2.282) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100610@unknown@formal@none@1@S@We do not compare our predictions to this dataset because such a threshold of TP/FP > 1 does not correspond to a posterior odds threshold > 1.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 9) (:start . 6)\n (:id . 44))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 17)\n (:start . 10) (:id . 45))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 33)\n (:start . 22) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 36) (:start . 34)\n (:id . 48))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 41) (:start . 37)\n (:id . 49))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 49)\n (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 57)\n (:start . 50) (:id . 51))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 62) (:start . 58)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n (:id . 53))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 74)\n (:start . 65) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n (:id . 55))\n ((:tag . "NNP") (:stem . "TP/FP") (:form . "TP/FP") (:end . 83) (:start . 78)\n (:id . 56))\n ((:tag . "SYM") (:stem . ">") (:form . ">") (:end . 85) (:start . 84)\n (:id . 57))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 87) (:start . 86)\n (:id . 58))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 92) (:start . 88)\n (:id . 59))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 96) (:start . 93)\n (:id . 60))\n ((:tag . "VB") (:stem . "correspond") (:form . "correspond") (:end . 107)\n (:start . 97) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 112) (:start . 111)\n (:id . 63))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 122)\n (:start . 113) (:id . 64))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 127) (:start . 123)\n (:id . 65))\n ((:tag . "VBP") (:stem . "threshold") (:form . "threshold") (:end . 137)\n (:start . 128) (:id . 66))\n ((:tag . "SYM") (:stem . ">") (:form . ">") (:end . 139) (:start . 138)\n (:id . 67))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 141) (:start . 140)\n (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n (:id . 69)))@@@1@28@((:ncues ((:id . :x2.284.1) (:span 93 96)) ((:id . :x2.284.2) (:span 6 9)))\n (:nscopes ((:id . :x2.284.1) (:span 93 141))\n ((:id . :x2.284.2) (:span 6 49)))\n (:identifiers (:sid . :s2.284) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100611@unknown@formal@none@1@S@Depending on the positive-to-negative ratio used in the datasets, TP/FP > 1 might correspond to an average posterior odds ratio of 1.@(((:tag . "VBG") (:stem . "depend") (:form . "Depending") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 12) (:start . 10)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "positive-to-negative")\n (:form . "positive-to-negative") (:end . 37) (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 43) (:start . 38)\n (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 48) (:start . 44)\n (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n (:id . 49))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 64)\n (:start . 56) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n (:id . 51))\n ((:tag . "NNP") (:stem . "TP/FP") (:form . "TP/FP") (:end . 71) (:start . 66)\n (:id . 52))\n ((:tag . "SYM") (:stem . ">") (:form . ">") (:end . 73) (:start . 72)\n (:id . 53))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 75) (:start . 74)\n (:id . 54))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 81) (:start . 76)\n (:id . 55))\n ((:tag . "VB") (:stem . "correspond") (:form . "correspond") (:end . 92)\n (:start . 82) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 95) (:start . 93)\n (:id . 57))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 98) (:start . 96)\n (:id . 58))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 106)\n (:start . 99) (:id . 59))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 116)\n (:start . 107) (:id . 60))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 121) (:start . 117)\n (:id . 61))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 127)\n (:start . 122) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 130) (:start . 128)\n (:id . 63))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 132) (:start . 131)\n (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n (:id . 65)))@@@1@24@((:hcues ((:id . :x2.285.1) (:span 76 81)))\n (:hscopes ((:id . :x2.285.1) (:span 76 132)))\n (:identifiers (:sid . :s2.285) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100612@unknown@formal@none@1@S@In contrast, the average posterior odds ratio of our LR400 dataset is above 700.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 24)\n (:start . 17) (:id . 46))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 34)\n (:start . 25) (:id . 47))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 39) (:start . 35)\n (:id . 48))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 45) (:start . 40)\n (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n (:id . 50))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 52) (:start . 49)\n (:id . 51))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 58) (:start . 53)\n (:id . 52))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 66)\n (:start . 59) (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 69) (:start . 67)\n (:id . 54))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 75) (:start . 70)\n (:id . 55))\n ((:tag . "CD") (:stem . "700") (:form . "700") (:end . 79) (:start . 76)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s2.286) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100613@unknown@formal@none@1@S@In comparison, by using a threshold of TP/FP > 1 in our test set, we predict over 1 000 000 human interactions.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 13)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 17) (:start . 15)\n (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 23) (:start . 18)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 25) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 35)\n (:start . 26) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n (:id . 49))\n ((:tag . "NNP") (:stem . "TP/FP") (:form . "TP/FP") (:end . 44) (:start . 39)\n (:id . 50))\n ((:tag . "SYM") (:stem . ">") (:form . ">") (:end . 46) (:start . 45)\n (:id . 51))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 48) (:start . 47)\n (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n (:id . 53))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 55) (:start . 52)\n (:id . 54))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 60) (:start . 56)\n (:id . 55))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 64) (:start . 61)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n (:id . 57))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 68) (:start . 66)\n (:id . 58))\n ((:tag . "VBP") (:stem . "predict") (:form . "predict") (:end . 76)\n (:start . 69) (:id . 59))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 81) (:start . 77)\n (:id . 60))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 83) (:start . 82)\n (:id . 61))\n ((:tag . "CD") (:stem . "000") (:form . "000") (:end . 87) (:start . 84)\n (:id . 62))\n ((:tag . "CD") (:stem . "000") (:form . "000") (:end . 91) (:start . 88)\n (:id . 63))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 97) (:start . 92)\n (:id . 64))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 110)\n (:start . 98) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x2.287.1) (:span 69 76)))\n (:hscopes ((:id . :x2.287.1) (:span 69 110)))\n (:identifiers (:sid . :s2.287) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100614@unknown@formal@none@1@S@We do not believe that the quality of this large number of predictions is high enough to warrant their publication since the great majority of these protein pairs achieve a posterior odds ratio below 1.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 9) (:start . 6)\n (:id . 44))\n ((:tag . "VB") (:stem . "believe") (:form . "believe") (:end . 17)\n (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n (:id . 46))\n ((:tag . 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"enough") (:end . 85)\n (:start . 79) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n (:id . 58))\n ((:tag . "VB") (:stem . "warrant") (:form . "warrant") (:end . 96)\n (:start . 89) (:id . 59))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 102)\n (:start . 97) (:id . 60))\n ((:tag . "NN") (:stem . "publication") (:form . "publication") (:end . 114)\n (:start . 103) (:id . 61))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 120)\n (:start . 115) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n (:id . 63))\n ((:tag . "JJ") (:stem . "great") (:form . "great") (:end . 130)\n (:start . 125) (:id . 64))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 139)\n (:start . 131) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n (:id . 66))\n ((:tag . "DT") (:stem . "these") (:form . 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(:end . 202) (:start . 201)\n (:id . 77)))@@@1@36@((:hcues ((:id . :x2.288.1) (:span 10 17)))\n (:ncues ((:id . :x2.288.2) (:span 6 9)))\n (:hscopes ((:id . :x2.288.1) (:span 10 114)))\n (:nscopes ((:id . :x2.288.2) (:span 6 114)))\n (:identifiers (:sid . :s2.288) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100615@unknown@formal@none@1@S@Independent validation@(((:tag . "JJ") (:stem . "independent") (:form . "Independent") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "validation") (:form . "validation") (:end . 22)\n (:start . 12) (:id . 43)))@@@1@2@((:identifiers (:sid . :s2.289) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100616@unknown@formal@none@1@S@Although the overlap between the LR400 dataset and the HPRD-derived positive training set is below 10% as shown in Figure 6C, the proportion of interactions common to these two sets is not equally distributed for all posterior odds ratios of interaction values.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 43))\n ((:tag . "NN") (:stem . "overlap") (:form . "overlap") (:end . 20)\n (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 28)\n (:start . 21) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n (:id . 46))\n ((:tag . 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"for") (:end . 212) (:start . 209)\n (:id . 78))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 216) (:start . 213)\n (:id . 79))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 226)\n (:start . 217) (:id . 80))\n ((:tag . "VBZ") (:stem . "odd") (:form . "odds") (:end . 231) (:start . 227)\n (:id . 81))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 238)\n (:start . 232) (:id . 82))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 241) (:start . 239)\n (:id . 83))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 253)\n (:start . 242) (:id . 84))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 260)\n (:start . 254) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 261) (:start . 260)\n (:id . 86)))@@@1@45@((:ncues ((:id . :x2.290.1) (:span 185 188)))\n (:nscopes ((:id . :x2.290.1) (:span 185 260)))\n (:identifiers (:sid . :s2.290) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100617@unknown@formal@none@1@S@As shown in Figure 7, while less than 3% of the protein pairs predicted to interact at posterior odds ratios between 1 and 2 overlap with the HPRD dataset used for training, this value increases to over 50% for the highest scoring subsets of the LR400 dataset.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 18)\n (:start . 12) (:id . 45))\n ((:tag . "CD") (:stem . "7") (:form . 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"IN") (:stem . "of") (:form . "of") (:end . 241) (:start . 239)\n (:id . 89))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 245) (:start . 242)\n (:id . 90))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 251)\n (:start . 246) (:id . 91))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 259)\n (:start . 252) (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 260) (:start . 259)\n (:id . 93)))@@@1@52@((:identifiers (:sid . :s2.291) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100618@unknown@formal@none@1@S@These highest scoring predictions receive high likelihood ratios of interaction from all four predictive modules and represent the strongest examples of interaction as evaluated by our predictor.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "JJS") (:stem . "high") (:form . 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"interaction") (:end . 164)\n (:start . 153) (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 167) (:start . 165)\n (:id . 64))\n ((:tag . "VBN") (:stem . "evaluate") (:form . "evaluated") (:end . 177)\n (:start . 168) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 180) (:start . 178)\n (:id . 66))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 184) (:start . 181)\n (:id . 67))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 194)\n (:start . 185) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s2.292) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100620@unknown@formal@none@1@S@The highest scoring predictions in the LR400 dataset thus mainly represent interactions present in the HPRD dataset as well as interactions between proteins that have strong sequence identity to these known interacting pairs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 11) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 19)\n (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 31)\n (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . 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"strong") (:end . 173)\n (:start . 167) (:id . 67))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 182)\n (:start . 174) (:id . 68))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 191)\n (:start . 183) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 194) (:start . 192)\n (:id . 70))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 200)\n (:start . 195) (:id . 71))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 206)\n (:start . 201) (:id . 72))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 218)\n (:start . 207) (:id . 73))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 224)\n (:start . 219) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s2.294) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100621@unknown@formal@none@1@S@However, as the posterior odds ratio decreases, the overlap between the predictions and the HPRD-derived training set decreases.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n (:id . 45))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 25)\n (:start . 16) (:id . 46))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 30) (:start . 26)\n (:id . 47))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 36) (:start . 31)\n (:id . 48))\n ((:tag . "VBZ") (:stem . "decrease") (:form . "decreases") (:end . 46)\n (:start . 37) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n (:id . 51))\n ((:tag . "NN") (:stem . "overlap") (:form . "overlap") (:end . 59)\n (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 67)\n (:start . 60) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n (:id . 54))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 83)\n (:start . 72) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n (:id . 57))\n ((:tag . "JJ") (:stem . "hprd-derived") (:form . "HPRD-derived") (:end . 104)\n (:start . 92) (:id . 58))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 113)\n (:start . 105) (:id . 59))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 117) (:start . 114)\n (:id . 60))\n ((:tag . "VBZ") (:stem . "decrease") (:form . "decreases") (:end . 127)\n (:start . 118) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.295) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100622@unknown@formal@none@1@S@Some subsets of quite high posterior odds have much smaller overlaps with the training set.@(((:tag . "DT") (:stem . "some") (:form . "Some") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "subset") (:form . "subsets") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "RB") (:stem . "quite") (:form . "quite") (:end . 21) (:start . 16)\n (:id . 45))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 26) (:start . 22)\n (:id . 46))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 36)\n (:start . 27) (:id . 47))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 41) (:start . 37)\n (:id . 48))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 46) (:start . 42)\n (:id . 49))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 51) (:start . 47)\n (:id . 50))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 59)\n (:start . 52) (:id . 51))\n ((:tag . "NNS") (:stem . "overlap") (:form . "overlaps") (:end . 68)\n (:start . 60) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 73) (:start . 69)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n (:id . 54))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 86)\n (:start . 78) (:id . 55))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 90) (:start . 87)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s2.296) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100623@unknown@formal@none@1@S@For example, interactions predicted at posterior odds ratios between 128 and 2048 have a 20 to 30% overlap with the training set as shown in Figure 7.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 25)\n (:start . 13) (:id . 45))\n ((:tag . 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"shown") (:end . 137)\n (:start . 132) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 140) (:start . 138)\n (:id . 68))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 147)\n (:start . 141) (:id . 69))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 149) (:start . 148)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s2.297) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100624@unknown@formal@none@1@S@Although many of these novel predictions have not been previously investigated in the literature, there exists experimental evidence supporting a subset of these predictions which is not present in the June 2006 version of the HPRD used to train our predictor, thus providing independent validation of our method.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 13) (:start . 9)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 22) (:start . 17)\n (:id . 45))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 28) (:start . 23)\n (:id . 46))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 40)\n (:start . 29) (:id . 47))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 45) (:start . 41)\n (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 54) (:start . 50)\n (:id . 50))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 65)\n (:start . 55) (:id . 51))\n ((:tag . "VBN") (:stem . "investigate") (:form . 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"the") (:end . 201) (:start . 198)\n (:id . 72))\n ((:tag . "NNP") (:stem . "June") (:form . "June") (:end . 206) (:start . 202)\n (:id . 73))\n ((:tag . "CD") (:stem . "2006") (:form . "2006") (:end . 211) (:start . 207)\n (:id . 74))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 219)\n (:start . 212) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 222) (:start . 220)\n (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 226) (:start . 223)\n (:id . 77))\n ((:tag . "NNP") (:stem . "HPRD") (:form . "HPRD") (:end . 231) (:start . 227)\n (:id . 78))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 236) (:start . 232)\n (:id . 79))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 239) (:start . 237)\n (:id . 80))\n ((:tag . "VB") (:stem . "train") (:form . "train") (:end . 245)\n (:start . 240) (:id . 81))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 249) (:start . 246)\n (:id . 82))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 259)\n (:start . 250) (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 260) (:start . 259)\n (:id . 84))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 265) (:start . 261)\n (:id . 85))\n ((:tag . "VBG") (:stem . "provide") (:form . "providing") (:end . 275)\n (:start . 266) (:id . 86))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 287)\n (:start . 276) (:id . 87))\n ((:tag . "NN") (:stem . "validation") (:form . "validation") (:end . 298)\n (:start . 288) (:id . 88))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 301) (:start . 299)\n (:id . 89))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 305) (:start . 302)\n (:id . 90))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 312)\n (:start . 306) (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 313) (:start . 312)\n (:id . 92)))@@@1@51@((:ncues ((:id . :x2.298.1) (:span 183 186))\n ((:id . :x2.298.2) (:span 46 49)))\n (:nscopes ((:id . :x2.298.1) (:span 183 259))\n ((:id . :x2.298.2) (:span 9 96)))\n (:identifiers (:sid . :s2.298) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100625@unknown@formal@none@1@S@Five such validated predictions are reported here:@(((:tag . "CD") (:stem . "five") (:form . "Five") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . "JJ") (:stem . "validated") (:form . "validated") (:end . 19)\n (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 31)\n (:start . 20) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n (:id . 46))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 44)\n (:start . 36) (:id . 47))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 49) (:start . 45)\n (:id . 48))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 50) (:start . 49)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s2.299) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100626@unknown@formal@none@1@S@Overlap of different subsets of the LR400 dataset with the HPRD-derived training set@(((:tag . "NN") (:stem . "overlap") (:form . "Overlap") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n (:id . 43))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 20)\n (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "subset") (:form . "subsets") (:end . 28)\n (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n (:id . 47))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 41) (:start . 36)\n (:id . 48))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 49)\n (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 54) (:start . 50)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n (:id . 51))\n ((:tag . "JJ") (:stem . "hprd-derived") (:form . "HPRD-derived") (:end . 71)\n (:start . 59) (:id . 52))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 80)\n (:start . 72) (:id . 53))\n ((:tag . "NN") (:stem . "set") (:form . 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"and") (:end . 254) (:start . 251)\n (:id . 85))\n ((:tag . "JJ") (:stem . "computational") (:form . "computational")\n (:end . 268) (:start . 255) (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 269) (:start . 268)\n (:id . 87))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 279)\n (:start . 270) (:id . 88))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 282) (:start . 280)\n (:id . 89))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 285) (:start . 283)\n (:id . 90))\n ((:tag . "CD") (:stem . "90") (:form . "90") (:end . 288) (:start . 286)\n (:id . 91))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 289) (:start . 288)\n (:id . 92))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 292) (:start . 290)\n (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 293) (:start . 292)\n (:id . 94)))@@@1@53@((:hcues ((:id . :x2.322.1) (:span 270 279)))\n (:hscopes ((:id . :x2.322.1) (:span 270 289)))\n (:identifiers (:sid . :s2.322) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100650@unknown@formal@none@1@S@We provide all our predictions ranked according to the posterior odds ratio of interaction in Additional File 3.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 30)\n (:start . 19) (:id . 46))\n ((:tag . "VBD") (:stem . "rank") (:form . "ranked") (:end . 37) (:start . 31)\n (:id . 47))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 47)\n (:start . 38) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n (:id . 50))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 64)\n (:start . 55) (:id . 51))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 69) (:start . 65)\n (:id . 52))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 75) (:start . 70)\n (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n (:id . 54))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 90)\n (:start . 79) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 93) (:start . 91)\n (:id . 56))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 104)\n (:start . 94) (:id . 57))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 109) (:start . 105)\n (:id . 58))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 111) (:start . 110)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s2.324) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100651@unknown@formal@none@1@S@It is thus possible to restrict the dataset to the highest scoring protein pairs (and only choose for example, protein pairs that have an estimated true positive rate of interaction above 90%).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 10) (:start . 6)\n (:id . 44))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 19)\n (:start . 11) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 22) (:start . 20)\n (:id . 46))\n ((:tag . "VB") (:stem . "restrict") (:form . "restrict") (:end . 31)\n (:start . 23) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n (:id . 48))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 43)\n (:start . 36) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 46) (:start . 44)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n (:id . 51))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 58)\n (:start . 51) (:id . 52))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 66)\n (:start . 59) (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 74)\n (:start . 67) (:id . 54))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 80) (:start . 75)\n (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n (:id . 57))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 90) (:start . 86)\n (:id . 58))\n ((:tag . "VB") (:stem . "choose") (:form . "choose") (:end . 97)\n (:start . 91) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 101) (:start . 98)\n (:id . 60))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 109)\n (:start . 102) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n (:id . 62))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 118)\n (:start . 111) (:id . 63))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 124)\n (:start . 119) (:id . 64))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 129) (:start . 125)\n (:id . 65))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 134) (:start . 130)\n (:id . 66))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 137) (:start . 135)\n (:id . 67))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 147)\n (:start . 138) (:id . 68))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 152) (:start . 148)\n (:id . 69))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 161)\n (:start . 153) (:id . 70))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 166) (:start . 162)\n (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 169) (:start . 167)\n (:id . 72))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 181)\n (:start . 170) (:id . 73))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 187)\n (:start . 182) (:id . 74))\n ((:tag . "CD") (:stem . "90") (:form . "90") (:end . 190) (:start . 188)\n (:id . 75))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 191) (:start . 190)\n (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 192) (:start . 191)\n (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n (:id . 78)))@@@1@37@((:hcues ((:id . :x2.325.1) (:span 138 147))\n ((:id . :x2.325.2) (:span 11 19)))\n (:hscopes ((:id . :x2.325.1) (:span 138 192))\n ((:id . :x2.325.2) (:span 11 192)))\n (:identifiers (:sid . :s2.325) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100652@unknown@formal@none@1@S@By making this human interaction prediction dataset publicly available, it is our hope that it will help to identify the most high-confidence interactions, leading to a more complete and accurate human interaction map.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBG") (:stem . "make") (:form . "making") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 32)\n (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 43)\n (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 51)\n (:start . 44) (:id . 48))\n ((:tag . "RB") (:stem . "publicly") (:form . "publicly") (:end . 60)\n (:start . 52) (:id . 49))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 70)\n (:start . 61) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n (:id . 51))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 74) (:start . 72)\n (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 77) (:start . 75)\n (:id . 53))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 81) (:start . 78)\n (:id . 54))\n ((:tag . "NN") (:stem . "hope") (:form . "hope") (:end . 86) (:start . 82)\n (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 91) (:start . 87)\n (:id . 56))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 94) (:start . 92)\n (:id . 57))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 99) (:start . 95)\n (:id . 58))\n ((:tag . "VB") (:stem . "help") (:form . "help") (:end . 104) (:start . 100)\n (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 107) (:start . 105)\n (:id . 60))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 116)\n (:start . 108) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n (:id . 62))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 125) (:start . 121)\n (:id . 63))\n ((:tag . "JJ") (:stem . "high-confidence") (:form . "high-confidence")\n (:end . 141) (:start . 126) (:id . 64))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 154)\n (:start . 142) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 155) (:start . 154)\n (:id . 66))\n ((:tag . "VBG") (:stem . "lead") (:form . "leading") (:end . 163)\n (:start . 156) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 166) (:start . 164)\n (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 168) (:start . 167)\n (:id . 69))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 173) (:start . 169)\n (:id . 70))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 182)\n (:start . 174) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 186) (:start . 183)\n (:id . 72))\n ((:tag . "JJ") (:stem . "accurate") (:form . "accurate") (:end . 195)\n (:start . 187) (:id . 73))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 201)\n (:start . 196) (:id . 74))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 213)\n (:start . 202) (:id . 75))\n ((:tag . "NN") (:stem . "map") (:form . "map") (:end . 217) (:start . 214)\n (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n (:id . 77)))@@@1@36@((:hcues ((:id . :x2.326.1) (:span 82 86)))\n (:hscopes ((:id . :x2.326.1) (:span 82 217)))\n (:identifiers (:sid . :s2.326) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100653@unknown@formal@none@1@S@Methods@(((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 7)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s2.327) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Title|)))@oe@9-2-2011 5100654@unknown@formal@none@1@S@Datasets@(((:tag . "NNP") (:stem . "Dataset") (:form . "Datasets") (:end . 8)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s2.328) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100655@unknown@formal@none@1@S@In order to investigate the likelihood of interaction of human proteins, 62322 human protein sequences were downloaded from the International Protein Index (IPI) database (version 3.16) 64.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "VB") (:stem . "investigate") (:form . "investigate") (:end . 23)\n (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n (:id . 46))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 38)\n (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n (:id . 48))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 53)\n (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n (:id . 50))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 62) (:start . 57)\n (:id . 51))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 71)\n (:start . 63) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n (:id . 53))\n ((:tag . "CD") (:stem . "62322") (:form . "62322") (:end . 78) (:start . 73)\n (:id . 54))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 84) (:start . 79)\n (:id . 55))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 92)\n (:start . 85) (:id . 56))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 102)\n (:start . 93) (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 107) (:start . 103)\n (:id . 58))\n ((:tag . "VBN") (:stem . "downloade") (:form . "downloaded") (:end . 118)\n (:start . 108) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 123) (:start . 119)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n (:id . 61))\n ((:tag . "NNP") (:stem . "International") (:form . "International")\n (:end . 141) (:start . 128) (:id . 62))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 149)\n (:start . 142) (:id . 63))\n ((:tag . "NNP") (:stem . "Index") (:form . "Index") (:end . 155)\n (:start . 150) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 157) (:start . 156)\n (:id . 65))\n ((:tag . "NNP") (:stem . "IPI") (:form . "IPI") (:end . 160) (:start . 157)\n (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 161) (:start . 160)\n (:id . 67))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 170)\n (:start . 162) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 172) (:start . 171)\n (:id . 69))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 179)\n (:start . 172) (:id . 70))\n ((:tag . "CD") (:stem . "3.16") (:form . "3.16") (:end . 184) (:start . 180)\n (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 185) (:start . 184)\n (:id . 72))\n ((:tag . "CD") (:stem . "64") (:form . "64") (:end . 188) (:start . 186)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s2.329) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100656@unknown@formal@none@1@S@Some of these proteins are alternative transcripts of the same gene but can have distinct interaction partners.@(((:tag . "DT") (:stem . "some") (:form . "Some") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 22)\n (:start . 14) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "JJ") (:stem . "alternative") (:form . "alternative") (:end . 38)\n (:start . 27) (:id . 47))\n ((:tag . "NNS") (:stem . "transcript") (:form . "transcripts") (:end . 50)\n (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n (:id . 50))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 62) (:start . 58)\n (:id . 51))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 67) (:start . 63)\n (:id . 52))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 71) (:start . 68)\n (:id . 53))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 75) (:start . 72)\n (:id . 54))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 80) (:start . 76)\n (:id . 55))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 89)\n (:start . 81) (:id . 56))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 101)\n (:start . 90) (:id . 57))\n ((:tag . "NNS") (:stem . "partner") (:form . "partners") (:end . 110)\n (:start . 102) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s2.330) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100657@unknown@formal@none@1@S@Known interactions were downloaded from the Human Protein Reference Database (HPRD; June 2006 version) 15.@(((:tag . "NN") (:stem . "known") (:form . "Known") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 18)\n (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 23) (:start . 19)\n (:id . 44))\n ((:tag . "VBN") (:stem . "downloade") (:form . "downloaded") (:end . 34)\n (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 39) (:start . 35)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n (:id . 47))\n ((:tag . "JJ") (:stem . "human") (:form . "Human") (:end . 49) (:start . 44)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 57)\n (:start . 50) (:id . 49))\n ((:tag . "NNP") (:stem . "Reference") (:form . "Reference") (:end . 67)\n (:start . 58) (:id . 50))\n ((:tag . "NNP") (:stem . "Database") (:form . "Database") (:end . 76)\n (:start . 68) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n (:id . 52))\n ((:tag . "NNP") (:stem . "HPRD") (:form . "HPRD") (:end . 82) (:start . 78)\n (:id . 53))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 83) (:start . 82)\n (:id . 54))\n ((:tag . "NNP") (:stem . "June") (:form . "June") (:end . 88) (:start . 84)\n (:id . 55))\n ((:tag . "CD") (:stem . "2006") (:form . "2006") (:end . 93) (:start . 89)\n (:id . 56))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 101)\n (:start . 94) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n (:id . 58))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 105) (:start . 103)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s2.331) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100658@unknown@formal@none@1@S@Duplicate interactions and self-interactions were not considered.@(((:tag . "JJ") (:stem . "duplicate") (:form . "Duplicate") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 22)\n (:start . 10) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n (:id . 44))\n ((:tag . "NNS") (:stem . "self-interaction") (:form . "self-interactions")\n (:end . 44) (:start . 27) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 49) (:start . 45)\n (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 53) (:start . 50)\n (:id . 47))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 64)\n (:start . 54) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n (:id . 49)))@@@1@8@((:ncues ((:id . :x2.332.1) (:span 50 53)))\n (:nscopes ((:id . :x2.332.1) (:span 0 64)))\n (:identifiers (:sid . :s2.332) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100660@unknown@formal@none@1@S@This resulted in 26896 distinct human protein interactions involving 7531 distinct human proteins present in the initial IPI dataset.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 16) (:start . 14)\n (:id . 44))\n ((:tag . "CD") (:stem . "26896") (:form . 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"to") (:end . 165) (:start . 163)\n (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 167) (:start . 166)\n (:id . 66))\n ((:tag . "JJ") (:stem . "localization-derived")\n (:form . "localization-derived") (:end . 188) (:start . 168) (:id . 67))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 197)\n (:start . 189) (:id . 68))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 205)\n (:start . 198) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s2.336) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100663@unknown@formal@none@1@S@Both non-interacting protein datasets were cleaned by removing all protein pairs that came from the positive dataset as well as protein pairs that were annotated as interacting in other databases (DIP 65: 679 interactions, BIND 66: 2650 interactions), or predicted to interact in other studies (OPHID 67: 21815 interactions).@(((:tag . "CC") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "non-interacting") (:form . "non-interacting")\n (:end . 20) (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 28)\n (:start . 21) (:id . 44))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 37)\n (:start . 29) (:id . 45))\n ((:tag . "VBD") (:stem . 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"interactions") (:end . 323)\n (:start . 311) (:id . 98))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 324) (:start . 323)\n (:id . 99))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 325) (:start . 324)\n (:id . 100)))@@@1@59@((:identifiers (:sid . :s2.337) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100664@unknown@formal@none@1@S@Of the 62322 human proteins from the initial IPI dataset, 22889 were characterized by at least one of the features that we considered to predict interaction (see the Features section).@(((:tag . "IN") (:stem . "of") (:form . "Of") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "CD") (:stem . "62322") (:form . "62322") (:end . 12) (:start . 7)\n (:id . 44))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "NNS") (:stem . 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(:end . 184) (:start . 183)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s2.338) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100665@unknown@formal@none@1@S@These 22889 human proteins are encoded by 16904 distinct genes and are referred to as the Informative Protein Set.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "22889") (:form . "22889") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 17) (:start . 12)\n (:id . 44))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 26)\n (:start . 18) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 38)\n (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . 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"NNP") (:stem . "Protein") (:form . "Protein") (:end . 109)\n (:start . 102) (:id . 59))\n ((:tag . "NNP") (:stem . "Set") (:form . "Set") (:end . 113) (:start . 110)\n (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s2.339) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100666@unknown@formal@none@1@S@The randomly-generated negative dataset used for the training and testing of the predictor was created by selecting protein pairs at random from the Informative Protein Set.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "randomly-generated") (:form . "randomly-generated")\n (:end . 22) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 31)\n (:start . 23) (:id . 44))\n ((:tag . "NN") (:stem . "dataset") (:form . 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"Protein") (:end . 168)\n (:start . 161) (:id . 66))\n ((:tag . "NNP") (:stem . "Set") (:form . "Set") (:end . 172) (:start . 169)\n (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s2.340) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100667@unknown@formal@none@1@S@In contrast, the localization-derived negative dataset was created by selecting protein pairs from the Informative Protein Set for which the HPRD 15 annotates one as being primarily in the plasma membrane and the other as primarily in the nucleus.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . 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"annotates") (:end . 158)\n (:start . 149) (:id . 65))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 162) (:start . 159)\n (:id . 66))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 165) (:start . 163)\n (:id . 67))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 171) (:start . 166)\n (:id . 68))\n ((:tag . "RB") (:stem . "primarily") (:form . "primarily") (:end . 181)\n (:start . 172) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 184) (:start . 182)\n (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 188) (:start . 185)\n (:id . 71))\n ((:tag . "NN") (:stem . "plasma") (:form . "plasma") (:end . 195)\n (:start . 189) (:id . 72))\n ((:tag . "NN") (:stem . "membrane") (:form . "membrane") (:end . 204)\n (:start . 196) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 208) (:start . 205)\n (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 212) (:start . 209)\n (:id . 75))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 218)\n (:start . 213) (:id . 76))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 221) (:start . 219)\n (:id . 77))\n ((:tag . "RB") (:stem . "primarily") (:form . "primarily") (:end . 231)\n (:start . 222) (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 234) (:start . 232)\n (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 238) (:start . 235)\n (:id . 80))\n ((:tag . "NN") (:stem . "nucleus") (:form . "nucleus") (:end . 246)\n (:start . 239) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 247) (:start . 246)\n (:id . 82)))@@@1@41@((:identifiers (:sid . :s2.341) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100668@unknown@formal@none@1@S@Training and testing was performed with 5-fold cross-validation.@(((:tag . "NN") (:stem . "training") (:form . "Training") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 12) (:start . 9)\n (:id . 43))\n ((:tag . "NN") (:stem . "testing") (:form . "testing") (:end . 20)\n (:start . 13) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 24) (:start . 21)\n (:id . 45))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 34)\n (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 39) (:start . 35)\n (:id . 47))\n ((:tag . "JJ") (:stem . "5-fold") (:form . "5-fold") (:end . 46)\n (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "cross-validation") (:form . "cross-validation")\n (:end . 63) (:start . 47) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 64) (:start . 63)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s2.342) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100670@unknown@formal@none@1@S@The predictions were compared to the literature-mined Ramani dataset 16, the orthology-derived Lehner prediction dataset 36 and the probabilistic Rhodes prediction dataset 46.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 20) (:start . 16)\n (:id . 44))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 29)\n (:start . 21) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 32) (:start . 30)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n (:id . 47))\n ((:tag . "JJ") (:stem . 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"36") (:form . "36") (:end . 123) (:start . 121)\n (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n (:id . 60))\n ((:tag . "JJ") (:stem . "probabilistic") (:form . "probabilistic")\n (:end . 145) (:start . 132) (:id . 61))\n ((:tag . "NNP") (:stem . "Rhodes") (:form . "Rhodes") (:end . 152)\n (:start . 146) (:id . 62))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 163)\n (:start . 153) (:id . 63))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 171)\n (:start . 164) (:id . 64))\n ((:tag . "CD") (:stem . "46") (:form . "46") (:end . 174) (:start . 172)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s2.344) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100671@unknown@formal@none@1@S@All three datasets identify the interactions by stating the names and/or gene locus IDs of the genes that encode the interacting proteins.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 18)\n (:start . 10) (:id . 44))\n ((:tag . "VBP") (:stem . "identify") (:form . "identify") (:end . 27)\n (:start . 19) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n (:id . 46))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 44)\n (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 47) (:start . 45)\n (:id . 48))\n ((:tag . "VBG") (:stem . "state") (:form . "stating") (:end . 55)\n (:start . 48) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n (:id . 50))\n ((:tag . "NNS") (:stem . "name") (:form . "names") (:end . 65) (:start . 60)\n (:id . 51))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 72)\n (:start . 66) (:id . 52))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 77) (:start . 73)\n (:id . 53))\n ((:tag . "NN") (:stem . "locus") (:form . "locus") (:end . 83) (:start . 78)\n (:id . 54))\n ((:tag . "NNS") (:stem . "id") (:form . "IDs") (:end . 87) (:start . 84)\n (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n (:id . 57))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 100) (:start . 95)\n (:id . 58))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 105) (:start . 101)\n (:id . 59))\n ((:tag . "VBP") (:stem . "encode") (:form . "encode") (:end . 112)\n (:start . 106) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n (:id . 61))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 128)\n (:start . 117) (:id . 62))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 137)\n (:start . 129) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.345) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100672@unknown@formal@none@1@S@In contrast, we work directly on the protein sequences and so related the gene annotations to our protein identifiers by extracting Entrez Gene IDs corresponding to the IPI protein entries from the IPI cross-reference files (for the IPI release 3.24) 64.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "VBP") (:stem . "work") (:form . "work") (:end . 20) (:start . 16)\n (:id . 46))\n ((:tag . "RB") (:stem . "directly") (:form . 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"JJ") (:stem . "bayesian") (:form . "Bayesian") (:end . 92)\n (:start . 84) (:id . 56))\n ((:tag . "NN") (:stem . "formalism") (:form . "formalism") (:end . 102)\n (:start . 93) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.354) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100681@unknown@formal@none@1@S@We are interested in determining the posterior odds ratio of interaction of two proteins, given the presence of the features we are considering.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "interested") (:form . "interested") (:end . 17)\n (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 20) (:start . 18)\n (:id . 45))\n ((:tag . 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",") (:end . 89) (:start . 88)\n (:id . 56))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 95) (:start . 90)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n (:id . 58))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 108)\n (:start . 100) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n (:id . 61))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 124)\n (:start . 116) (:id . 62))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 127) (:start . 125)\n (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 131) (:start . 128)\n (:id . 64))\n ((:tag . "VBG") (:stem . "consider") (:form . "considering") (:end . 143)\n (:start . 132) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s2.355) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100682@unknown@formal@none@1@S@This posterior odds ratio can be re-written using Bayes rule: Opost = P(I|f1,..., fn)P(~I|f1,..., fn)=P(f1,..., fn|I)∗P(I)P(f1,..., fn)P(f1,..., fn|~I)∗P(~I)P(f1,..., fn)=P(f1,..., fn|I)∗P(I)P(f,..., fn|~I∗P(~I)=P(I)P(~I∗P(f1,..., fn|I)P(f1,..., fn|~I)=Oprior∗LR(1,...,fn) where I is a binary variable representing interaction, ~I represents non-interaction, f1 through fn are the features we are considering, Oprior is the prior odds ratio and LR is the likelihood ratio.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 14)\n (:start . 5) (:id . 43))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . 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"odds") (:end . 434) (:start . 430)\n (:id . 117))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 440)\n (:start . 435) (:id . 118))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 444) (:start . 441)\n (:id . 119))\n ((:tag . "NNP") (:stem . "LR") (:form . "LR") (:end . 447) (:start . 445)\n (:id . 120))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 450) (:start . 448)\n (:id . 121))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 454) (:start . 451)\n (:id . 122))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 465)\n (:start . 455) (:id . 123))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 471)\n (:start . 466) (:id . 124))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 472) (:start . 471)\n (:id . 125)))@@@1@84@((:identifiers (:sid . :s2.356) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100683@unknown@formal@none@1@S@If the features considered are independent, the likelihood ratio LR can be calculated as the product of the individual likelihood ratios with respect to the features considered separately.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 15)\n (:start . 7) (:id . 44))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 26)\n (:start . 16) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "JJ") (:stem . "independent") (:form . 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"product") (:form . "product") (:end . 100)\n (:start . 93) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n (:id . 60))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 118)\n (:start . 108) (:id . 61))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 129)\n (:start . 119) (:id . 62))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 136)\n (:start . 130) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 141) (:start . 137)\n (:id . 64))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 149)\n (:start . 142) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 152) (:start . 150)\n (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 156) (:start . 153)\n (:id . 67))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 165)\n (:start . 157) (:id . 68))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 176)\n (:start . 166) (:id . 69))\n ((:tag . "RB") (:stem . "separately") (:form . "separately") (:end . 187)\n (:start . 177) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s2.357) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100684@unknown@formal@none@1@S@If the features are not independent, all possible combinations of all states of these features must be considered, which can be computationally quite intensive.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 15)\n (:start . 7) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 23) (:start . 20)\n (:id . 46))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 35)\n (:start . 24) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n (:id . 48))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 40) (:start . 37)\n (:id . 49))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 49)\n (:start . 41) (:id . 50))\n ((:tag . "NNS") (:stem . "combination") (:form . "combinations") (:end . 62)\n (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n (:id . 52))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 69) (:start . 66)\n (:id . 53))\n ((:tag . "NNS") (:stem . "state") (:form . "states") (:end . 76)\n (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n (:id . 55))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 85) (:start . 80)\n (:id . 56))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 94)\n (:start . 86) (:id . 57))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 99) (:start . 95)\n (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 102) (:start . 100)\n (:id . 59))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 113)\n (:start . 103) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 120)\n (:start . 115) (:id . 62))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 124) (:start . 121)\n (:id . 63))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 127) (:start . 125)\n (:id . 64))\n ((:tag . "RB") (:stem . "computationally") (:form . "computationally")\n (:end . 143) (:start . 128) (:id . 65))\n ((:tag . "RB") (:stem . "quite") (:form . "quite") (:end . 149)\n (:start . 144) (:id . 66))\n ((:tag . "JJ") (:stem . "intensive") (:form . "intensive") (:end . 159)\n (:start . 150) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n (:id . 68)))@@@1@27@((:hcues ((:id . :x2.358.1) (:span 121 124)))\n (:ncues ((:id . :x2.358.2) (:span 20 23)))\n (:hscopes ((:id . :x2.358.1) (:span 121 159)))\n (:nscopes ((:id . :x2.358.2) (:span 20 35)))\n (:identifiers (:sid . :s2.358) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100685@unknown@formal@none@1@S@In the independent case, the likelihood ratio can be calculated as: LR(f1,...,fn)=[P(f1,..., fn|I)P(f1,..., fn|~I)]=∏i=1n[P(fi|I)P(fi~I)]@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . 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", fn|~I)]=∏i=1n[P(fi|I)P(fi~I)") (:end . 136) (:start . 106)\n (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 137) (:start . 136)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.359) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100686@unknown@formal@none@1@S@The likelihood ratios for the different features considered can be estimated by evaluating the ratio of the proportion of interacting and non-interacting proteins for which a particular state of the feature is true in the training set (i.e. by determining to which bin of the feature the protein pair belongs, for every protein pair in the positive and negative training sets).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "ratio") (:form . 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"evaluating") (:end . 90)\n (:start . 80) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n (:id . 55))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 100) (:start . 95)\n (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n (:id . 58))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 118)\n (:start . 108) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n (:id . 60))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 133)\n (:start . 122) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n (:id . 62))\n ((:tag . "JJ") (:stem . "non-interacting") (:form . "non-interacting")\n (:end . 153) (:start . 138) (:id . 63))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 162)\n (:start . 154) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 166) (:start . 163)\n (:id . 65))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 172)\n (:start . 167) (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 174) (:start . 173)\n (:id . 67))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 185)\n (:start . 175) (:id . 68))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 191)\n (:start . 186) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 194) (:start . 192)\n (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 198) (:start . 195)\n (:id . 71))\n ((:tag . "NN") (:stem . "feature") (:form . "feature") (:end . 206)\n (:start . 199) (:id . 72))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 209) (:start . 207)\n (:id . 73))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 214) (:start . 210)\n (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 217) (:start . 215)\n (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 221) (:start . 218)\n (:id . 76))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 230)\n (:start . 222) (:id . 77))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 234) (:start . 231)\n (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 236) (:start . 235)\n (:id . 79))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 240) (:start . 236)\n (:id . 80))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 243) (:start . 241)\n (:id . 81))\n ((:tag . "VBG") (:stem . "determine") (:form . "determining") (:end . 255)\n (:start . 244) (:id . 82))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 258) (:start . 256)\n (:id . 83))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 264)\n (:start . 259) (:id . 84))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 268) (:start . 265)\n (:id . 85))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 271) (:start . 269)\n (:id . 86))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 275) (:start . 272)\n (:id . 87))\n ((:tag . "NN") (:stem . "feature") (:form . "feature") (:end . 283)\n (:start . 276) (:id . 88))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 287) (:start . 284)\n (:id . 89))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 295)\n (:start . 288) (:id . 90))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 300) (:start . 296)\n (:id . 91))\n ((:tag . "VBZ") (:stem . "belong") (:form . "belongs") (:end . 308)\n (:start . 301) (:id . 92))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 309) (:start . 308)\n (:id . 93))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 313) (:start . 310)\n (:id . 94))\n ((:tag . "DT") (:stem . "every") (:form . "every") (:end . 319)\n (:start . 314) (:id . 95))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 327)\n (:start . 320) (:id . 96))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 332) (:start . 328)\n (:id . 97))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 335) (:start . 333)\n (:id . 98))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 339) (:start . 336)\n (:id . 99))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 348)\n (:start . 340) (:id . 100))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 352) (:start . 349)\n (:id . 101))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 361)\n (:start . 353) (:id . 102))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 370)\n (:start . 362) (:id . 103))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 375) (:start . 371)\n (:id . 104))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 376) (:start . 375)\n (:id . 105))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 377) (:start . 376)\n (:id . 106)))@@@1@65@((:identifiers (:sid . :s2.360) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100687@unknown@formal@none@1@S@More precisely, the training step consisted of calculating the respective proportions of positive and negative examples that fall into each bin of the feature(s) considered (i.e. that have a particular state).@(((:tag . "RBR") (:stem . "more") (:form . "More") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "precisely") (:form . "precisely") (:end . 14)\n (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 28)\n (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "VBD") (:stem . "consist") (:form . "consisted") (:end . 43)\n (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n (:id . 49))\n ((:tag . "VBG") (:stem . "calculate") (:form . "calculating") (:end . 58)\n (:start . 47) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n (:id . 51))\n ((:tag . "JJ") (:stem . "respective") (:form . "respective") (:end . 73)\n (:start . 63) (:id . 52))\n ((:tag . "NNS") (:stem . "proportion") (:form . "proportions") (:end . 85)\n (:start . 74) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n (:id . 54))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 97)\n (:start . 89) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n (:id . 56))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 110)\n (:start . 102) (:id . 57))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 119)\n (:start . 111) (:id . 58))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 124) (:start . 120)\n (:id . 59))\n ((:tag . "VBP") (:stem . "fall") (:form . "fall") (:end . 129) (:start . 125)\n (:id . 60))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 134) (:start . 130)\n (:id . 61))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 139) (:start . 135)\n (:id . 62))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 143) (:start . 140)\n (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 146) (:start . 144)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 150) (:start . 147)\n (:id . 65))\n ((:tag . "NN") (:stem . "feature(s)") (:form . "feature(s)") (:end . 161)\n (:start . 151) (:id . 66))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 172)\n (:start . 162) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 174) (:start . 173)\n (:id . 68))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 178) (:start . 174)\n (:id . 69))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 183) (:start . 179)\n (:id . 70))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 188) (:start . 184)\n (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 190) (:start . 189)\n (:id . 72))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 201)\n (:start . 191) (:id . 73))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 207)\n (:start . 202) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 208) (:start . 207)\n (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s2.361) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100688@unknown@formal@none@1@S@The likelihood ratio of interaction for a given state is simply the ratio of the proportion of all positives that have that state divided by the proportion of all negatives that have that same state.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 20) (:start . 15)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 45))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 35)\n (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 39) (:start . 36)\n (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 41) (:start . 40)\n (:id . 48))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 47) (:start . 42)\n (:id . 49))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 53) (:start . 48)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 56) (:start . 54)\n (:id . 51))\n ((:tag . "RB") (:stem . "simply") (:form . "simply") (:end . 63)\n (:start . 57) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n (:id . 53))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 73) (:start . 68)\n (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n (:id . 56))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 91)\n (:start . 81) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n (:id . 58))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 98) (:start . 95)\n (:id . 59))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 108)\n (:start . 99) (:id . 60))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 113) (:start . 109)\n (:id . 61))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 118) (:start . 114)\n (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 123) (:start . 119)\n (:id . 63))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 129)\n (:start . 124) (:id . 64))\n ((:tag . "VBN") (:stem . "divide") (:form . "divided") (:end . 137)\n (:start . 130) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 140) (:start . 138)\n (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n (:id . 67))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 155)\n (:start . 145) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 158) (:start . 156)\n (:id . 69))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 162) (:start . 159)\n (:id . 70))\n ((:tag . "NNS") (:stem . "negative") (:form . "negatives") (:end . 172)\n (:start . 163) (:id . 71))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 177) (:start . 173)\n (:id . 72))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 182) (:start . 178)\n (:id . 73))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 187) (:start . 183)\n (:id . 74))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 192) (:start . 188)\n (:id . 75))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 198)\n (:start . 193) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 199) (:start . 198)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s2.362) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100690@unknown@formal@none@1@S@Additionally, when no data are available for a specific feature (for a given pair of proteins), the likelihood of the feature is set to 1.0.@(((:tag . "RB") (:stem . "additionally") (:form . "Additionally") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 43))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 26) (:start . 22)\n (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 30) (:start . 27)\n (:id . 47))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 40)\n (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 44) (:start . 41)\n (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 46) (:start . 45)\n (:id . 50))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 55)\n (:start . 47) (:id . 51))\n ((:tag . "NN") (:stem . "feature") (:form . "feature") (:end . 63)\n (:start . 56) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 68) (:start . 65)\n (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 70) (:start . 69)\n (:id . 55))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 76) (:start . 71)\n (:id . 56))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 81) (:start . 77)\n (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 93)\n (:start . 85) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 94) (:start . 93)\n (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n (:id . 62))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 110)\n (:start . 100) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n (:id . 65))\n ((:tag . "NN") (:stem . "feature") (:form . "feature") (:end . 125)\n (:start . 118) (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 128) (:start . 126)\n (:id . 67))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 132) (:start . 129)\n (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 135) (:start . 133)\n (:id . 69))\n ((:tag . "CD") (:stem . "1.0") (:form . "1.0") (:end . 139) (:start . 136)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n (:id . 71)))@@@1@30@((:ncues ((:id . :x2.364.1) (:span 19 21)))\n (:nscopes ((:id . :x2.364.1) (:span 19 94)))\n (:identifiers (:sid . :s2.364) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100691@unknown@formal@none@1@S@For a detailed calculation of the likelihoods see Additional File 4.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 5) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "detailed") (:form . "detailed") (:end . 14)\n (:start . 6) (:id . 44))\n ((:tag . "NN") (:stem . "calculation") (:form . "calculation") (:end . 26)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 47))\n ((:tag . "NNS") (:stem . "likelihood") (:form . "likelihoods") (:end . 45)\n (:start . 34) (:id . 48))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 60)\n (:start . 50) (:id . 50))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 65) (:start . 61)\n (:id . 51))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 67) (:start . 66)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.365) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100692@unknown@formal@none@1@S@Prior odds ratio estimate@(((:tag . "JJ") (:stem . "prior") (:form . "Prior") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 16) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "estimate") (:form . "estimate") (:end . 25)\n (:start . 17) (:id . 45)))@@@1@4@((:identifiers (:sid . :s2.366) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100693@unknown@formal@none@1@S@The prior odds ratio (Oprior) is difficult to estimate because we do not know all the true interactions, even for a small subset of proteins.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Oprior") (:form . "Oprior") (:end . 28)\n (:start . 22) (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 29) (:start . 28)\n (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 32) (:start . 30)\n (:id . 49))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 42)\n (:start . 33) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 45) (:start . 43)\n (:id . 51))\n ((:tag . "VB") (:stem . "estimate") (:form . "estimate") (:end . 54)\n (:start . 46) (:id . 52))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 62)\n (:start . 55) (:id . 53))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 65) (:start . 63)\n (:id . 54))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 68) (:start . 66)\n (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 72) (:start . 69)\n (:id . 56))\n ((:tag . "VB") (:stem . "know") (:form . "know") (:end . 77) (:start . 73)\n (:id . 57))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 81) (:start . 78)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n (:id . 59))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 90) (:start . 86)\n (:id . 60))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 103)\n (:start . 91) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n (:id . 62))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 109) (:start . 105)\n (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 113) (:start . 110)\n (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 115) (:start . 114)\n (:id . 65))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 121)\n (:start . 116) (:id . 66))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 128)\n (:start . 122) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n (:id . 68))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 140)\n (:start . 132) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n (:id . 70)))@@@1@29@((:ncues ((:id . :x2.367.1) (:span 69 72)))\n (:nscopes ((:id . :x2.367.1) (:span 69 140)))\n (:identifiers (:sid . :s2.367) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100694@unknown@formal@none@1@S@The prior odds ratio of interaction for yeast was estimated by combining all protein-protein interactions (but only those related to direct physical interactions, and no entries derived by synthetic lethal-type experiments) from the BIND, DIP and GRID databases 656669.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 46))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 35)\n (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 45) (:start . 40)\n (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 49) (:start . 46)\n (:id . 50))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 59)\n (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 62) (:start . 60)\n (:id . 52))\n ((:tag . "VBG") (:stem . "combine") (:form . "combining") (:end . 72)\n (:start . 63) (:id . 53))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 76) (:start . 73)\n (:id . 54))\n ((:tag . "JJ") (:stem . "protein-protein") (:form . "protein-protein")\n (:end . 92) (:start . 77) (:id . 55))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 105)\n (:start . 93) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n (:id . 57))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 110) (:start . 107)\n (:id . 58))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 115) (:start . 111)\n (:id . 59))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 121)\n (:start . 116) (:id . 60))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 129)\n (:start . 122) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 132) (:start . 130)\n (:id . 62))\n ((:tag . "VB") (:stem . "direct") (:form . "direct") (:end . 139)\n (:start . 133) (:id . 63))\n ((:tag . "JJ") (:stem . "physical") (:form . "physical") (:end . 148)\n (:start . 140) (:id . 64))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 161)\n (:start . 149) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 162) (:start . 161)\n (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 166) (:start . 163)\n (:id . 67))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 169) (:start . 167)\n (:id . 68))\n ((:tag . "NNS") (:stem . "entry") (:form . "entries") (:end . 177)\n (:start . 170) (:id . 69))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 185)\n (:start . 178) (:id . 70))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 188) (:start . 186)\n (:id . 71))\n ((:tag . "JJ") (:stem . "synthetic") (:form . "synthetic") (:end . 198)\n (:start . 189) (:id . 72))\n ((:tag . "JJ") (:stem . "lethal-type") (:form . "lethal-type") (:end . 210)\n (:start . 199) (:id . 73))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 222)\n (:start . 211) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 223) (:start . 222)\n (:id . 75))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 228) (:start . 224)\n (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 232) (:start . 229)\n (:id . 77))\n ((:tag . "NNP") (:stem . "BIND") (:form . "BIND") (:end . 237) (:start . 233)\n (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 238) (:start . 237)\n (:id . 79))\n ((:tag . "NNP") (:stem . "DIP") (:form . "DIP") (:end . 242) (:start . 239)\n (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 246) (:start . 243)\n (:id . 81))\n ((:tag . "NNP") (:stem . "GRID") (:form . "GRID") (:end . 251) (:start . 247)\n (:id . 82))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 261)\n (:start . 252) (:id . 83))\n ((:tag . "CD") (:stem . "656669") (:form . "656669") (:end . 268)\n (:start . 262) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 269) (:start . 268)\n (:id . 85)))@@@1@44@((:ncues ((:id . :x2.368.1) (:span 167 169)))\n (:nscopes ((:id . :x2.368.1) (:span 167 261)))\n (:identifiers (:sid . :s2.368) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100695@unknown@formal@none@1@S@This subset of interactions contains 36466 distinct interactions involving 5202 distinct proteins, thus resulting in a prior odds ratio of 1/370.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 27)\n (:start . 15) (:id . 45))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 36)\n (:start . 28) (:id . 46))\n ((:tag . "CD") (:stem . "36466") (:form . "36466") (:end . 42) (:start . 37)\n (:id . 47))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 51)\n (:start . 43) (:id . 48))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 64)\n (:start . 52) (:id . 49))\n ((:tag . "VBG") (:stem . "involve") (:form . "involving") (:end . 74)\n (:start . 65) (:id . 50))\n ((:tag . "CD") (:stem . "5202") (:form . "5202") (:end . 79) (:start . 75)\n (:id . 51))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 88)\n (:start . 80) (:id . 52))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 97)\n (:start . 89) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n (:id . 54))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 103) (:start . 99)\n (:id . 55))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 113)\n (:start . 104) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 116) (:start . 114)\n (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 118) (:start . 117)\n (:id . 58))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 124)\n (:start . 119) (:id . 59))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 129) (:start . 125)\n (:id . 60))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 135)\n (:start . 130) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n (:id . 62))\n ((:tag . "CD") (:stem . "1/370") (:form . "1/370") (:end . 144)\n (:start . 139) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.369) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100696@unknown@formal@none@1@S@This is most likely a conservative estimate since a certain proportion of interactions remain unknown and so when more data become available, the prior odds ratio will increase.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "RB") (:stem . "likely") (:form . "likely") (:end . 19)\n (:start . 13) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 21) (:start . 20)\n (:id . 46))\n ((:tag . "JJ") (:stem . "conservative") (:form . "conservative") (:end . 34)\n (:start . 22) (:id . 47))\n ((:tag . "NN") (:stem . "estimate") (:form . "estimate") (:end . 43)\n (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 49) (:start . 44)\n (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n (:id . 50))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 59)\n (:start . 52) (:id . 51))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 70)\n (:start . 60) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n (:id . 53))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 86)\n (:start . 74) (:id . 54))\n ((:tag . "VBP") (:stem . "remain") (:form . "remain") (:end . 93)\n (:start . 87) (:id . 55))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 101)\n (:start . 94) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 105) (:start . 102)\n (:id . 57))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 108) (:start . 106)\n (:id . 58))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 113) (:start . 109)\n (:id . 59))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 118) (:start . 114)\n (:id . 60))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 123)\n (:start . 119) (:id . 61))\n ((:tag . "VBP") (:stem . "become") (:form . "become") (:end . 130)\n (:start . 124) (:id . 62))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 140)\n (:start . 131) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n (:id . 65))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 151)\n (:start . 146) (:id . 66))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 156) (:start . 152)\n (:id . 67))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 162)\n (:start . 157) (:id . 68))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 167) (:start . 163)\n (:id . 69))\n ((:tag . "VB") (:stem . "increase") (:form . "increase") (:end . 176)\n (:start . 168) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n (:id . 71)))@@@1@30@((:hcues ((:id . :x2.370.1) (:span 94 101)) ((:id . :x2.370.2) (:span 13 19)))\n (:hscopes ((:id . :x2.370.1) (:span 50 101))\n ((:id . :x2.370.2) (:span 13 43)))\n (:identifiers (:sid . :s2.370) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100697@unknown@formal@none@1@S@For human proteins, 12191 distinct interactions were recovered, involving 5164 human proteins from the September 2005 version of the HPRD 15 and 26896 distinct interactions involving 7531 human proteins from the June 2006 version, leading respectively to prior odds estimates of 1/1093 and 1/1053.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 18)\n (:start . 10) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n (:id . 45))\n ((:tag . "CD") (:stem . "12191") (:form . "12191") (:end . 25) (:start . 20)\n (:id . 46))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 34)\n (:start . 26) (:id . 47))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 47)\n (:start . 35) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 52) (:start . 48)\n (:id . 49))\n ((:tag . "VBN") (:stem . "recover") (:form . "recovered") (:end . 62)\n (:start . 53) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n (:id . 51))\n ((:tag . "VBG") (:stem . "involve") (:form . "involving") (:end . 73)\n (:start . 64) (:id . 52))\n ((:tag . "CD") (:stem . "5164") (:form . "5164") (:end . 78) (:start . 74)\n (:id . 53))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 84) (:start . 79)\n (:id . 54))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 93)\n (:start . 85) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 98) (:start . 94)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n (:id . 57))\n ((:tag . "NNP") (:stem . "September") (:form . "September") (:end . 112)\n (:start . 103) (:id . 58))\n ((:tag . "CD") (:stem . "2005") (:form . "2005") (:end . 117) (:start . 113)\n (:id . 59))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 125)\n (:start . 118) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 128) (:start . 126)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n (:id . 62))\n ((:tag . "NNP") (:stem . "HPRD") (:form . "HPRD") (:end . 137) (:start . 133)\n (:id . 63))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 140) (:start . 138)\n (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 144) (:start . 141)\n (:id . 65))\n ((:tag . "CD") (:stem . "26896") (:form . "26896") (:end . 150)\n (:start . 145) (:id . 66))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 159)\n (:start . 151) (:id . 67))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 172)\n (:start . 160) (:id . 68))\n ((:tag . "VBG") (:stem . "involve") (:form . "involving") (:end . 182)\n (:start . 173) (:id . 69))\n ((:tag . "CD") (:stem . "7531") (:form . "7531") (:end . 187) (:start . 183)\n (:id . 70))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 193)\n (:start . 188) (:id . 71))\n ((:tag . "NNS") (:stem . "protein") (:form . 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"Features") (:end . 8)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s2.376) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100703@unknown@formal@none@1@S@Seven distinct features combined into five modules were investigated as summarized in Table 1 and described below.@(((:tag . "CD") (:stem . "seven") (:form . "Seven") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 14)\n (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 23)\n (:start . 15) (:id . 44))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 32)\n (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 37) (:start . 33)\n (:id . 46))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 42) (:start . 38)\n (:id . 47))\n ((:tag . "NNS") (:stem . "module") (:form . 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".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s2.377) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100704@unknown@formal@none@1@S@1.@(((:tag . "LS") (:stem . "1") (:form . "1") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 2) (:start . 1) (:id . 43)))@@@1@2@((:identifiers (:sid . :s2.378) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5100705@unknown@formal@none@1@S@Expression module@(((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "module") (:form . 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"Expression") (:form . "Expression") (:end . 56)\n (:start . 46) (:id . 49))\n ((:tag . "NNP") (:stem . "Omnibus") (:form . "Omnibus") (:end . 64)\n (:start . 57) (:id . 50))\n ((:tag . "CD") (:stem . "70") (:form . "70") (:end . 67) (:start . 65)\n (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s2.380) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100707@unknown@formal@none@1@S@The GDS596 dataset was used which examines gene expression profiles from 79 physiologically normal tissues obtained from various sources 71.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "GDS596") (:form . "GDS596") (:end . 10)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 18)\n (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 27) (:start . 23)\n (:id . 46))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 33) (:start . 28)\n (:id . 47))\n ((:tag . "VBZ") (:stem . "examine") (:form . "examines") (:end . 42)\n (:start . 34) (:id . 48))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 47) (:start . 43)\n (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 58)\n (:start . 48) (:id . 50))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 67)\n (:start . 59) (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 72) (:start . 68)\n (:id . 52))\n ((:tag . "CD") (:stem . "79") (:form . "79") (:end . 75) (:start . 73)\n (:id . 53))\n ((:tag . "RB") (:stem . "physiologically") (:form . "physiologically")\n (:end . 91) (:start . 76) (:id . 54))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 98)\n (:start . 92) (:id . 55))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 106)\n (:start . 99) (:id . 56))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 115)\n (:start . 107) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 120) (:start . 116)\n (:id . 58))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 128)\n (:start . 121) (:id . 59))\n ((:tag . "NNS") (:stem . "source") (:form . "sources") (:end . 136)\n (:start . 129) (:id . 60))\n ((:tag . "CD") (:stem . "71") (:form . "71") (:end . 139) (:start . 137)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.381) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100708@unknown@formal@none@1@S@Expression data were recovered for 10642 distinct transcripts in 158 different arrays (2 arrays per tissue).@(((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 15) (:start . 11)\n (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 20) (:start . 16)\n (:id . 44))\n ((:tag . "VBN") (:stem . "recover") (:form . "recovered") (:end . 30)\n (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 34) (:start . 31)\n (:id . 46))\n ((:tag . "CD") (:stem . "10642") (:form . "10642") (:end . 40) (:start . 35)\n (:id . 47))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 49)\n (:start . 41) (:id . 48))\n ((:tag . "NNS") (:stem . "transcript") (:form . "transcripts") (:end . 61)\n (:start . 50) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n (:id . 50))\n ((:tag . "CD") (:stem . "158") (:form . "158") (:end . 68) (:start . 65)\n (:id . 51))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 78)\n (:start . 69) (:id . 52))\n ((:tag . "NNS") (:stem . "array") (:form . "arrays") (:end . 85)\n (:start . 79) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n (:id . 54))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 88) (:start . 87)\n (:id . 55))\n ((:tag . "NNS") (:stem . "array") (:form . "arrays") (:end . 95)\n (:start . 89) (:id . 56))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 99) (:start . 96)\n (:id . 57))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 106)\n (:start . 100) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s2.382) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100710@unknown@formal@none@1@S@2.@(((:tag . "LS") (:stem . "2") (:form . "2") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 2) (:start . 1) (:id . 43)))@@@1@2@((:identifiers (:sid . :s2.384) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5100711@unknown@formal@none@1@S@Orthology module@(((:tag . "NNP") (:stem . "Orthology") (:form . "Orthology") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 16)\n (:start . 10) (:id . 43)))@@@1@2@((:identifiers (:sid . :s2.385) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100712@unknown@formal@none@1@S@Orthology maps between human and yeast, worm and fly were downloaded from the InParanoid database 72.@(((:tag . "NNP") (:stem . "Orthology") (:form . "Orthology") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "map") (:form . "maps") (:end . 14) (:start . 10)\n (:id . 43))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 22)\n (:start . 15) (:id . 44))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 28) (:start . 23)\n (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n (:id . 46))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 38) (:start . 33)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n (:id . 48))\n ((:tag . "NN") (:stem . "worm") (:form . "worm") (:end . 44) (:start . 40)\n (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n (:id . 50))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 52) (:start . 49)\n (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 57) (:start . 53)\n (:id . 52))\n ((:tag . "VBN") (:stem . "downloade") (:form . "downloaded") (:end . 68)\n (:start . 58) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 73) (:start . 69)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n (:id . 55))\n ((:tag . "NN") (:stem . "inparanoid") (:form . "InParanoid") (:end . 88)\n (:start . 78) (:id . 56))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 97)\n (:start . 89) (:id . 57))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 100) (:start . 98)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s2.386) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100713@unknown@formal@none@1@S@Interaction datasets for model organisms were downloaded from the BIND 66, DIP 65 and GRID 69 databases.@(((:tag . "NNP") (:stem . "Interaction") (:form . "Interaction") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 20)\n (:start . 12) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 24) (:start . 21)\n (:id . 44))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 30) (:start . 25)\n (:id . 45))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 40)\n (:start . 31) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 45) (:start . 41)\n (:id . 47))\n ((:tag . "VBN") (:stem . "downloade") (:form . "downloaded") (:end . 56)\n (:start . 46) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 61) (:start . 57)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n (:id . 50))\n ((:tag . "NNP") (:stem . "BIND") (:form . "BIND") (:end . 70) (:start . 66)\n (:id . 51))\n ((:tag . "CD") (:stem . "66") (:form . "66") (:end . 73) (:start . 71)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n (:id . 53))\n ((:tag . "NNP") (:stem . "DIP") (:form . "DIP") (:end . 78) (:start . 75)\n (:id . 54))\n ((:tag . "CD") (:stem . "65") (:form . "65") (:end . 81) (:start . 79)\n (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n (:id . 56))\n ((:tag . "NN") (:stem . "grid") (:form . "GRID") (:end . 90) (:start . 86)\n (:id . 57))\n ((:tag . "CD") (:stem . "69") (:form . "69") (:end . 93) (:start . 91)\n (:id . 58))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 103)\n (:start . 94) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s2.387) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100714@unknown@formal@none@1@S@Orthology interaction data were classified into 13 bins.@(((:tag . "NNP") (:stem . "Orthology") (:form . "Orthology") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 21)\n (:start . 10) (:id . 43))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 26) (:start . 22)\n (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 31) (:start . 27)\n (:id . 45))\n ((:tag . "VBN") (:stem . "classify") (:form . "classified") (:end . 42)\n (:start . 32) (:id . 46))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 47) (:start . 43)\n (:id . 47))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 50) (:start . 48)\n (:id . 48))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 55) (:start . 51)\n (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s2.388) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100715@unknown@formal@none@1@S@High, medium and low confidence bins were defined for human protein pairs that have interacting orthologs in either yeast, fly or worm (for a total of 9 bins).@(((:tag . "JJ") (:stem . "high") (:form . "High") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 12) (:start . 6)\n (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 20) (:start . 17)\n (:id . 46))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 31)\n (:start . 21) (:id . 47))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 36) (:start . 32)\n (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 41) (:start . 37)\n (:id . 49))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 49)\n (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 53) (:start . 50)\n (:id . 51))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 59) (:start . 54)\n (:id . 52))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 67)\n (:start . 60) (:id . 53))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 73) (:start . 68)\n (:id . 54))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 78) (:start . 74)\n (:id . 55))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 83) (:start . 79)\n (:id . 56))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 95)\n (:start . 84) (:id . 57))\n ((:tag . "NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 105)\n (:start . 96) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n (:id . 59))\n ((:tag . "DT") (:stem . "either") (:form . "either") (:end . 115)\n (:start . 109) (:id . 60))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 121)\n (:start . 116) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n (:id . 62))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 126) (:start . 123)\n (:id . 63))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 129) (:start . 127)\n (:id . 64))\n ((:tag . "NN") (:stem . "worm") (:form . "worm") (:end . 134) (:start . 130)\n (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 136) (:start . 135)\n (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 139) (:start . 136)\n (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 141) (:start . 140)\n (:id . 68))\n ((:tag . "NN") (:stem . "total") (:form . "total") (:end . 147)\n (:start . 142) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 150) (:start . 148)\n (:id . 70))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 152) (:start . 151)\n (:id . 71))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 157) (:start . 153)\n (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s2.389) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100716@unknown@formal@none@1@S@The high confidence bins were populated by human protein pairs that have interacting orthologs that both achieve an InParanoid score of 1 (i.e. both proteins involved in an interaction in another organism are respectively the best orthology match for the two human proteins under consideration).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 19)\n (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 24) (:start . 20)\n (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 29) (:start . 25)\n (:id . 46))\n ((:tag . "VBN") (:stem . "populate") (:form . "populated") (:end . 39)\n (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 42) (:start . 40)\n (:id . 48))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 48) (:start . 43)\n (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 56)\n (:start . 49) (:id . 50))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 62) (:start . 57)\n (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 67) (:start . 63)\n (:id . 52))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 72) (:start . 68)\n (:id . 53))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 84)\n (:start . 73) (:id . 54))\n ((:tag . "NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 94)\n (:start . 85) (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 99) (:start . 95)\n (:id . 56))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 104) (:start . 100)\n (:id . 57))\n ((:tag . "VBP") (:stem . "achieve") (:form . "achieve") (:end . 112)\n (:start . 105) (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 115) (:start . 113)\n (:id . 59))\n ((:tag . "JJ") (:stem . "inparanoid") (:form . "InParanoid") (:end . 126)\n (:start . 116) (:id . 60))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 132)\n (:start . 127) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 135) (:start . 133)\n (:id . 62))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 137) (:start . 136)\n (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n (:id . 64))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 143) (:start . 139)\n (:id . 65))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 148) (:start . 144)\n (:id . 66))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 157)\n (:start . 149) (:id . 67))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 166)\n (:start . 158) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 169) (:start . 167)\n (:id . 69))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 172) (:start . 170)\n (:id . 70))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 184)\n (:start . 173) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 187) (:start . 185)\n (:id . 72))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 195)\n (:start . 188) (:id . 73))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 204)\n (:start . 196) (:id . 74))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 208) (:start . 205)\n (:id . 75))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 221)\n (:start . 209) (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 225) (:start . 222)\n (:id . 77))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 230) (:start . 226)\n (:id . 78))\n ((:tag . "NN") (:stem . "orthology") (:form . "orthology") (:end . 240)\n (:start . 231) (:id . 79))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 246)\n (:start . 241) (:id . 80))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 250) (:start . 247)\n (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 254) (:start . 251)\n (:id . 82))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 258) (:start . 255)\n (:id . 83))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 264)\n (:start . 259) (:id . 84))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 273)\n (:start . 265) (:id . 85))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 279)\n (:start . 274) (:id . 86))\n ((:tag . "NN") (:stem . "consideration") (:form . "consideration")\n (:end . 293) (:start . 280) (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 294) (:start . 293)\n (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 295) (:start . 294)\n (:id . 89)))@@@1@48@((:identifiers (:sid . :s2.390) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100717@unknown@formal@none@1@S@The medium confidence bins were populated by human protein pairs that have interacting orthologs but only one of the interacting orthologs has an InParanoid score of 1.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 21)\n (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 26) (:start . 22)\n (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 31) (:start . 27)\n (:id . 46))\n ((:tag . "VBN") (:stem . "populate") (:form . "populated") (:end . 41)\n (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 44) (:start . 42)\n (:id . 48))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 50) (:start . 45)\n (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 58)\n (:start . 51) (:id . 50))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 64) (:start . 59)\n (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 69) (:start . 65)\n (:id . 52))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 74) (:start . 70)\n (:id . 53))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 86)\n (:start . 75) (:id . 54))\n ((:tag . "NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 96)\n (:start . 87) (:id . 55))\n ((:tag . "CC") (:stem . "but") (:form . 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"1") (:end . 148) (:start . 147)\n (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n (:id . 66))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 154) (:start . 150)\n (:id . 67))\n ((:tag . "DT") (:stem . "neither") (:form . "neither") (:end . 162)\n (:start . 155) (:id . 68))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 165) (:start . 163)\n (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 169) (:start . 166)\n (:id . 70))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 174) (:start . 170)\n (:id . 71))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 180)\n (:start . 175) (:id . 72))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 184) (:start . 181)\n (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 188) (:start . 185)\n (:id . 74))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 192) (:start . 189)\n (:id . 75))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 198)\n (:start . 193) (:id . 76))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 207)\n (:start . 199) (:id . 77))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 213)\n (:start . 208) (:id . 78))\n ((:tag . "NN") (:stem . "consideration") (:form . "consideration")\n (:end . 227) (:start . 214) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 228) (:start . 227)\n (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n (:id . 81)))@@@1@40@((:ncues ((:id . :x2.392.1) (:span 119 126)))\n (:nscopes ((:id . :x2.392.1) (:span 119 148)))\n (:identifiers (:sid . :s2.392) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100720@unknown@formal@none@1@S@3.@(((:tag . "LS") (:stem . "3") (:form . "3") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 2) (:start . 1) (:id . 43)))@@@1@2@((:identifiers (:sid . :s2.394) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5100721@unknown@formal@none@1@S@Combined module@(((:tag . "VBN") (:stem . "combine") (:form . "Combined") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 15) (:start . 9)\n (:id . 43)))@@@1@2@((:identifiers (:sid . :s2.395) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100722@unknown@formal@none@1@S@This module incorporates three distinct features in a non-naïve Bayesian framework: subcellular localization, domain co-occurrence and post-translational modification co-occurrence.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "module") (:form . 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":") (:end . 83) (:start . 82)\n (:id . 53))\n ((:tag . "JJ") (:stem . "subcellular") (:form . "subcellular") (:end . 95)\n (:start . 84) (:id . 54))\n ((:tag . "NN") (:stem . "localization") (:form . "localization") (:end . 108)\n (:start . 96) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 116)\n (:start . 110) (:id . 57))\n ((:tag . "NN") (:stem . "co-occurrence") (:form . "co-occurrence")\n (:end . 130) (:start . 117) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n (:id . 59))\n ((:tag . "JJ") (:stem . "post-translational") (:form . "post-translational")\n (:end . 153) (:start . 135) (:id . 60))\n ((:tag . "NN") (:stem . "modification") (:form . "modification") (:end . 166)\n (:start . 154) (:id . 61))\n ((:tag . "NN") (:stem . "co-occurrence") (:form . "co-occurrence")\n (:end . 180) (:start . 167) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s2.396) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100723@unknown@formal@none@1@S@Subcellular localization@(((:tag . "JJ") (:stem . "subcellular") (:form . "Subcellular") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "localization") (:form . 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"which") (:end . 485)\n (:start . 480) (:id . 115))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 491)\n (:start . 486) (:id . 116))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 496) (:start . 492)\n (:id . 117))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 499) (:start . 497)\n (:id . 118))\n ((:tag . "NN") (:stem . "localization") (:form . "localization") (:end . 512)\n (:start . 500) (:id . 119))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 524)\n (:start . 513) (:id . 120))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 525) (:start . 524)\n (:id . 121)))@@@1@80@((:ncues ((:id . :x2.398.1) (:span 497 499)))\n (:nscopes ((:id . :x2.398.1) (:span 497 524)))\n (:identifiers (:sid . :s2.398) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100725@unknown@formal@none@1@S@Neighboring compartments were chosen as compartment pairs sharing a high proportion of proteins, as investigated previously 54.@(((:tag . "VBG") (:stem . "neighbor") (:form . "Neighboring") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "compartment") (:form . "compartments") (:end . 24)\n (:start . 12) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 29) (:start . 25)\n (:id . 44))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 36)\n (:start . 30) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 39) (:start . 37)\n (:id . 46))\n ((:tag . "NN") (:stem . "compartment") (:form . 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(:end . 137) (:start . 136)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.401) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100728@unknown@formal@none@1@S@Chi-square scores were calculated for all pairs of domains/motifs that occurred in the training data and were then grouped into 5 bins of increasing value.@(((:tag . "JJ") (:stem . "chi-square") (:form . "Chi-square") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 17)\n (:start . 11) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 22) (:start . 18)\n (:id . 44))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 33)\n (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 37) (:start . 34)\n (:id . 46))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 41) (:start . 38)\n (:id . 47))\n ((:tag . "NNS") (:stem . 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(:end . 155) (:start . 154)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.402) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100730@unknown@formal@none@1@S@When protein pairs contained more than one domain pair, the domain pair assigned to the highest Chi-square score bin was used to assign a likelihood of interaction.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 28)\n (:start . 19) (:id . 45))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 33) (:start . 29)\n (:id . 46))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 38) (:start . 34)\n (:id . 47))\n ((:tag . "CD") (:stem . 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"JJ") (:stem . "chi-square") (:form . "Chi-square") (:end . 106)\n (:start . 96) (:id . 59))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 112)\n (:start . 107) (:id . 60))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 116) (:start . 113)\n (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 120) (:start . 117)\n (:id . 62))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 125) (:start . 121)\n (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 128) (:start . 126)\n (:id . 64))\n ((:tag . "VB") (:stem . "assign") (:form . "assign") (:end . 135)\n (:start . 129) (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 137) (:start . 136)\n (:id . 66))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 148)\n (:start . 138) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n (:id . 68))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 163)\n (:start . 152) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s2.404) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100731@unknown@formal@none@1@S@Post-translational modification (PTM) pair co-occurrence@(((:tag . "JJ") (:stem . "post-translational") (:form . "Post-translational")\n (:end . 18) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "modification") (:form . "modification") (:end . 31)\n (:start . 19) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 33) (:start . 32)\n (:id . 44))\n ((:tag . "NNP") (:stem . "PTM") (:form . "PTM") (:end . 36) (:start . 33)\n (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 37) (:start . 36)\n (:id . 46))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 42) (:start . 38)\n (:id . 47))\n ((:tag . "NN") (:stem . "co-occurrence") (:form . "co-occurrence")\n (:end . 56) (:start . 43) (:id . 48)))@@@1@7@((:identifiers (:sid . :s2.405) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100732@unknown@formal@none@1@S@Likelihoods were assessed using a PTM pair enrichment score calculated as the probability of co-occurrence of two specific PTMs in all pairs of interacting protein pairs divided by the probability of occurrence of both of these PTMs separately: PTM_score=P(PTM[i],PTM[j]|I)P(PTM[i]|I)∗P(PTM[j]|I) where PTM[i] and PTM[j] are distinct PTMs and I is the set of all interacting proteins that were used to train the predictor.@(((:tag . "NNP") (:stem . "Likelihood") (:form . "Likelihoods") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 16) (:start . 12)\n (:id . 43))\n ((:tag . "VBN") (:stem . "assess") (:form . 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"the") (:form . "the") (:end . 351) (:start . 348)\n (:id . 94))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 355) (:start . 352)\n (:id . 95))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 358) (:start . 356)\n (:id . 96))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 362) (:start . 359)\n (:id . 97))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 374)\n (:start . 363) (:id . 98))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 383)\n (:start . 375) (:id . 99))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 388) (:start . 384)\n (:id . 100))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 393) (:start . 389)\n (:id . 101))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 398) (:start . 394)\n (:id . 102))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 401) (:start . 399)\n (:id . 103))\n ((:tag . "VB") (:stem . "train") (:form . "train") (:end . 407)\n (:start . 402) (:id . 104))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 411) (:start . 408)\n (:id . 105))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 421)\n (:start . 412) (:id . 106))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 422) (:start . 421)\n (:id . 107)))@@@1@66@((:identifiers (:sid . :s2.406) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100733@unknown@formal@none@1@S@The annotations of PTMs in human proteins were downloaded from UniProt 76 and HPRD 15.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "annotation") (:form . "annotations") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n (:id . 44))\n ((:tag . "NNS") (:stem . "ptm") (:form . "PTMs") (:end . 23) (:start . 19)\n (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 32) (:start . 27)\n (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 41)\n (:start . 33) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 46) (:start . 42)\n (:id . 49))\n ((:tag . "VBN") (:stem . "downloade") (:form . "downloaded") (:end . 57)\n (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 62) (:start . 58)\n (:id . 51))\n ((:tag . "NNP") (:stem . "UniProt") (:form . "UniProt") (:end . 70)\n (:start . 63) (:id . 52))\n ((:tag . "CD") (:stem . "76") (:form . "76") (:end . 73) (:start . 71)\n (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n (:id . 54))\n ((:tag . "NNP") (:stem . "HPRD") (:form . "HPRD") (:end . 82) (:start . 78)\n (:id . 55))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 85) (:start . 83)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s2.407) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100734@unknown@formal@none@1@S@PTM instances described as "predicted", "probable" or "possible" were excluded, leaving 3439 distinct proteins with PTM annotations in the training set.@(((:tag . "NNP") (:stem . "PTM") (:form . "PTM") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 23)\n (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 26) (:start . 24)\n (:id . 45))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 28) (:start . 27)\n (:id . 46))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 37)\n (:start . 28) (:id . 47))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 38) (:start . 37)\n (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n (:id . 49))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 41) (:start . 40)\n (:id . 50))\n ((:tag . "JJ") (:stem . "probable") (:form . "probable") (:end . 49)\n (:start . 41) (:id . 51))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 50) (:start . 49)\n (:id . 52))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 53) (:start . 51)\n (:id . 53))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 55) (:start . 54)\n (:id . 54))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 63)\n (:start . 55) (:id . 55))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 64) (:start . 63)\n (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 69) (:start . 65)\n (:id . 57))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 78)\n (:start . 70) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n (:id . 59))\n ((:tag . "VBG") (:stem . "leave") (:form . "leaving") (:end . 87)\n (:start . 80) (:id . 60))\n ((:tag . "CD") (:stem . "3439") (:form . "3439") (:end . 92) (:start . 88)\n (:id . 61))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 101)\n (:start . 93) (:id . 62))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 110)\n (:start . 102) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 115) (:start . 111)\n (:id . 64))\n ((:tag . "NN") (:stem . "ptm") (:form . "PTM") (:end . 119) (:start . 116)\n (:id . 65))\n ((:tag . "NNS") (:stem . "annotation") (:form . "annotations") (:end . 131)\n (:start . 120) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 134) (:start . 132)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n (:id . 68))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 147)\n (:start . 139) (:id . 69))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 151) (:start . 148)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s2.408) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100735@unknown@formal@none@1@S@The PTM pair enrichment scores were grouped into 4 bins of increasing value.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "PTM") (:form . "PTM") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 23)\n (:start . 13) (:id . 45))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 30)\n (:start . 24) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 35) (:start . 31)\n (:id . 47))\n ((:tag . "VBN") (:stem . "group") (:form . "grouped") (:end . 43)\n (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 48) (:start . 44)\n (:id . 49))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 50) (:start . 49)\n (:id . 50))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 55) (:start . 51)\n (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n (:id . 52))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 69)\n (:start . 59) (:id . 53))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 75) (:start . 70)\n (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.409) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100736@unknown@formal@none@1@S@The localization, co-occurrence of domains, and PTMs were considered simultaneously to measure their predictive power in assessing the likelihood of protein interaction.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "localization") (:form . "localization") (:end . 16)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 44))\n ((:tag . "NN") (:stem . "co-occurrence") (:form . "co-occurrence")\n (:end . 31) (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n (:id . 46))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 42)\n (:start . 35) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n (:id . 49))\n ((:tag . "NNP") (:stem . "PTM") (:form . "PTMs") (:end . 52) (:start . 48)\n (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 57) (:start . 53)\n (:id . 51))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 68)\n (:start . 58) (:id . 52))\n ((:tag . "RB") (:stem . "simultaneously") (:form . "simultaneously")\n (:end . 83) (:start . 69) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 86) (:start . 84)\n (:id . 54))\n ((:tag . "VB") (:stem . "measure") (:form . "measure") (:end . 94)\n (:start . 87) (:id . 55))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 100)\n (:start . 95) (:id . 56))\n ((:tag . "JJ") (:stem . "predictive") (:form . "predictive") (:end . 111)\n (:start . 101) (:id . 57))\n ((:tag . "NN") (:stem . "power") (:form . "power") (:end . 117)\n (:start . 112) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 120) (:start . 118)\n (:id . 59))\n ((:tag . "VBG") (:stem . "assess") (:form . "assessing") (:end . 130)\n (:start . 121) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n (:id . 61))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 145)\n (:start . 135) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 148) (:start . 146)\n (:id . 63))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 156)\n (:start . 149) (:id . 64))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 168)\n (:start . 157) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s2.410) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100737@unknown@formal@none@1@S@To do this, all possible combinations of the 4 localization bins, 5 chi-square domain-co-occurrence bins and 4 PTM_score bins were investigated and are referred to as the combined module.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "do") (:form . "do") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 10) (:start . 6)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 45))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 15) (:start . 12)\n (:id . 46))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 24)\n (:start . 16) (:id . 47))\n ((:tag . "NNS") (:stem . "combination") (:form . "combinations") (:end . 37)\n (:start . 25) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n (:id . 50))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 46) (:start . 45)\n (:id . 51))\n ((:tag . "NN") (:stem . "localization") (:form . "localization") (:end . 59)\n (:start . 47) (:id . 52))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 64) (:start . 60)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n (:id . 54))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 67) (:start . 66)\n (:id . 55))\n ((:tag . "JJ") (:stem . "chi-square") (:form . "chi-square") (:end . 78)\n (:start . 68) (:id . 56))\n ((:tag . "NN") (:stem . "domain-co-occurrence")\n (:form . "domain-co-occurrence") (:end . 99) (:start . 79) (:id . 57))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 104) (:start . 100)\n (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n (:id . 59))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 110) (:start . 109)\n (:id . 60))\n ((:tag . "NNP") (:stem . "PTM_score") (:form . "PTM_score") (:end . 120)\n (:start . 111) (:id . 61))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 125) (:start . 121)\n (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 130) (:start . 126)\n (:id . 63))\n ((:tag . "VBN") (:stem . "investigate") (:form . "investigated") (:end . 143)\n (:start . 131) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 147) (:start . 144)\n (:id . 65))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 151) (:start . 148)\n (:id . 66))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 160)\n (:start . 152) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 163) (:start . 161)\n (:id . 68))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 166) (:start . 164)\n (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 170) (:start . 167)\n (:id . 70))\n ((:tag . "JJ") (:stem . "combined") (:form . "combined") (:end . 179)\n (:start . 171) (:id . 71))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 186)\n (:start . 180) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s2.411) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100738@unknown@formal@none@1@S@4.@(((:tag . "LS") (:stem . "4") (:form . "4") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 2) (:start . 1) (:id . 43)))@@@1@2@((:identifiers (:sid . :s2.412) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5100740@unknown@formal@none@1@S@It has been suggested that unstructured regions of proteins are often involved in binding interactions, particularly in the case of transient interactions 77.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "VBN") (:stem . "suggest") (:form . "suggested") (:end . 21)\n (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n (:id . 46))\n ((:tag . "JJ") (:stem . "unstructured") (:form . "unstructured") (:end . 39)\n (:start . 27) (:id . 47))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 47)\n (:start . 40) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n (:id . 49))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 59)\n (:start . 51) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 63) (:start . 60)\n (:id . 51))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 69) (:start . 64)\n (:id . 52))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 78)\n (:start . 70) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n (:id . 54))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 89)\n (:start . 82) (:id . 55))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 102)\n (:start . 90) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n (:id . 57))\n ((:tag . "RB") (:stem . "particularly") (:form . "particularly") (:end . 116)\n (:start . 104) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 119) (:start . 117)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n (:id . 60))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 128) (:start . 124)\n (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n (:id . 62))\n ((:tag . "JJ") (:stem . "transient") (:form . "transient") (:end . 141)\n (:start . 132) (:id . 63))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 154)\n (:start . 142) (:id . 64))\n ((:tag . "CD") (:stem . "77") (:form . "77") (:end . 157) (:start . 155)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x2.414.1) (:span 12 21)))\n (:hscopes ((:id . :x2.414.1) (:span 12 154)))\n (:identifiers (:sid . :s2.414) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100741@unknown@formal@none@1@S@Protein intrinsic disorder was predicted for all proteins considered by using the VSL2B predictor 78.@(((:tag . "NN") (:stem . "protein") (:form . "Protein") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "intrinsic") (:form . "intrinsic") (:end . 17)\n (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "disorder") (:form . "disorder") (:end . 26)\n (:start . 18) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 30) (:start . 27)\n (:id . 45))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 40)\n (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 44) (:start . 41)\n (:id . 47))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 48) (:start . 45)\n (:id . 48))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 57)\n (:start . 49) (:id . 49))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 68)\n (:start . 58) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 71) (:start . 69)\n (:id . 51))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 77) (:start . 72)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n (:id . 53))\n ((:tag . "NNP") (:stem . "VSL2B") (:form . "VSL2B") (:end . 87) (:start . 82)\n (:id . 54))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 97)\n (:start . 88) (:id . 55))\n ((:tag . "CD") (:stem . "78") (:form . "78") (:end . 100) (:start . 98)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s2.415) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100742@unknown@formal@none@1@S@The disorder score for protein pairs was then calculated as the sum of percent disorder for each protein of the pair.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "disorder") (:form . "disorder") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 30)\n (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 36) (:start . 31)\n (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 40) (:start . 37)\n (:id . 48))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 45) (:start . 41)\n (:id . 49))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 56)\n (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 59) (:start . 57)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n (:id . 52))\n ((:tag . "NN") (:stem . "sum") (:form . "sum") (:end . 67) (:start . 64)\n (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n (:id . 54))\n ((:tag . "NN") (:stem . "percent") (:form . "percent") (:end . 78)\n (:start . 71) (:id . 55))\n ((:tag . "NN") (:stem . "disorder") (:form . "disorder") (:end . 87)\n (:start . 79) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 91) (:start . 88)\n (:id . 57))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 96) (:start . 92)\n (:id . 58))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 104)\n (:start . 97) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n (:id . 61))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 116) (:start . 112)\n (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s2.416) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100743@unknown@formal@none@1@S@Disorder scores were grouped into 6 bins of increasing value.@(((:tag . "NN") (:stem . "disorder") (:form . "Disorder") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 15) (:start . 9)\n (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 20) (:start . 16)\n (:id . 44))\n ((:tag . "VBN") (:stem . "group") (:form . "grouped") (:end . 28)\n (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 33) (:start . 29)\n (:id . 46))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 35) (:start . 34)\n (:id . 47))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 40) (:start . 36)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n (:id . 49))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 54)\n (:start . 44) (:id . 50))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 60) (:start . 55)\n (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 61) (:start . 60)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s2.417) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100744@unknown@formal@none@1@S@The Expression, Orthology, Combined and Disorder modules are referred collectively as the Group A modules.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Expression") (:form . "Expression") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Orthology") (:form . "Orthology") (:end . 25)\n (:start . 16) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Combined") (:form . "Combined") (:end . 35)\n (:start . 27) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Disorder") (:form . "Disorder") (:end . 48)\n (:start . 40) (:id . 49))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 56)\n (:start . 49) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 60) (:start . 57)\n (:id . 51))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 69)\n (:start . 61) (:id . 52))\n ((:tag . "RB") (:stem . "collectively") (:form . "collectively") (:end . 82)\n (:start . 70) (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 85) (:start . 83)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Group") (:form . "Group") (:end . 95) (:start . 90)\n (:id . 56))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 97) (:start . 96)\n (:id . 57))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 105)\n (:start . 98) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s2.418) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100745@unknown@formal@none@1@S@Likelihood ratios for each of the Group A modules are illustrated in Figure 1A (see Additional File 4 for complete likelihood ratios for every possible state of these modules and for detailed calculations of these likelihood ratios).@(((:tag . "NN") (:stem . "likelihood") (:form . "Likelihood") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 17)\n (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 21) (:start . 18)\n (:id . 44))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 26) (:start . 22)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Group") (:form . "Group") (:end . 39) (:start . 34)\n (:id . 48))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 41) (:start . 40)\n (:id . 49))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 49)\n (:start . 42) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 53) (:start . 50)\n (:id . 51))\n ((:tag . "VBN") (:stem . "illustrate") (:form . "illustrated") (:end . 65)\n (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 75)\n (:start . 69) (:id . 54))\n ((:tag . "NN") (:stem . "1a") (:form . "1A") (:end . 78) (:start . 76)\n (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 80) (:start . 79)\n (:id . 56))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 83) (:start . 80)\n (:id . 57))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 94)\n (:start . 84) (:id . 58))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 99) (:start . 95)\n (:id . 59))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 101) (:start . 100)\n (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 105) (:start . 102)\n (:id . 61))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 114)\n (:start . 106) (:id . 62))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 125)\n (:start . 115) (:id . 63))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 132)\n (:start . 126) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 136) (:start . 133)\n (:id . 65))\n ((:tag . "DT") (:stem . "every") (:form . "every") (:end . 142)\n (:start . 137) (:id . 66))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 151)\n (:start . 143) (:id . 67))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 157)\n (:start . 152) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 160) (:start . 158)\n (:id . 69))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 166)\n (:start . 161) (:id . 70))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 174)\n (:start . 167) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 178) (:start . 175)\n (:id . 72))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 182) (:start . 179)\n (:id . 73))\n ((:tag . "JJ") (:stem . "detailed") (:form . "detailed") (:end . 191)\n (:start . 183) (:id . 74))\n ((:tag . "NNS") (:stem . "calculation") (:form . "calculations") (:end . 204)\n (:start . 192) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 207) (:start . 205)\n (:id . 76))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 213)\n (:start . 208) (:id . 77))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 224)\n (:start . 214) (:id . 78))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 231)\n (:start . 225) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 232) (:start . 231)\n (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 233) (:start . 232)\n (:id . 81)))@@@1@40@((:identifiers (:sid . :s2.419) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100746@unknown@formal@none@1@S@5.@(((:tag . "LS") (:stem . "5") (:form . "5") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 2) (:start . 1) (:id . 43)))@@@1@2@((:identifiers (:sid . :s2.420) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5100747@unknown@formal@none@1@S@Transitive module@(((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 17)\n (:start . 11) (:id . 43)))@@@1@2@((:identifiers (:sid . :s2.421) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100748@unknown@formal@none@1@S@The transitive module works on the premise that a pair of proteins is more likely to interact if it shares interacting partners.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "transitive") (:form . "transitive") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 21)\n (:start . 15) (:id . 44))\n ((:tag . "VBZ") (:stem . "work") (:form . "works") (:end . 27) (:start . 22)\n (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "NN") (:stem . "premise") (:form . "premise") (:end . 42)\n (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 47) (:start . 43)\n (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n (:id . 50))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 54) (:start . 50)\n (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n (:id . 52))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 66)\n (:start . 58) (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 69) (:start . 67)\n (:id . 54))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 74) (:start . 70)\n (:id . 55))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 81)\n (:start . 75) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 84) (:start . 82)\n (:id . 57))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 93)\n (:start . 85) (:id . 58))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 96) (:start . 94)\n (:id . 59))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 99) (:start . 97)\n (:id . 60))\n ((:tag . "VBZ") (:stem . "share") (:form . "shares") (:end . 106)\n (:start . 100) (:id . 61))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 118)\n (:start . 107) (:id . 62))\n ((:tag . "NNS") (:stem . "partner") (:form . "partners") (:end . 127)\n (:start . 119) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n (:id . 64)))@@@1@23@((:hcues ((:id . :x2.422.1) (:span 75 81)))\n (:hscopes ((:id . :x2.422.1) (:span 48 127)))\n (:identifiers (:sid . :s2.422) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100750@unknown@formal@none@1@S@Thus, the transitive module takes as input the product of the likelihood ratios of all other modules considered by the predictor (as illustrated in Figure 1B).@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n (:id . 44))\n ((:tag . "JJ") (:stem . "transitive") (:form . "transitive") (:end . 20)\n (:start . 10) (:id . 45))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 27)\n (:start . 21) (:id . 46))\n ((:tag . "VBZ") (:stem . "take") (:form . "takes") (:end . 33) (:start . 28)\n (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 36) (:start . 34)\n (:id . 48))\n ((:tag . "NN") (:stem . "input") (:form . "input") (:end . 42) (:start . 37)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n (:id . 50))\n ((:tag . "NN") (:stem . "product") (:form . "product") (:end . 54)\n (:start . 47) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n (:id . 53))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 72)\n (:start . 62) (:id . 54))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 79)\n (:start . 73) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 86) (:start . 83)\n (:id . 57))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 92) (:start . 87)\n (:id . 58))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 100)\n (:start . 93) (:id . 59))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 111)\n (:start . 101) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 114) (:start . 112)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n (:id . 62))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 128)\n (:start . 119) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 132) (:start . 130)\n (:id . 65))\n ((:tag . "VBN") (:stem . "illustrate") (:form . "illustrated") (:end . 144)\n (:start . 133) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 147) (:start . 145)\n (:id . 67))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 154)\n (:start . 148) (:id . 68))\n ((:tag . "NN") (:stem . "1b") (:form . "1B") (:end . 157) (:start . 155)\n (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s2.424) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100751@unknown@formal@none@1@S@For each pair of proteins in the training set, the product of the likelihood ratios from all other modules (referred to as the preliminary score (PS) in Figure 1) was calculated for all protein pairs neighboring the pair (i.e. all protein pairs which involve one protein from the initial protein pair under study and for which it is possible to calculate such a score).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 25)\n (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 28) (:start . 26)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n (:id . 48))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 41)\n (:start . 33) (:id . 49))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 45) (:start . 42)\n (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n (:id . 52))\n ((:tag . "NN") (:stem . "product") (:form . "product") (:end . 58)\n (:start . 51) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n (:id . 55))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 76)\n (:start . 66) (:id . 56))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 83)\n (:start . 77) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 88) (:start . 84)\n (:id . 58))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 92) (:start . 89)\n (:id . 59))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 98) (:start . 93)\n (:id . 60))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 106)\n (:start . 99) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n (:id . 62))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 116)\n (:start . 108) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 119) (:start . 117)\n (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 122) (:start . 120)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n (:id . 66))\n ((:tag . "JJ") (:stem . "preliminary") (:form . "preliminary") (:end . 138)\n (:start . 127) (:id . 67))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 144)\n (:start . 139) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 146) (:start . 145)\n (:id . 69))\n ((:tag . "NNP") (:stem . "PS") (:form . "PS") (:end . 148) (:start . 146)\n (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 152) (:start . 150)\n (:id . 72))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 159)\n (:start . 153) (:id . 73))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 161) (:start . 160)\n (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n (:id . 75))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 166) (:start . 163)\n (:id . 76))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 177)\n (:start . 167) (:id . 77))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 181) (:start . 178)\n (:id . 78))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 185) (:start . 182)\n (:id . 79))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 193)\n (:start . 186) (:id . 80))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 199)\n (:start . 194) (:id . 81))\n ((:tag . "VBG") (:stem . "neighbor") (:form . "neighboring") (:end . 211)\n (:start . 200) (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 215) (:start . 212)\n (:id . 83))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 220) (:start . 216)\n (:id . 84))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 222) (:start . 221)\n (:id . 85))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 226) (:start . 222)\n (:id . 86))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 230) (:start . 227)\n (:id . 87))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 238)\n (:start . 231) (:id . 88))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 244)\n (:start . 239) (:id . 89))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 250)\n (:start . 245) (:id . 90))\n ((:tag . "VBP") (:stem . "involve") (:form . "involve") (:end . 258)\n (:start . 251) (:id . 91))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 262) (:start . 259)\n (:id . 92))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 270)\n (:start . 263) (:id . 93))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 275) (:start . 271)\n (:id . 94))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 279) (:start . 276)\n (:id . 95))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 287)\n (:start . 280) (:id . 96))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 295)\n (:start . 288) (:id . 97))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 300) (:start . 296)\n (:id . 98))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 306)\n (:start . 301) (:id . 99))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 312)\n (:start . 307) (:id . 100))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 316) (:start . 313)\n (:id . 101))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 320) (:start . 317)\n (:id . 102))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 326)\n (:start . 321) (:id . 103))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 329) (:start . 327)\n (:id . 104))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 332) (:start . 330)\n (:id . 105))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 341)\n (:start . 333) (:id . 106))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 344) (:start . 342)\n (:id . 107))\n ((:tag . "VB") (:stem . "calculate") (:form . "calculate") (:end . 354)\n (:start . 345) (:id . 108))\n ((:tag . "PDT") (:stem . "such") (:form . "such") (:end . 359) (:start . 355)\n (:id . 109))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 361) (:start . 360)\n (:id . 110))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 367)\n (:start . 362) (:id . 111))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 368) (:start . 367)\n (:id . 112))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 369) (:start . 368)\n (:id . 113)))@@@1@72@((:hcues ((:id . :x2.425.1) (:span 333 341)))\n (:hscopes ((:id . :x2.425.1) (:span 333 367)))\n (:identifiers (:sid . :s2.425) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100752@unknown@formal@none@1@S@All preliminary scores above 10 were kept.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "preliminary") (:form . "preliminary") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 22)\n (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 28) (:start . 23)\n (:id . 45))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 31) (:start . 29)\n (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 36) (:start . 32)\n (:id . 47))\n ((:tag . "VBN") (:stem . "keep") (:form . "kept") (:end . 41) (:start . 37)\n (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 42) (:start . 41)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s2.426) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100753@unknown@formal@none@1@S@This parameter was determined empirically.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "parameter") (:form . "parameter") (:end . 14)\n (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 18) (:start . 15)\n (:id . 44))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 29)\n (:start . 19) (:id . 45))\n ((:tag . "RB") (:stem . "empirically") (:form . "empirically") (:end . 41)\n (:start . 30) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 42) (:start . 41)\n (:id . 47)))@@@1@6@((:identifiers (:sid . :s2.427) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100754@unknown@formal@none@1@S@A neighborhood topology score T was then calculated as follows:@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "neighborhood") (:form . "neighborhood") (:end . 14)\n (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "topology") (:form . "topology") (:end . 23)\n (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 29) (:start . 24)\n (:id . 45))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 31) (:start . 30)\n (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 35) (:start . 32)\n (:id . 47))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 40) (:start . 36)\n (:id . 48))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 51)\n (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 54) (:start . 52)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 62)\n (:start . 55) (:id . 51))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 63) (:start . 62)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s2.428) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100755@unknown@formal@none@1@S@Transitive module hypothesis@(((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 17)\n (:start . 11) (:id . 43))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 28)\n (:start . 18) (:id . 44)))@@@1@3@((:identifiers (:sid . :s2.429) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|FigureLegend|)))@oe@9-2-2011 5100756@unknown@formal@none@1@S@Transitive module hypothesis.@(((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 17)\n (:start . 11) (:id . 43))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 28)\n (:start . 18) (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 29) (:start . 28)\n (:id . 45)))@@@1@4@((:identifiers (:sid . :s2.430) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100757@unknown@formal@none@1@S@The Transitive module investigates whether two proteins (such as i and j) that share many common interactors and have few additional interactors that are not common to both proteins are more likely to interact than two proteins (such as i' and j') that share few common interactors.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 21)\n (:start . 15) (:id . 44))\n ((:tag . "NNS") (:stem . "investigate") (:form . "investigates") (:end . 34)\n (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 42)\n (:start . 35) (:id . 46))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 46) (:start . 43)\n (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 55)\n (:start . 47) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n (:id . 49))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 61) (:start . 57)\n (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 64) (:start . 62)\n (:id . 51))\n ((:tag . "NNP") (:stem . "i") (:form . "i") (:end . 66) (:start . 65)\n (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n (:id . 53))\n ((:tag . "NNP") (:stem . "j") (:form . "j") (:end . 72) (:start . 71)\n (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 73) (:start . 72)\n (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 78) (:start . 74)\n (:id . 56))\n ((:tag . "VBP") (:stem . "share") (:form . "share") (:end . 84) (:start . 79)\n (:id . 57))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 89) (:start . 85)\n (:id . 58))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 96)\n (:start . 90) (:id . 59))\n ((:tag . "NNS") (:stem . "interactor") (:form . "interactors") (:end . 108)\n (:start . 97) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n (:id . 61))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 117) (:start . 113)\n (:id . 62))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 121) (:start . 118)\n (:id . 63))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 132)\n (:start . 122) (:id . 64))\n ((:tag . "NNS") (:stem . "interactor") (:form . "interactors") (:end . 144)\n (:start . 133) (:id . 65))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 149) (:start . 145)\n (:id . 66))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 153) (:start . 150)\n (:id . 67))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 157) (:start . 154)\n (:id . 68))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 164)\n (:start . 158) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 167) (:start . 165)\n (:id . 70))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 172) (:start . 168)\n (:id . 71))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 181)\n (:start . 173) (:id . 72))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 185) (:start . 182)\n (:id . 73))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 190) (:start . 186)\n (:id . 74))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 197)\n (:start . 191) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 200) (:start . 198)\n (:id . 76))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 209)\n (:start . 201) (:id . 77))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 214) (:start . 210)\n (:id . 78))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 218) (:start . 215)\n (:id . 79))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 227)\n (:start . 219) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 229) (:start . 228)\n (:id . 81))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 233) (:start . 229)\n (:id . 82))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 236) (:start . 234)\n (:id . 83))\n ((:tag . "NNP") (:stem . "i") (:form . "i") (:end . 238) (:start . 237)\n (:id . 84))\n ((:tag . "POS") (:stem . "'") (:form . "’") (:end . 239) (:start . 238)\n (:id . 85))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 243) (:start . 240)\n (:id . 86))\n ((:tag . "NNP") (:stem . "j") (:form . "j") (:end . 245) (:start . 244)\n (:id . 87))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 246) (:start . 245)\n (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 247) (:start . 246)\n (:id . 89))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 252) (:start . 248)\n (:id . 90))\n ((:tag . "VBP") (:stem . "share") (:form . "share") (:end . 258)\n (:start . 253) (:id . 91))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 262) (:start . 259)\n (:id . 92))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 269)\n (:start . 263) (:id . 93))\n ((:tag . "NNS") (:stem . "interactor") (:form . "interactors") (:end . 281)\n (:start . 270) (:id . 94))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 282) (:start . 281)\n (:id . 95)))@@@1@54@((:hcues ((:id . :x2.431.2) (:span 191 197))\n ((:id . :x2.431.3) (:span 35 42)))\n (:ncues ((:id . :x2.431.1) (:span 154 157)))\n (:hscopes ((:id . :x2.431.2) (:span 43 281))\n ((:id . :x2.431.3) (:span 35 281)))\n (:nscopes ((:id . :x2.431.1) (:span 154 181)))\n (:identifiers (:sid . :s2.431) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100758@unknown@formal@none@1@S@T=∑e∈Ecse1+|Ei\\Ec|+|Ej\\Ec| where Ec is the set of edges that connect proteins i and j to their common interactors, Ei is the set of edges that involve protein i, se is the score (likelihood ratio) of edge e and Ei\\Ec refers to the set difference of Ei and Ec.@(((:tag . "NNP") (:stem . "T=∑e∈Ecse1+|Ei\\\\Ec|+|Ej\\\\Ec|")\n (:form . "T=∑e∈Ecse1+|Ei\\\\Ec|+|Ej\\\\Ec|") (:end . 26) (:start . 0)\n (:id . 42))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 32) (:start . 27)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Ec") (:form . "Ec") (:end . 35) (:start . 33)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 38) (:start . 36)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n (:id . 46))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 46) (:start . 43)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n (:id . 48))\n ((:tag . "NNS") (:stem . "edge") (:form . "edges") (:end . 55) (:start . 50)\n (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 60) (:start . 56)\n (:id . 50))\n ((:tag . "VBP") (:stem . "connect") (:form . "connect") (:end . 68)\n (:start . 61) (:id . 51))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 77)\n (:start . 69) (:id . 52))\n ((:tag . "NN") (:stem . "i") (:form . "i") (:end . 79) (:start . 78)\n (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n (:id . 54))\n ((:tag . "NN") (:stem . "j") (:form . "j") (:end . 85) (:start . 84)\n (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n (:id . 56))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 94)\n (:start . 89) (:id . 57))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 101)\n (:start . 95) (:id . 58))\n ((:tag . "NNS") (:stem . "interactor") (:form . "interactors") (:end . 113)\n (:start . 102) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n (:id . 60))\n ((:tag . "NNP") (:stem . "Ei") (:form . "Ei") (:end . 117) (:start . 115)\n (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 120) (:start . 118)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n (:id . 63))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 128) (:start . 125)\n (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n (:id . 65))\n ((:tag . "NNS") (:stem . "edge") (:form . "edges") (:end . 137)\n (:start . 132) (:id . 66))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 142) (:start . 138)\n (:id . 67))\n ((:tag . "VBP") (:stem . "involve") (:form . "involve") (:end . 150)\n (:start . 143) (:id . 68))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 158)\n (:start . 151) (:id . 69))\n ((:tag . "NN") (:stem . "i") (:form . "i") (:end . 160) (:start . 159)\n (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n (:id . 71))\n ((:tag . "NN") (:stem . "se") (:form . "se") (:end . 164) (:start . 162)\n (:id . 72))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 167) (:start . 165)\n (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 171) (:start . 168)\n (:id . 74))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 177)\n (:start . 172) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 179) (:start . 178)\n (:id . 76))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 189)\n (:start . 179) (:id . 77))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 195)\n (:start . 190) (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 196) (:start . 195)\n (:id . 79))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 199) (:start . 197)\n (:id . 80))\n ((:tag . "NN") (:stem . "edge") (:form . "edge") (:end . 204) (:start . 200)\n (:id . 81))\n ((:tag . "NN") (:stem . "e") (:form . "e") (:end . 206) (:start . 205)\n (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 210) (:start . 207)\n (:id . 83))\n ((:tag . "NNP") (:stem . "Ei\\\\Ec") (:form . "Ei\\\\Ec") (:end . 216)\n (:start . 211) (:id . 84))\n ((:tag . "VBZ") (:stem . "refer") (:form . "refers") (:end . 223)\n (:start . 217) (:id . 85))\n ((:tag . "TO") (:stem . "to") (:form . 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(:end . 259) (:start . 258)\n (:id . 94)))@@@1@53@((:identifiers (:sid . :s2.432) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100760@unknown@formal@none@1@S@Additionally, the topology score T of a pair of proteins increases as the proportion of likely interactors that these two proteins share increases.@(((:tag . "RB") (:stem . "additionally") (:form . "Additionally") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "topology") (:form . "topology") (:end . 26)\n (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 32) (:start . 27)\n (:id . 46))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 34) (:start . 33)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . 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(:end . 147) (:start . 146)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s2.434) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100761@unknown@formal@none@1@S@The topology scores were grouped into 5 bins of increasing value.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "topology") (:form . "topology") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 19)\n (:start . 13) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 24) (:start . 20)\n (:id . 45))\n ((:tag . "VBN") (:stem . "group") (:form . "grouped") (:end . 32)\n (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 37) (:start . 33)\n (:id . 47))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 39) (:start . 38)\n (:id . 48))\n ((:tag . "NNS") (:stem . "bin") (:form . 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(:end . 135) (:start . 134)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.437) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100764@unknown@formal@none@1@S@Accordingly, the likelihood ratio the transitive module outputs for a given protein pair is independent of the likelihood ratio calculated by the Group A modules for this same protein pair.@(((:tag . "RB") (:stem . "accordingly") (:form . "Accordingly") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 27)\n (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 33) (:start . 28)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n (:id . 47))\n ((:tag . 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"for") (:end . 165) (:start . 162)\n (:id . 68))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 170) (:start . 166)\n (:id . 69))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 175) (:start . 171)\n (:id . 70))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 183)\n (:start . 176) (:id . 71))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 188) (:start . 184)\n (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s2.438) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100765@unknown@formal@none@1@S@Correlation analysis@(((:tag . "NN") (:stem . "correlation") (:form . "Correlation") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 20)\n (:start . 12) (:id . 43)))@@@1@2@((:identifiers (:sid . :s2.439) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100766@unknown@formal@none@1@S@The Pearson correlation between pairs of modules was estimated by taking 150 samples of 10000 protein pairs each and calculating the Pearson correlation of the likelihood ratios for the two modules considered, for each sample.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 23)\n (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 31)\n (:start . 24) (:id . 45))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 37) (:start . 32)\n (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n (:id . 47))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 48)\n (:start . 41) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 52) (:start . 49)\n (:id . 49))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 62)\n (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 65) (:start . 63)\n (:id . 51))\n ((:tag . "VBG") (:stem . "take") (:form . "taking") (:end . 72) (:start . 66)\n (:id . 52))\n ((:tag . "CD") (:stem . "150") (:form . "150") (:end . 76) (:start . 73)\n (:id . 53))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 84)\n (:start . 77) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n (:id . 55))\n ((:tag . "CD") (:stem . "10000") (:form . "10000") (:end . 93) (:start . 88)\n (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 101)\n (:start . 94) (:id . 57))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 107)\n (:start . 102) (:id . 58))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 112) (:start . 108)\n (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n (:id . 60))\n ((:tag . "VBG") (:stem . "calculate") (:form . "calculating") (:end . 128)\n (:start . 117) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n (:id . 62))\n ((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 140)\n (:start . 133) (:id . 63))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 152)\n (:start . 141) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n (:id . 66))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 170)\n (:start . 160) (:id . 67))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 177)\n (:start . 171) (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 181) (:start . 178)\n (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 185) (:start . 182)\n (:id . 70))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 189) (:start . 186)\n (:id . 71))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 197)\n (:start . 190) (:id . 72))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 208)\n (:start . 198) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 209) (:start . 208)\n (:id . 74))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 213) (:start . 210)\n (:id . 75))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 218) (:start . 214)\n (:id . 76))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 225)\n (:start . 219) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 226) (:start . 225)\n (:id . 78)))@@@1@37@((:identifiers (:sid . :s2.440) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100767@unknown@formal@none@1@S@The reported correlation values are the average of the 150 experiments.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 24)\n (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 31)\n (:start . 25) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 47))\n ((:tag . "NN") (:stem . "average") (:form . "average") (:end . 47)\n (:start . 40) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n (:id . 50))\n ((:tag . "CD") (:stem . "150") (:form . "150") (:end . 58) (:start . 55)\n (:id . 51))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 70)\n (:start . 59) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.441) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100768@unknown@formal@none@1@S@Samples of the protein pair space were taken instead of considering the whole space as this was more computationally tractable.@(((:tag . "NNS") (:stem . "sample") (:form . "Samples") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . 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"NN") (:stem . "space") (:form . "space") (:end . 83) (:start . 78)\n (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 86) (:start . 84)\n (:id . 56))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 91) (:start . 87)\n (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 95) (:start . 92)\n (:id . 58))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 100) (:start . 96)\n (:id . 59))\n ((:tag . "RB") (:stem . "computationally") (:form . "computationally")\n (:end . 116) (:start . 101) (:id . 60))\n ((:tag . "JJ") (:stem . "tractable") (:form . "tractable") (:end . 126)\n (:start . 117) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n (:id . 62)))@@@1@21@((:ncues ((:id . :x2.442.1) (:span 45 55)))\n (:nscopes ((:id . :x2.442.1) (:span 45 83)))\n (:identifiers (:sid . :s2.442) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100770@unknown@formal@none@1@S@The accuracy of the predictors was measured by performing five-fold cross validation experiments in which the datasets were randomly divided into five non-overlapping sets, four of which were used to train the predictor while the fifth was used to test the prediction accuracy.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "NNS") (:stem . 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"DT") (:stem . "the") (:form . "the") (:end . 229) (:start . 226)\n (:id . 77))\n ((:tag . "NN") (:stem . "fifth") (:form . "fifth") (:end . 235)\n (:start . 230) (:id . 78))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 239) (:start . 236)\n (:id . 79))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 244) (:start . 240)\n (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 247) (:start . 245)\n (:id . 81))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 252) (:start . 248)\n (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 256) (:start . 253)\n (:id . 83))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 267)\n (:start . 257) (:id . 84))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 276)\n (:start . 268) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 277) (:start . 276)\n (:id . 86)))@@@1@45@((:identifiers (:sid . :s2.444) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100771@unknown@formal@none@1@S@The accuracy reported is the average measured for all combinations of training and testing sets using these five sets.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 21)\n (:start . 13) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 24) (:start . 22)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "NN") (:stem . "average") (:form . "average") (:end . 36)\n (:start . 29) (:id . 47))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 45)\n (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 53) (:start . 50)\n (:id . 50))\n ((:tag . "NNS") (:stem . "combination") (:form . "combinations") (:end . 66)\n (:start . 54) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n (:id . 52))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 78)\n (:start . 70) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n (:id . 54))\n ((:tag . "NN") (:stem . "testing") (:form . "testing") (:end . 90)\n (:start . 83) (:id . 55))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 95) (:start . 91)\n (:id . 56))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 101) (:start . 96)\n (:id . 57))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 107)\n (:start . 102) (:id . 58))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 112) (:start . 108)\n (:id . 59))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 117) (:start . 113)\n (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s2.445) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100772@unknown@formal@none@1@S@Testing was done by predicting the total likelihood scores for all protein pairs in the test set using the models computed in the training phase and then counting the number of pairs that were well predicted.@(((:tag . "NNP") (:stem . "Testing") (:form . "Testing") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 11) (:start . 8)\n (:id . 43))\n ((:tag . "VBN") (:stem . "do") (:form . "done") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . 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(:end . 67) (:start . 66)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.447) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100774@unknown@formal@none@1@S@Receiver operator characteristic (ROC) curves plot the true positive rate versus the false positive rate over their full range of possible values.@(((:tag . "NN") (:stem . "receiver") (:form . "Receiver") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "operator") (:form . "operator") (:end . 17)\n (:start . 9) (:id . 43))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n (:end . 32) (:start . 18) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 34) (:start . 33)\n (:id . 45))\n ((:tag . "NNP") (:stem . "ROC") (:form . "ROC") (:end . 37) (:start . 34)\n (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 38) (:start . 37)\n (:id . 47))\n ((:tag . "VBZ") (:stem . "curve") (:form . 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"IN") (:stem . "over") (:form . "over") (:end . 109) (:start . 105)\n (:id . 59))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 115)\n (:start . 110) (:id . 60))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 120) (:start . 116)\n (:id . 61))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 126)\n (:start . 121) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n (:id . 63))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 138)\n (:start . 130) (:id . 64))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 145)\n (:start . 139) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s2.448) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100775@unknown@formal@none@1@S@In some circumstances, it is more informative to use partial ROC curves (ROCn curves) which illustrate the number of true positives identified by the predictor that score higher than the n highest scoring negatives, plotted for all values from 0 to n.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NNS") (:stem . "circumstance") (:form . "circumstances")\n (:end . 21) (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n (:id . 45))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 25) (:start . 23)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . 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"ith") (:end . 218) (:start . 215)\n (:id . 88))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 226)\n (:start . 219) (:id . 89))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 234)\n (:start . 227) (:id . 90))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 243)\n (:start . 235) (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 244) (:start . 243)\n (:id . 92)))@@@1@51@((:identifiers (:sid . :s2.454) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100781@unknown@formal@none@1@S@A novel ensemble learning method for de novo computational identification of DNA binding sites@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 7) (:start . 2)\n (:id . 43))\n ((:tag . "NN") (:stem . "ensemble") (:form . 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"binding") (:end . 88)\n (:start . 81) (:id . 54))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 94) (:start . 89)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.1) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011 5100782@unknown@formal@none@1@S@Abstract@(((:tag . "NN") (:stem . "abstract") (:form . "Abstract") (:end . 8)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s3.2) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100783@unknown@formal@none@1@S@Background@(((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 10)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s3.3) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5100784@unknown@formal@none@1@S@Despite the diversity of motif representations and search algorithms, the de novo computational identification of transcription factor binding sites remains constrained by the limited accuracy of existing algorithms and the need for user-specified input parameters that describe the motif being sought.@(((:tag . "IN") (:stem . "despite") (:form . "Despite") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n (:id . 43))\n ((:tag . "NN") (:stem . "diversity") (:form . "diversity") (:end . 21)\n (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n (:id . 45))\n ((:tag . "NN") (:stem . "motif") (:form . 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(:end . 302) (:start . 301)\n (:id . 84)))@@@1@43@((:identifiers (:sid . :s3.4) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100785@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s3.5) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5100786@unknown@formal@none@1@S@We present a novel ensemble learning method, SCOPE, that is based on the assumption that transcription factor binding sites belong to one of three broad classes of motifs:: non-degenerate, degenerate and gapped motifs.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "present") (:form . "present") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . 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"JJ") (:stem . "degenerate") (:form . "degenerate") (:end . 199)\n (:start . 189) (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 203) (:start . 200)\n (:id . 77))\n ((:tag . "JJ") (:stem . "gapped") (:form . "gapped") (:end . 210)\n (:start . 204) (:id . 78))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 217)\n (:start . 211) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n (:id . 80)))@@@1@39@((:hcues ((:id . :x3.6.1) (:span 73 83)))\n (:hscopes ((:id . :x3.6.1) (:span 73 217)))\n (:identifiers (:sid . :s3.6) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100787@unknown@formal@none@1@S@SCOPE employs a unified scoring metric to combine the results from three motif finding algorithms each aimed at the discovery of one of these classes of motifs.@(((:tag . "NN") (:stem . "scope") (:form . 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"DT") (:stem . "the") (:form . "the") (:end . 211) (:start . 208)\n (:id . 75))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 216) (:start . 212)\n (:id . 76))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n (:end . 230) (:start . 217) (:id . 77))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 237)\n (:start . 231) (:id . 78))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 239) (:start . 238)\n (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 240) (:start . 239)\n (:id . 80)))@@@1@39@((:identifiers (:sid . :s3.17) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100798@unknown@formal@none@1@S@The problem thus simplifies to the identification of overrepresented motifs in a given set of upstream sequences.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "problem") (:form . "problem") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "simplify") (:form . "simplifies") (:end . 27)\n (:start . 17) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n (:end . 49) (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n (:id . 49))\n ((:tag . "JJ") (:stem . "overrepresented") (:form . "overrepresented")\n (:end . 68) (:start . 53) (:id . 50))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 75)\n (:start . 69) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 80) (:start . 79)\n (:id . 53))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 86) (:start . 81)\n (:id . 54))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 90) (:start . 87)\n (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n (:id . 56))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 102)\n (:start . 94) (:id . 57))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 112)\n (:start . 103) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.18) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100800@unknown@formal@none@1@S@Most recent programs represent motifs as position weight matrices (PWMs), which record the frequency of each base at every position in the motif.@(((:tag . "JJS") (:stem . "most") (:form . "Most") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 20)\n (:start . 12) (:id . 44))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 30)\n (:start . 21) (:id . 45))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 37)\n (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 40) (:start . 38)\n (:id . 47))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 49)\n (:start . 41) (:id . 48))\n ((:tag . "NN") (:stem . "weight") (:form . "weight") (:end . 56)\n (:start . 50) (:id . 49))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 65)\n (:start . 57) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n (:id . 51))\n ((:tag . "NNP") (:stem . "PWM") (:form . "PWMs") (:end . 71) (:start . 67)\n (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n (:id . 54))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 79) (:start . 74)\n (:id . 55))\n ((:tag . "VBP") (:stem . "record") (:form . "record") (:end . 86)\n (:start . 80) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n (:id . 57))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 100)\n (:start . 91) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n (:id . 59))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 108) (:start . 104)\n (:id . 60))\n ((:tag . "NN") (:stem . "base") (:form . "base") (:end . 113) (:start . 109)\n (:id . 61))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 116) (:start . 114)\n (:id . 62))\n ((:tag . "DT") (:stem . "every") (:form . "every") (:end . 122)\n (:start . 117) (:id . 63))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 131)\n (:start . 123) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 134) (:start . 132)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n (:id . 66))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 144)\n (:start . 139) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s3.20) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100801@unknown@formal@none@1@S@Other motif finding programs have relied on the use of consensus motif models (in which every base is represented by a letter of the 15-letter IUPAC code, which accounts for degeneracies as well as single bases) or k-mismatch motif models (in which a non-degenerate word with at most k allowed mismatches is used to represent the word).@(((:tag . "JJ") (:stem . "other") (:form . "Other") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 19)\n (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 28)\n (:start . 20) (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 33) (:start . 29)\n (:id . 46))\n ((:tag . "VBN") (:stem . "rely") (:form . "relied") (:end . 40) (:start . 34)\n (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 43) (:start . 41)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n (:id . 49))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 51) (:start . 48)\n (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n (:id . 51))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 64)\n (:start . 55) (:id . 52))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 70) (:start . 65)\n (:id . 53))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 77)\n (:start . 71) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 87) (:start . 82)\n (:id . 57))\n ((:tag . "DT") (:stem . "every") (:form . "every") (:end . 93) (:start . 88)\n (:id . 58))\n ((:tag . "NN") (:stem . "base") (:form . "base") (:end . 98) (:start . 94)\n (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 101) (:start . 99)\n (:id . 60))\n ((:tag . "VBN") (:stem . "represent") (:form . "represented") (:end . 113)\n (:start . 102) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 116) (:start . 114)\n (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 118) (:start . 117)\n (:id . 63))\n ((:tag . "NN") (:stem . "letter") (:form . "letter") (:end . 125)\n (:start . 119) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 128) (:start . 126)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n (:id . 66))\n ((:tag . "NN") (:stem . "15-letter") (:form . "15-letter") (:end . 142)\n (:start . 133) (:id . 67))\n ((:tag . "NNP") (:stem . "IUPAC") (:form . "IUPAC") (:end . 148)\n (:start . 143) (:id . 68))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 153) (:start . 149)\n (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 154) (:start . 153)\n (:id . 70))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 160)\n (:start . 155) (:id . 71))\n ((:tag . "VBZ") (:stem . "account") (:form . "accounts") (:end . 169)\n (:start . 161) (:id . 72))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 173) (:start . 170)\n (:id . 73))\n ((:tag . "NNS") (:stem . "degeneracy") (:form . "degeneracies") (:end . 186)\n (:start . 174) (:id . 74))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 189) (:start . 187)\n (:id . 75))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 194) (:start . 190)\n (:id . 76))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 197) (:start . 195)\n (:id . 77))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 204)\n (:start . 198) (:id . 78))\n ((:tag . "NNS") (:stem . "base") (:form . "bases") (:end . 210)\n (:start . 205) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 211) (:start . 210)\n (:id . 80))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 214) (:start . 212)\n (:id . 81))\n ((:tag . "JJ") (:stem . "k-mismatch") (:form . "k-mismatch") (:end . 225)\n (:start . 215) (:id . 82))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 231)\n (:start . 226) (:id . 83))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 238)\n (:start . 232) (:id . 84))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 240) (:start . 239)\n (:id . 85))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 242) (:start . 240)\n (:id . 86))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 248)\n (:start . 243) (:id . 87))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 250) (:start . 249)\n (:id . 88))\n ((:tag . "JJ") (:stem . "non-degenerate") (:form . "non-degenerate")\n (:end . 265) (:start . 251) (:id . 89))\n ((:tag . "NN") (:stem . "word") (:form . "word") (:end . 270) (:start . 266)\n (:id . 90))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 275) (:start . 271)\n (:id . 91))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 278) (:start . 276)\n (:id . 92))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 283) (:start . 279)\n (:id . 93))\n ((:tag . "NN") (:stem . "k") (:form . "k") (:end . 285) (:start . 284)\n (:id . 94))\n ((:tag . "VBN") (:stem . "allow") (:form . "allowed") (:end . 293)\n (:start . 286) (:id . 95))\n ((:tag . "NNS") (:stem . "mismatch") (:form . "mismatches") (:end . 304)\n (:start . 294) (:id . 96))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 307) (:start . 305)\n (:id . 97))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 312) (:start . 308)\n (:id . 98))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 315) (:start . 313)\n (:id . 99))\n ((:tag . "VB") (:stem . "represent") (:form . "represent") (:end . 325)\n (:start . 316) (:id . 100))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 329) (:start . 326)\n (:id . 101))\n ((:tag . "NN") (:stem . "word") (:form . "word") (:end . 334) (:start . 330)\n (:id . 102))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 335) (:start . 334)\n (:id . 103))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 336) (:start . 335)\n (:id . 104)))@@@1@63@((:identifiers (:sid . :s3.21) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100802@unknown@formal@none@1@S@Regardless of the motif model used, a search for all overrepresented motifs of any length and degree of degeneracy leads to a dauntingly large search space.@(((:tag . "RB") (:stem . "regardless") (:form . "Regardless") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 23) (:start . 18)\n (:id . 45))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 29) (:start . 24)\n (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 34) (:start . 30)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n (:id . 49))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 44)\n (:start . 38) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 48) (:start . 45)\n (:id . 51))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 52) (:start . 49)\n (:id . 52))\n ((:tag . "JJ") (:stem . "overrepresented") (:form . "overrepresented")\n (:end . 68) (:start . 53) (:id . 53))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 75)\n (:start . 69) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n (:id . 55))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 82) (:start . 79)\n (:id . 56))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 89)\n (:start . 83) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n (:id . 58))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 100)\n (:start . 94) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n (:id . 60))\n ((:tag . "NN") (:stem . "degeneracy") (:form . "degeneracy") (:end . 114)\n (:start . 104) (:id . 61))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 120)\n (:start . 115) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 123) (:start . 121)\n (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 125) (:start . 124)\n (:id . 64))\n ((:tag . "RB") (:stem . "dauntingly") (:form . "dauntingly") (:end . 136)\n (:start . 126) (:id . 65))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 142)\n (:start . 137) (:id . 66))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 149)\n (:start . 143) (:id . 67))\n ((:tag . "NN") (:stem . "space") (:form . "space") (:end . 155)\n (:start . 150) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s3.22) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100803@unknown@formal@none@1@S@Thus, motif finding algorithms restrict their search space by using simplified motif representations, employing heuristic search strategies that are prone to local optima, or invoking additional parameters to limit the search space and thereby pass some of the optimization process off to the user 3.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 11) (:start . 6)\n (:id . 44))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 19)\n (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 30)\n (:start . 20) (:id . 46))\n ((:tag . "VBP") (:stem . "restrict") (:form . "restrict") (:end . 39)\n (:start . 31) (:id . 47))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 45)\n (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 52)\n (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "space") (:form . "space") (:end . 58) (:start . 53)\n (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 61) (:start . 59)\n (:id . 51))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 67) (:start . 62)\n (:id . 52))\n ((:tag . "JJ") (:stem . "simplified") (:form . "simplified") (:end . 78)\n (:start . 68) (:id . 53))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 84) (:start . 79)\n (:id . 54))\n ((:tag . "NNS") (:stem . "representation") (:form . "representations")\n (:end . 100) (:start . 85) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n (:id . 56))\n ((:tag . "VBG") (:stem . "employ") (:form . "employing") (:end . 111)\n (:start . 102) (:id . 57))\n ((:tag . "JJ") (:stem . "heuristic") (:form . "heuristic") (:end . 121)\n (:start . 112) (:id . 58))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 128)\n (:start . 122) (:id . 59))\n ((:tag . "NNS") (:stem . "strategy") (:form . "strategies") (:end . 139)\n (:start . 129) (:id . 60))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 144) (:start . 140)\n (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 148) (:start . 145)\n (:id . 62))\n ((:tag . "JJ") (:stem . "prone") (:form . "prone") (:end . 154)\n (:start . 149) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 157) (:start . 155)\n (:id . 64))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 163)\n (:start . 158) (:id . 65))\n ((:tag . "NNS") (:stem . "optimum") (:form . "optima") (:end . 170)\n (:start . 164) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 174) (:start . 172)\n (:id . 68))\n ((:tag . "VBG") (:stem . "invoke") (:form . "invoking") (:end . 183)\n (:start . 175) (:id . 69))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 194)\n (:start . 184) (:id . 70))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 205)\n (:start . 195) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 208) (:start . 206)\n (:id . 72))\n ((:tag . "VB") (:stem . "limit") (:form . "limit") (:end . 214)\n (:start . 209) (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 218) (:start . 215)\n (:id . 74))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 225)\n (:start . 219) (:id . 75))\n ((:tag . "NN") (:stem . "space") (:form . 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"to") (:end . 288) (:start . 286)\n (:id . 86))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 292) (:start . 289)\n (:id . 87))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 297) (:start . 293)\n (:id . 88))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 299) (:start . 298)\n (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 300) (:start . 299)\n (:id . 90)))@@@1@49@((:identifiers (:sid . :s3.23) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100804@unknown@formal@none@1@S@Program parameters (such as motif length, number of occurrences and orientation) that cannot be reasonably specified by the user without prior knowledge about the true binding sites are referred to as nuisance parameters 4.@(((:tag . "NN") (:stem . "program") (:form . "Program") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "parameter") (:form . 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"orientation") (:form . "orientation") (:end . 79)\n (:start . 68) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 85) (:start . 81)\n (:id . 56))\n ((:tag . "NN") (:stem . "cannot") (:form . "cannot") (:end . 92)\n (:start . 86) (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 95) (:start . 93)\n (:id . 58))\n ((:tag . "RB") (:stem . "reasonably") (:form . "reasonably") (:end . 106)\n (:start . 96) (:id . 59))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 116)\n (:start . 107) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 119) (:start . 117)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n (:id . 62))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 128) (:start . 124)\n (:id . 63))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 136)\n (:start . 129) (:id . 64))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 142)\n (:start . 137) (:id . 65))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 152)\n (:start . 143) (:id . 66))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 158)\n (:start . 153) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 162) (:start . 159)\n (:id . 68))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 167) (:start . 163)\n (:id . 69))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 175)\n (:start . 168) (:id . 70))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 181)\n (:start . 176) (:id . 71))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 185) (:start . 182)\n (:id . 72))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 194)\n (:start . 186) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 197) (:start . 195)\n (:id . 74))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 200) (:start . 198)\n (:id . 75))\n ((:tag . "NN") (:stem . "nuisance") (:form . "nuisance") (:end . 209)\n (:start . 201) (:id . 76))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 220)\n (:start . 210) (:id . 77))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 222) (:start . 221)\n (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 223) (:start . 222)\n (:id . 79)))@@@1@38@((:ncues ((:id . :x3.24.1) (:span 129 136)) ((:id . :x3.24.2) (:span 86 92)))\n (:nscopes ((:id . :x3.24.1) (:span 129 181))\n ((:id . :x3.24.2) (:span 81 181)))\n (:identifiers (:sid . :s3.24) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100805@unknown@formal@none@1@S@Selection of the correct settings for these parameters is a crucial step in motif finding, and is often assumed to be the domain of experts.@(((:tag . "NN") (:stem . "selection") (:form . "Selection") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "correct") (:form . "correct") (:end . 24)\n (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "setting") (:form . "settings") (:end . 33)\n (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 37) (:start . 34)\n (:id . 47))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 43) (:start . 38)\n (:id . 48))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 54)\n (:start . 44) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 57) (:start . 55)\n (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 59) (:start . 58)\n (:id . 51))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 67)\n (:start . 60) (:id . 52))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 72) (:start . 68)\n (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 75) (:start . 73)\n (:id . 54))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 81) (:start . 76)\n (:id . 55))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 89)\n (:start . 82) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 97) (:start . 95)\n (:id . 59))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 103) (:start . 98)\n (:id . 60))\n ((:tag . "VBN") (:stem . "assume") (:form . "assumed") (:end . 111)\n (:start . 104) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 114) (:start . 112)\n (:id . 62))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 117) (:start . 115)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n (:id . 64))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 128)\n (:start . 122) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n (:id . 66))\n ((:tag . "NNS") (:stem . "expert") (:form . "experts") (:end . 139)\n (:start . 132) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n (:id . 68)))@@@1@27@((:hcues ((:id . :x3.25.1) (:span 104 111)))\n (:hscopes ((:id . :x3.25.1) (:span 95 139)))\n (:identifiers (:sid . :s3.25) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100806@unknown@formal@none@1@S@In a recent evaluation, Hu and colleagues 4 compared the performance of five motif finders on a single prokaryotic genome, systematically exploring the effects of nuisance parameters, including expected motif length and number of occurrences.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 11) (:start . 5)\n (:id . 44))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 22)\n (:start . 12) (:id . 45))\n ((:tag . ",") (:stem . 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"effects") (:end . 159)\n (:start . 152) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 162) (:start . 160)\n (:id . 68))\n ((:tag . "NN") (:stem . "nuisance") (:form . "nuisance") (:end . 171)\n (:start . 163) (:id . 69))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 182)\n (:start . 172) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 183) (:start . 182)\n (:id . 71))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 193)\n (:start . 184) (:id . 72))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 202)\n (:start . 194) (:id . 73))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 208)\n (:start . 203) (:id . 74))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 215)\n (:start . 209) (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 219) (:start . 216)\n (:id . 76))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 226)\n (:start . 220) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 229) (:start . 227)\n (:id . 78))\n ((:tag . "NNS") (:stem . "occurrence") (:form . "occurrences") (:end . 241)\n (:start . 230) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 242) (:start . 241)\n (:id . 80)))@@@1@39@((:identifiers (:sid . :s3.26) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100807@unknown@formal@none@1@S@Every motif finder they tested was found to be sensitive to values used for these parameters.@(((:tag . "DT") (:stem . "every") (:form . "Every") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "finder") (:form . "finder") (:end . 18)\n (:start . 12) (:id . 44))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 23) (:start . 19)\n (:id . 45))\n ((:tag . "VBD") (:stem . "test") (:form . "tested") (:end . 30) (:start . 24)\n (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 40) (:start . 35)\n (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 43) (:start . 41)\n (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 46) (:start . 44)\n (:id . 50))\n ((:tag . "JJ") (:stem . "sensitive") (:form . "sensitive") (:end . 56)\n (:start . 47) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n (:id . 52))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 66)\n (:start . 60) (:id . 53))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 71) (:start . 67)\n (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 75) (:start . 72)\n (:id . 55))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 81) (:start . 76)\n (:id . 56))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 92)\n (:start . 82) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.27) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100808@unknown@formal@none@1@S@Guidance on the specific parameter settings to use for given motif finding situations is not provided in most publications presenting motif finders.@(((:tag . "NN") (:stem . "guidance") (:form . "Guidance") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 11) (:start . 9)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 24)\n (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "parameter") (:form . "parameter") (:end . 34)\n (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "setting") (:form . "settings") (:end . 43)\n (:start . 35) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 46) (:start . 44)\n (:id . 48))\n ((:tag . "VB") (:stem . "use") (:form . "use") (:end . 50) (:start . 47)\n (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 54) (:start . 51)\n (:id . 50))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 60) (:start . 55)\n (:id . 51))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 66) (:start . 61)\n (:id . 52))\n ((:tag . "VBG") (:stem . "find") (:form . "finding") (:end . 74)\n (:start . 67) (:id . 53))\n ((:tag . "NNS") (:stem . "situation") (:form . "situations") (:end . 85)\n (:start . 75) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 88) (:start . 86)\n (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 92) (:start . 89)\n (:id . 56))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 101)\n (:start . 93) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 104) (:start . 102)\n (:id . 58))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 109) (:start . 105)\n (:id . 59))\n ((:tag . "NNS") (:stem . "publication") (:form . "publications") (:end . 122)\n (:start . 110) (:id . 60))\n ((:tag . "VBG") (:stem . "present") (:form . "presenting") (:end . 133)\n (:start . 123) (:id . 61))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 139)\n (:start . 134) (:id . 62))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 147)\n (:start . 140) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n (:id . 64)))@@@1@23@((:ncues ((:id . :x3.28.1) (:span 89 92)))\n (:nscopes ((:id . :x3.28.1) (:span 0 147)))\n (:identifiers (:sid . :s3.28) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100810@unknown@formal@none@1@S@Nuisance parameters complicate the interpretation of performance comparisons as well.@(((:tag . "NN") (:stem . "nuisance") (:form . "Nuisance") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 19)\n (:start . 9) (:id . 43))\n ((:tag . "VBP") (:stem . "complicate") (:form . "complicate") (:end . 30)\n (:start . 20) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 45))\n ((:tag . "NN") (:stem . "interpretation") (:form . "interpretation")\n (:end . 49) (:start . 35) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n (:id . 47))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 64)\n (:start . 53) (:id . 48))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 76)\n (:start . 65) (:id . 49))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 79) (:start . 77)\n (:id . 50))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 84) (:start . 80)\n (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s3.30) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100811@unknown@formal@none@1@S@A recent large-scale performance comparison between thirteen different motif finding tools used expert knowledge in setting the parameters for every program 5.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 8) (:start . 2)\n (:id . 43))\n ((:tag . "JJ") (:stem . "large-scale") (:form . "large-scale") (:end . 20)\n (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 32)\n (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 43)\n (:start . 33) (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 51)\n (:start . 44) (:id . 47))\n ((:tag . "CD") (:stem . "thirteen") (:form . "thirteen") (:end . 60)\n (:start . 52) (:id . 48))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 70)\n (:start . 61) (:id . 49))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 76) (:start . 71)\n (:id . 50))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 84)\n (:start . 77) (:id . 51))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 90) (:start . 85)\n (:id . 52))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 95) (:start . 91)\n (:id . 53))\n ((:tag . "JJ") (:stem . "expert") (:form . "expert") (:end . 102)\n (:start . 96) (:id . 54))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 112)\n (:start . 103) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n (:id . 56))\n ((:tag . "VBG") (:stem . "set") (:form . "setting") (:end . 123)\n (:start . 116) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n (:id . 58))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 138)\n (:start . 128) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 142) (:start . 139)\n (:id . 60))\n ((:tag . "DT") (:stem . "every") (:form . "every") (:end . 148)\n (:start . 143) (:id . 61))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 156)\n (:start . 149) (:id . 62))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 158) (:start . 157)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.31) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100812@unknown@formal@none@1@S@Several of the programs contributing to the performance comparison were run with different parameter settings for each regulon, and in some cases, motifs were hand filtered as a post-processing step.@(((:tag . "JJ") (:stem . "several") (:form . "Several") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "VBG") (:stem . "contribute") (:form . "contributing") (:end . 36)\n (:start . 24) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n (:id . 48))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 55)\n (:start . 44) (:id . 49))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 66)\n (:start . 56) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 71) (:start . 67)\n (:id . 51))\n ((:tag . "VBN") (:stem . "run") (:form . "run") (:end . 75) (:start . 72)\n (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 80) (:start . 76)\n (:id . 53))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 90)\n (:start . 81) (:id . 54))\n ((:tag . "NN") (:stem . "parameter") (:form . "parameter") (:end . 100)\n (:start . 91) (:id . 55))\n ((:tag . "NNS") (:stem . "setting") (:form . "settings") (:end . 109)\n (:start . 101) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 113) (:start . 110)\n (:id . 57))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 118) (:start . 114)\n (:id . 58))\n ((:tag . "NN") (:stem . "regulon") (:form . "regulon") (:end . 126)\n (:start . 119) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 131) (:start . 128)\n (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 134) (:start . 132)\n (:id . 62))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 139) (:start . 135)\n (:id . 63))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 145)\n (:start . 140) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n (:id . 65))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 153)\n (:start . 147) (:id . 66))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 158) (:start . 154)\n (:id . 67))\n ((:tag . "NN") (:stem . "hand") (:form . "hand") (:end . 163) (:start . 159)\n (:id . 68))\n ((:tag . "VBN") (:stem . "filter") (:form . "filtered") (:end . 172)\n (:start . 164) (:id . 69))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 175) (:start . 173)\n (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 177) (:start . 176)\n (:id . 71))\n ((:tag . "JJ") (:stem . "post-processing") (:form . "post-processing")\n (:end . 193) (:start . 178) (:id . 72))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 198) (:start . 194)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 199) (:start . 198)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.32) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100813@unknown@formal@none@1@S@Such performance comparisons evaluate not just algorithms but also the expertise of the users, making it difficult for a first-time user to select a motif finder on a principled basis.@(((:tag . "JJ") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 16)\n (:start . 5) (:id . 43))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 28)\n (:start . 17) (:id . 44))\n ((:tag . "VBP") (:stem . "evaluate") (:form . "evaluate") (:end . 37)\n (:start . 29) (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 41) (:start . 38)\n (:id . 46))\n ((:tag . "RB") (:stem . "just") (:form . "just") (:end . 46) (:start . 42)\n (:id . 47))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 57)\n (:start . 47) (:id . 48))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 61) (:start . 58)\n (:id . 49))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 66) (:start . 62)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n (:id . 51))\n ((:tag . "NN") (:stem . "expertise") (:form . "expertise") (:end . 80)\n (:start . 71) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n (:id . 54))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 93) (:start . 88)\n (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n (:id . 56))\n ((:tag . "VBG") (:stem . "make") (:form . "making") (:end . 101)\n (:start . 95) (:id . 57))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 104) (:start . 102)\n (:id . 58))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 114)\n (:start . 105) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 118) (:start . 115)\n (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 120) (:start . 119)\n (:id . 61))\n ((:tag . "JJ") (:stem . "first-time") (:form . "first-time") (:end . 131)\n (:start . 121) (:id . 62))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 136) (:start . 132)\n (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 139) (:start . 137)\n (:id . 64))\n ((:tag . "VB") (:stem . "select") (:form . "select") (:end . 146)\n (:start . 140) (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 148) (:start . 147)\n (:id . 66))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 154)\n (:start . 149) (:id . 67))\n ((:tag . "NN") (:stem . "finder") (:form . "finder") (:end . 161)\n (:start . 155) (:id . 68))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 164) (:start . 162)\n (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 166) (:start . 165)\n (:id . 70))\n ((:tag . "JJ") (:stem . "principled") (:form . "principled") (:end . 177)\n (:start . 167) (:id . 71))\n ((:tag . "NN") (:stem . "basis") (:form . "basis") (:end . 183)\n (:start . 178) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s3.33) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100814@unknown@formal@none@1@S@A key result of the Tompa, et al. study was the finding that all of the motif finders had roughly the same average performance under a wide range of conditions and test statistics 5.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 5) (:start . 2)\n (:id . 43))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 12) (:start . 6)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Tompa") (:form . "Tompa") (:end . 25) (:start . 20)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n (:id . 48))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 29) (:start . 27)\n (:id . 49))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 33) (:start . 30)\n (:id . 50))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 39) (:start . 34)\n (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 43) (:start . 40)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n (:id . 53))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 55)\n (:start . 48) (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 60) (:start . 56)\n (:id . 55))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 64) (:start . 61)\n (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n (:id . 58))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 77) (:start . 72)\n (:id . 59))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 85)\n (:start . 78) (:id . 60))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 89) (:start . 86)\n (:id . 61))\n ((:tag . "RB") (:stem . "roughly") (:form . "roughly") (:end . 97)\n (:start . 90) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n (:id . 63))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 106) (:start . 102)\n (:id . 64))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 114)\n (:start . 107) (:id . 65))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 126)\n (:start . 115) (:id . 66))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 132)\n (:start . 127) (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 134) (:start . 133)\n (:id . 68))\n ((:tag . "JJ") (:stem . "wide") (:form . "wide") (:end . 139) (:start . 135)\n (:id . 69))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 145)\n (:start . 140) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 148) (:start . 146)\n (:id . 71))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 159)\n (:start . 149) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 163) (:start . 160)\n (:id . 73))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 168) (:start . 164)\n (:id . 74))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 179)\n (:start . 169) (:id . 75))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 181) (:start . 180)\n (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s3.34) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100815@unknown@formal@none@1@S@This finding was particularly notable because the motif finders studied employed a wide range of motif representations, scoring functions and search strategies and all were operated under the most favorable conditions possible.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "RB") (:stem . "particularly") (:form . "particularly") (:end . 29)\n (:start . 17) (:id . 45))\n ((:tag . "JJ") (:stem . "notable") (:form . "notable") (:end . 37)\n (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 45)\n (:start . 38) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n (:id . 48))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 55) (:start . 50)\n (:id . 49))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 63)\n (:start . 56) (:id . 50))\n ((:tag . "VBN") (:stem . "study") (:form . "studied") (:end . 71)\n (:start . 64) (:id . 51))\n ((:tag . "VBD") (:stem . "employ") (:form . "employed") (:end . 80)\n (:start . 72) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 82) (:start . 81)\n (:id . 53))\n ((:tag . "JJ") (:stem . "wide") (:form . "wide") (:end . 87) (:start . 83)\n (:id . 54))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 93) (:start . 88)\n (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n (:id . 56))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 102) (:start . 97)\n (:id . 57))\n ((:tag . "NNS") (:stem . "representation") (:form . "representations")\n (:end . 118) (:start . 103) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n (:id . 59))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 127)\n (:start . 120) (:id . 60))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 137)\n (:start . 128) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 141) (:start . 138)\n (:id . 62))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 148)\n (:start . 142) (:id . 63))\n ((:tag . "NNS") (:stem . "strategy") (:form . "strategies") (:end . 159)\n (:start . 149) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 163) (:start . 160)\n (:id . 65))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 167) (:start . 164)\n (:id . 66))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 172) (:start . 168)\n (:id . 67))\n ((:tag . "VBN") (:stem . "operate") (:form . "operated") (:end . 181)\n (:start . 173) (:id . 68))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 187)\n (:start . 182) (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 191) (:start . 188)\n (:id . 70))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 196) (:start . 192)\n (:id . 71))\n ((:tag . "JJ") (:stem . "favorable") (:form . "favorable") (:end . 206)\n (:start . 197) (:id . 72))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 217)\n (:start . 207) (:id . 73))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 226)\n (:start . 218) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s3.35) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100816@unknown@formal@none@1@S@Although the average performance of the programs did not differ significantly, the authors found that, for each pair of programs, each program performed better than the other on some subset of the data 5.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 43))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 20)\n (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 32)\n (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 47))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 48)\n (:start . 40) (:id . 48))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 52) (:start . 49)\n (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 56) (:start . 53)\n (:id . 50))\n ((:tag . "VB") (:stem . "differ") (:form . "differ") (:end . 63)\n (:start . 57) (:id . 51))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 77) (:start . 64) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n (:id . 54))\n ((:tag . "NNS") (:stem . "author") (:form . "authors") (:end . 90)\n (:start . 83) (:id . 55))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 96) (:start . 91)\n (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 101) (:start . 97)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 106) (:start . 103)\n (:id . 59))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 111) (:start . 107)\n (:id . 60))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 116) (:start . 112)\n (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n (:id . 62))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 128)\n (:start . 120) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n (:id . 64))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 134) (:start . 130)\n (:id . 65))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 142)\n (:start . 135) (:id . 66))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 152)\n (:start . 143) (:id . 67))\n ((:tag . "JJR") (:stem . "good") (:form . "better") (:end . 159)\n (:start . 153) (:id . 68))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 164) (:start . 160)\n (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n (:id . 70))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 174)\n (:start . 169) (:id . 71))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 177) (:start . 175)\n (:id . 72))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 182) (:start . 178)\n (:id . 73))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 189)\n (:start . 183) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 192) (:start . 190)\n (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 196) (:start . 193)\n (:id . 76))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 201)\n (:start . 197) (:id . 77))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 203) (:start . 202)\n (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n (:id . 79)))@@@1@38@((:identifiers (:sid . :s3.36) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100817@unknown@formal@none@1@S@Previous studies over smaller numbers of motif finders have found that no program clearly stands out as superior to the others and each program outperforms all others on some subset of the regulons 678.@(((:tag . "JJ") (:stem . "previous") (:form . "Previous") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 16)\n (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 21) (:start . 17)\n (:id . 44))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 29)\n (:start . 22) (:id . 45))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 37)\n (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n (:id . 47))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 46) (:start . 41)\n (:id . 48))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 54)\n (:start . 47) (:id . 49))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 59) (:start . 55)\n (:id . 50))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 65) (:start . 60)\n (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 70) (:start . 66)\n (:id . 52))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 73) (:start . 71)\n (:id . 53))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 81)\n (:start . 74) (:id . 54))\n ((:tag . "RB") (:stem . "clearly") (:form . "clearly") (:end . 89)\n (:start . 82) (:id . 55))\n ((:tag . "VBZ") (:stem . "stand") (:form . "stands") (:end . 96)\n (:start . 90) (:id . 56))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 100) (:start . 97)\n (:id . 57))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 103) (:start . 101)\n (:id . 58))\n ((:tag . "JJ") (:stem . "superior") (:form . "superior") (:end . 112)\n (:start . 104) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 115) (:start . 113)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n (:id . 61))\n ((:tag . "NNS") (:stem . "other") (:form . "others") (:end . 126)\n (:start . 120) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n (:id . 63))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 135) (:start . 131)\n (:id . 64))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 143)\n (:start . 136) (:id . 65))\n ((:tag . "VBZ") (:stem . "outperform") (:form . "outperforms") (:end . 155)\n (:start . 144) (:id . 66))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 159) (:start . 156)\n (:id . 67))\n ((:tag . "NNS") (:stem . "other") (:form . "others") (:end . 166)\n (:start . 160) (:id . 68))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 169) (:start . 167)\n (:id . 69))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 174) (:start . 170)\n (:id . 70))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 181)\n (:start . 175) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 184) (:start . 182)\n (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 188) (:start . 185)\n (:id . 73))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 197)\n (:start . 189) (:id . 74))\n ((:tag . "CD") (:stem . "678") (:form . "678") (:end . 201) (:start . 198)\n (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n (:id . 76)))@@@1@35@((:ncues ((:id . :x3.37.1) (:span 71 73)))\n (:nscopes ((:id . :x3.37.1) (:span 71 126)))\n (:identifiers (:sid . :s3.37) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100818@unknown@formal@none@1@S@This diversity of performance has led a number of authors to speculate that ensemble methods, comprising multiple motif finders, may lead to improvements in accuracy 158.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "diversity") (:form . "diversity") (:end . 14)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n (:id . 44))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 29)\n (:start . 18) (:id . 45))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 33) (:start . 30)\n (:id . 46))\n ((:tag . "VBN") (:stem . "lead") (:form . "led") (:end . 37) (:start . 34)\n (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 39) (:start . 38)\n (:id . 48))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 46)\n (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n (:id . 50))\n ((:tag . "NNS") (:stem . "author") (:form . "authors") (:end . 57)\n (:start . 50) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n (:id . 52))\n ((:tag . "VB") (:stem . "speculate") (:form . "speculate") (:end . 70)\n (:start . 61) (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 75) (:start . 71)\n (:id . 54))\n ((:tag . "JJ") (:stem . "ensemble") (:form . "ensemble") (:end . 84)\n (:start . 76) (:id . 55))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 92)\n (:start . 85) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n (:id . 57))\n ((:tag . "VBG") (:stem . "comprise") (:form . "comprising") (:end . 104)\n (:start . 94) (:id . 58))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 113)\n (:start . 105) (:id . 59))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 119)\n (:start . 114) (:id . 60))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 127)\n (:start . 120) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n (:id . 62))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 132) (:start . 129)\n (:id . 63))\n ((:tag . "VB") (:stem . "lead") (:form . "lead") (:end . 137) (:start . 133)\n (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 140) (:start . 138)\n (:id . 65))\n ((:tag . "NNS") (:stem . "improvement") (:form . "improvements") (:end . 153)\n (:start . 141) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 156) (:start . 154)\n (:id . 67))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 165)\n (:start . 157) (:id . 68))\n ((:tag . "CD") (:stem . "158") (:form . "158") (:end . 169) (:start . 166)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x3.38.1) (:span 129 132)) ((:id . :x3.38.2) (:span 61 70)))\n (:hscopes ((:id . :x3.38.1) (:span 129 165))\n ((:id . :x3.38.2) (:span 61 165)))\n (:identifiers (:sid . :s3.38) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100820@unknown@formal@none@1@S@The final predictions are chosen from the ensemble of methods by a learning rule, which may be as simple as finding the maximum score from all the methods, or as complex as optimizing a weighted scoring scheme from among the methods.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 21)\n (:start . 10) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 32)\n (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 37) (:start . 33)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n (:id . 48))\n ((:tag . "NN") (:stem . "ensemble") (:form . "ensemble") (:end . 50)\n (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n (:id . 50))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 61)\n (:start . 54) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 64) (:start . 62)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 66) (:start . 65)\n (:id . 53))\n ((:tag . "NN") (:stem . 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"JJ") (:stem . "maximum") (:form . "maximum") (:end . 127)\n (:start . 120) (:id . 65))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 133)\n (:start . 128) (:id . 66))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 138) (:start . 134)\n (:id . 67))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 142) (:start . 139)\n (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n (:id . 69))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 154)\n (:start . 147) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 155) (:start . 154)\n (:id . 71))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 158) (:start . 156)\n (:id . 72))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 161) (:start . 159)\n (:id . 73))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 169)\n (:start . 162) (:id . 74))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 172) (:start . 170)\n (:id . 75))\n ((:tag . "VBG") (:stem . "optimize") (:form . "optimizing") (:end . 183)\n (:start . 173) (:id . 76))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 185) (:start . 184)\n (:id . 77))\n ((:tag . "JJ") (:stem . "weighted") (:form . "weighted") (:end . 194)\n (:start . 186) (:id . 78))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 202)\n (:start . 195) (:id . 79))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 209)\n (:start . 203) (:id . 80))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 214) (:start . 210)\n (:id . 81))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 220)\n (:start . 215) (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 224) (:start . 221)\n (:id . 83))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 232)\n (:start . 225) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 233) (:start . 232)\n (:id . 85)))@@@1@44@((:hcues ((:id . :x3.40.1) (:span 88 91)))\n (:hscopes ((:id . :x3.40.1) (:span 88 232)))\n (:identifiers (:sid . :s3.40) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100821@unknown@formal@none@1@S@The construction of this learning rule is key to the performance of an ensemble learning method, as the performance of an ensemble method with an ineffective learning rule will be the average of the performance of its component algorithms.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "construction") (:form . "construction") (:end . 16)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 24) (:start . 20)\n (:id . 45))\n ((:tag . "NN") (:stem . "learning") (:form . "learning") (:end . 33)\n (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "rule") (:form . "rule") (:end . 38) (:start . 34)\n (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 41) (:start . 39)\n (:id . 48))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 45) (:start . 42)\n (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n (:id . 51))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 64)\n (:start . 53) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n (:id . 53))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 70) (:start . 68)\n (:id . 54))\n ((:tag . "JJ") (:stem . "ensemble") (:form . "ensemble") (:end . 79)\n (:start . 71) (:id . 55))\n ((:tag . "NN") (:stem . "learning") (:form . "learning") (:end . 88)\n (:start . 80) (:id . 56))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 95)\n (:start . 89) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 99) (:start . 97)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n (:id . 60))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 115)\n (:start . 104) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 118) (:start . 116)\n (:id . 62))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 121) (:start . 119)\n (:id . 63))\n ((:tag . "JJ") (:stem . "ensemble") (:form . "ensemble") (:end . 130)\n (:start . 122) (:id . 64))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 137)\n (:start . 131) (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 142) (:start . 138)\n (:id . 66))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 145) (:start . 143)\n (:id . 67))\n ((:tag . "JJ") (:stem . "ineffective") (:form . "ineffective") (:end . 157)\n (:start . 146) (:id . 68))\n ((:tag . "NN") (:stem . "learning") (:form . "learning") (:end . 166)\n (:start . 158) (:id . 69))\n ((:tag . "NN") (:stem . "rule") (:form . "rule") (:end . 171) (:start . 167)\n (:id . 70))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 176) (:start . 172)\n (:id . 71))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 179) (:start . 177)\n (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 183) (:start . 180)\n (:id . 73))\n ((:tag . "NN") (:stem . "average") (:form . "average") (:end . 191)\n (:start . 184) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 194) (:start . 192)\n (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 198) (:start . 195)\n (:id . 76))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 210)\n (:start . 199) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 213) (:start . 211)\n (:id . 78))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 217) (:start . 214)\n (:id . 79))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 227)\n (:start . 218) (:id . 80))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 238)\n (:start . 228) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 239) (:start . 238)\n (:id . 82)))@@@1@41@((:identifiers (:sid . :s3.41) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100822@unknown@formal@none@1@S@In this context, we note that Tompa et al. 5 found that, although every motif finding program tested had some regulons on which its performance was clearly superior, it was not possible a priori to predict which motif finder represented the best choice under any given set of conditions 5.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 15)\n (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 19) (:start . 17)\n (:id . 46))\n ((:tag . "VBP") (:stem . 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"under") (:end . 258)\n (:start . 253) (:id . 88))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 262) (:start . 259)\n (:id . 89))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 268)\n (:start . 263) (:id . 90))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 272) (:start . 269)\n (:id . 91))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 275) (:start . 273)\n (:id . 92))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 286)\n (:start . 276) (:id . 93))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 288) (:start . 287)\n (:id . 94))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 289) (:start . 288)\n (:id . 95)))@@@1@54@((:hcues ((:id . :x3.42.1) (:span 177 185)))\n (:ncues ((:id . :x3.42.2) (:span 173 176)))\n (:hscopes ((:id . :x3.42.1) (:span 177 286)))\n (:nscopes ((:id . :x3.42.2) (:span 173 286)))\n (:identifiers (:sid . :s3.42) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100823@unknown@formal@none@1@S@This observation serves to illustrate the challenges to the construction of an effective learning rule.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 16)\n (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "serve") (:form . "serves") (:end . 23)\n (:start . 17) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 26) (:start . 24)\n (:id . 45))\n ((:tag . "VB") (:stem . "illustrate") (:form . "illustrate") (:end . 37)\n (:start . 27) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n (:id . 47))\n ((:tag . "NNS") (:stem . "challenge") (:form . "challenges") (:end . 52)\n (:start . 42) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 55) (:start . 53)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n (:id . 50))\n ((:tag . "NN") (:stem . "construction") (:form . "construction") (:end . 72)\n (:start . 60) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 78) (:start . 76)\n (:id . 53))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 88)\n (:start . 79) (:id . 54))\n ((:tag . "NN") (:stem . "learning") (:form . "learning") (:end . 97)\n (:start . 89) (:id . 55))\n ((:tag . "NN") (:stem . "rule") (:form . "rule") (:end . 102) (:start . 98)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.43) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100824@unknown@formal@none@1@S@To the best of our knowledge, only one study to date has explored ensemble learning in motif finding.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 45))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 18) (:start . 15)\n (:id . 46))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 28)\n (:start . 19) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n (:id . 48))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 34) (:start . 30)\n (:id . 49))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 38) (:start . 35)\n (:id . 50))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 44) (:start . 39)\n (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n (:id . 52))\n ((:tag . "NN") (:stem . "date") (:form . "date") (:end . 52) (:start . 48)\n (:id . 53))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 56) (:start . 53)\n (:id . 54))\n ((:tag . "VBN") (:stem . "explore") (:form . "explored") (:end . 65)\n (:start . 57) (:id . 55))\n ((:tag . "JJ") (:stem . "ensemble") (:form . "ensemble") (:end . 74)\n (:start . 66) (:id . 56))\n ((:tag . "NN") (:stem . "learning") (:form . "learning") (:end . 83)\n (:start . 75) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n (:id . 58))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 92) (:start . 87)\n (:id . 59))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 100)\n (:start . 93) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s3.44) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100825@unknown@formal@none@1@S@Hu, Li and Kihara 4 described a simple ensemble method wherein the component programs were random restarts of the same stochastic algorithm (such as Gibbs sampling or Expectation Maximization) and the learning rule was a voting scheme in which the results of each random restart cast a "vote" for which positions in the DNA sequence should be part of the final reported motif (hereafter, we refer to this as the HLK method).@(((:tag . "NNP") (:stem . "Hu") (:form . "Hu") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . 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"to") (:end . 399) (:start . 397)\n (:id . 115))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 404) (:start . 400)\n (:id . 116))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 407) (:start . 405)\n (:id . 117))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 411) (:start . 408)\n (:id . 118))\n ((:tag . "NNP") (:stem . "HLK") (:form . "HLK") (:end . 415) (:start . 412)\n (:id . 119))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 422)\n (:start . 416) (:id . 120))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 423) (:start . 422)\n (:id . 121))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 424) (:start . 423)\n (:id . 122)))@@@1@81@((:identifiers (:sid . :s3.45) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100826@unknown@formal@none@1@S@Under this scheme, the authors found that ensemble learning resulted in an increase in performance ranging from 6 to 45%.@(((:tag . "IN") (:stem . "under") (:form . "Under") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 17)\n (:start . 11) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 46))\n ((:tag . "NNS") (:stem . "author") (:form . "authors") (:end . 30)\n (:start . 23) (:id . 47))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 36) (:start . 31)\n (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 41) (:start . 37)\n (:id . 49))\n ((:tag . "JJ") (:stem . "ensemble") (:form . "ensemble") (:end . 50)\n (:start . 42) (:id . 50))\n ((:tag . "NN") (:stem . "learning") (:form . "learning") (:end . 59)\n (:start . 51) (:id . 51))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 68)\n (:start . 60) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 71) (:start . 69)\n (:id . 53))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 74) (:start . 72)\n (:id . 54))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 83)\n (:start . 75) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n (:id . 56))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 98)\n (:start . 87) (:id . 57))\n ((:tag . "VBG") (:stem . "range") (:form . "ranging") (:end . 106)\n (:start . 99) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 111) (:start . 107)\n (:id . 59))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 113) (:start . 112)\n (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 116) (:start . 114)\n (:id . 61))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 119) (:start . 117)\n (:id . 62))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 120) (:start . 119)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.46) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100827@unknown@formal@none@1@S@The HLK voting method provides a framework wherein a number of different motifs finders can be combined under the heuristic that if several motif finders make the same (or overlapping) prediction, then that prediction is accurate.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "HLK") (:form . "HLK") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "voting") (:form . "voting") (:end . 14) (:start . 8)\n (:id . 44))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 21)\n (:start . 15) (:id . 45))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 30)\n (:start . 22) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n (:id . 47))\n ((:tag . "NN") (:stem . "framework") (:form . "framework") (:end . 42)\n (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "wherein") (:form . "wherein") (:end . 50)\n (:start . 43) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n (:id . 50))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 59)\n (:start . 53) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n (:id . 52))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 72)\n (:start . 63) (:id . 53))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 79)\n (:start . 73) (:id . 54))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 87)\n (:start . 80) (:id . 55))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 91) (:start . 88)\n (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 94) (:start . 92)\n (:id . 57))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 103)\n (:start . 95) (:id . 58))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 109)\n (:start . 104) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n (:id . 60))\n ((:tag . "JJ") (:stem . "heuristic") (:form . "heuristic") (:end . 123)\n (:start . 114) (:id . 61))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 128) (:start . 124)\n (:id . 62))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 131) (:start . 129)\n (:id . 63))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 139)\n (:start . 132) (:id . 64))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 145)\n (:start . 140) (:id . 65))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 153)\n (:start . 146) (:id . 66))\n ((:tag . "VBP") (:stem . "make") (:form . "make") (:end . 158) (:start . 154)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 162) (:start . 159)\n (:id . 68))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 167) (:start . 163)\n (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 169) (:start . 168)\n (:id . 70))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 171) (:start . 169)\n (:id . 71))\n ((:tag . "VBG") (:stem . "overlap") (:form . "overlapping") (:end . 183)\n (:start . 172) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 184) (:start . 183)\n (:id . 73))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 195)\n (:start . 185) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 196) (:start . 195)\n (:id . 75))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 201) (:start . 197)\n (:id . 76))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 206) (:start . 202)\n (:id . 77))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 217)\n (:start . 207) (:id . 78))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 220) (:start . 218)\n (:id . 79))\n ((:tag . "JJ") (:stem . "accurate") (:form . "accurate") (:end . 229)\n (:start . 221) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 230) (:start . 229)\n (:id . 81)))@@@1@40@((:hcues ((:id . :x3.47.1) (:span 88 91)))\n (:hscopes ((:id . :x3.47.1) (:span 51 229)))\n (:identifiers (:sid . :s3.47) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100828@unknown@formal@none@1@S@Here we present a novel ensemble motif finder based on a different conceptual approach.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "VBP") (:stem . "present") (:form . "present") (:end . 15)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 23) (:start . 18)\n (:id . 46))\n ((:tag . "JJ") (:stem . "ensemble") (:form . "ensemble") (:end . 32)\n (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 38) (:start . 33)\n (:id . 48))\n ((:tag . "NN") (:stem . "finder") (:form . "finder") (:end . 45)\n (:start . 39) (:id . 49))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 51) (:start . 46)\n (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 54) (:start . 52)\n (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 56) (:start . 55)\n (:id . 52))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 66)\n (:start . 57) (:id . 53))\n ((:tag . "JJ") (:stem . "conceptual") (:form . "conceptual") (:end . 77)\n (:start . 67) (:id . 54))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 86)\n (:start . 78) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s3.48) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100830@unknown@formal@none@1@S@Thus, our ensemble uses three specialized algorithms whose search spaces restrict them to each of these three local optima (BEAM for non-degenerate motifs, PRISM for degenerate motifs and SPACER for bipartite motifs).@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 9) (:start . 6)\n (:id . 44))\n ((:tag . "NN") (:stem . "ensemble") (:form . "ensemble") (:end . 18)\n (:start . 10) (:id . 45))\n ((:tag . "VBZ") (:stem . "use") (:form . "uses") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 29) (:start . 24)\n (:id . 47))\n ((:tag . "VBN") (:stem . "specialize") (:form . "specialized") (:end . 41)\n (:start . 30) (:id . 48))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 52)\n (:start . 42) (:id . 49))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 58) (:start . 53)\n (:id . 50))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 65)\n (:start . 59) (:id . 51))\n ((:tag . "NNS") (:stem . "space") (:form . "spaces") (:end . 72)\n (:start . 66) (:id . 52))\n ((:tag . "VBP") (:stem . "restrict") (:form . "restrict") (:end . 81)\n (:start . 73) (:id . 53))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 86) (:start . 82)\n (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n (:id . 55))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 94) (:start . 90)\n (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n (:id . 57))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 103) (:start . 98)\n (:id . 58))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 109)\n (:start . 104) (:id . 59))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 115)\n (:start . 110) (:id . 60))\n ((:tag . "NNS") (:stem . "optimum") (:form . "optima") (:end . 122)\n (:start . 116) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 124) (:start . 123)\n (:id . 62))\n ((:tag . "NNP") (:stem . "BEAM") (:form . "BEAM") (:end . 128) (:start . 124)\n (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 132) (:start . 129)\n (:id . 64))\n ((:tag . "JJ") (:stem . "non-degenerate") (:form . "non-degenerate")\n (:end . 147) (:start . 133) (:id . 65))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 154)\n (:start . 148) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 155) (:start . 154)\n (:id . 67))\n ((:tag . "NN") (:stem . "prism") (:form . "PRISM") (:end . 161)\n (:start . 156) (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 165) (:start . 162)\n (:id . 69))\n ((:tag . "JJ") (:stem . "degenerate") (:form . "degenerate") (:end . 176)\n (:start . 166) (:id . 70))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 183)\n (:start . 177) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 187) (:start . 184)\n (:id . 72))\n ((:tag . "NN") (:stem . "spacer") (:form . "SPACER") (:end . 194)\n (:start . 188) (:id . 73))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 198) (:start . 195)\n (:id . 74))\n ((:tag . "JJ") (:stem . "bipartite") (:form . "bipartite") (:end . 208)\n (:start . 199) (:id . 75))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 215)\n (:start . 209) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 216) (:start . 215)\n (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 217) (:start . 216)\n (:id . 78)))@@@1@37@((:identifiers (:sid . :s3.50) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100831@unknown@formal@none@1@S@We have previously demonstrated that the greedy search strategies employed by each of these methods allow them to reliably search their respective motif domains without the use of nuisance parameters, as the algorithms themselves efficiently optimize the parameters that are typically forced on the users 101112.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 18)\n (:start . 8) (:id . 44))\n ((:tag . "VBN") (:stem . "demonstrate") (:form . "demonstrated") (:end . 31)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 36) (:start . 32)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n (:id . 47))\n ((:tag . "JJ") (:stem . "greedy") (:form . "greedy") (:end . 47)\n (:start . 41) (:id . 48))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 54)\n (:start . 48) (:id . 49))\n ((:tag . "NNS") (:stem . "strategy") (:form . "strategies") (:end . 65)\n (:start . 55) (:id . 50))\n ((:tag . "VBN") (:stem . "employ") (:form . "employed") (:end . 74)\n (:start . 66) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 77) (:start . 75)\n (:id . 52))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 82) (:start . 78)\n (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n (:id . 54))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 91) (:start . 86)\n (:id . 55))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 99)\n (:start . 92) (:id . 56))\n ((:tag . "VBP") (:stem . "allow") (:form . "allow") (:end . 105)\n (:start . 100) (:id . 57))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 110) (:start . 106)\n (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 113) (:start . 111)\n (:id . 59))\n ((:tag . "RB") (:stem . "reliably") (:form . "reliably") (:end . 122)\n (:start . 114) (:id . 60))\n ((:tag . "VB") (:stem . "search") (:form . "search") (:end . 129)\n (:start . 123) (:id . 61))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 135)\n (:start . 130) (:id . 62))\n ((:tag . "JJ") (:stem . "respective") (:form . "respective") (:end . 146)\n (:start . 136) (:id . 63))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 152)\n (:start . 147) (:id . 64))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 160)\n (:start . 153) (:id . 65))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 168)\n (:start . 161) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 172) (:start . 169)\n (:id . 67))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 176) (:start . 173)\n (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 179) (:start . 177)\n (:id . 69))\n ((:tag . "NN") (:stem . "nuisance") (:form . "nuisance") (:end . 188)\n (:start . 180) (:id . 70))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 199)\n (:start . 189) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 200) (:start . 199)\n (:id . 72))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 203) (:start . 201)\n (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 207) (:start . 204)\n (:id . 74))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 218)\n (:start . 208) (:id . 75))\n ((:tag . "PRP") (:stem . "themselves") (:form . "themselves") (:end . 229)\n (:start . 219) (:id . 76))\n ((:tag . "RB") (:stem . "efficiently") (:form . "efficiently") (:end . 241)\n (:start . 230) (:id . 77))\n ((:tag . "VBP") (:stem . "optimize") (:form . "optimize") (:end . 250)\n (:start . 242) (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 254) (:start . 251)\n (:id . 79))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 265)\n (:start . 255) (:id . 80))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 270) (:start . 266)\n (:id . 81))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 274) (:start . 271)\n (:id . 82))\n ((:tag . "RB") (:stem . "typically") (:form . "typically") (:end . 284)\n (:start . 275) (:id . 83))\n ((:tag . "VBN") (:stem . "force") (:form . "forced") (:end . 291)\n (:start . 285) (:id . 84))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 294) (:start . 292)\n (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 298) (:start . 295)\n (:id . 86))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 304)\n (:start . 299) (:id . 87))\n ((:tag . "CD") (:stem . "101112") (:form . "101112") (:end . 311)\n (:start . 305) (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 312) (:start . 311)\n (:id . 89)))@@@1@48@((:ncues ((:id . :x3.51.1) (:span 161 168)))\n (:nscopes ((:id . :x3.51.1) (:span 161 199)))\n (:identifiers (:sid . :s3.51) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100832@unknown@formal@none@1@S@The results of these component algorithms are then combined using a learning rule that is simply the maximum score returned by each component algorithm.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 30)\n (:start . 21) (:id . 46))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 41)\n (:start . 31) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 45) (:start . 42)\n (:id . 48))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 50) (:start . 46)\n (:id . 49))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 59)\n (:start . 51) (:id . 50))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 65) (:start . 60)\n (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 67) (:start . 66)\n (:id . 52))\n ((:tag . "NN") (:stem . "learning") (:form . "learning") (:end . 76)\n (:start . 68) (:id . 53))\n ((:tag . "NN") (:stem . "rule") (:form . "rule") (:end . 81) (:start . 77)\n (:id . 54))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 86) (:start . 82)\n (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 89) (:start . 87)\n (:id . 56))\n ((:tag . "RB") (:stem . "simply") (:form . "simply") (:end . 96)\n (:start . 90) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n (:id . 58))\n ((:tag . "JJ") (:stem . "maximum") (:form . "maximum") (:end . 108)\n (:start . 101) (:id . 59))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 114)\n (:start . 109) (:id . 60))\n ((:tag . "VBN") (:stem . "return") (:form . "returned") (:end . 123)\n (:start . 115) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 126) (:start . 124)\n (:id . 62))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 131) (:start . 127)\n (:id . 63))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 141)\n (:start . 132) (:id . 64))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 151)\n (:start . 142) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.52) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100833@unknown@formal@none@1@S@To make comparisons possible, the motif scores returned by each algorithm are penalized according to the complexity of the motif.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "make") (:form . "make") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 19)\n (:start . 8) (:id . 44))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 28)\n (:start . 20) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 47))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 39) (:start . 34)\n (:id . 48))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 46)\n (:start . 40) (:id . 49))\n ((:tag . "VBN") (:stem . "return") (:form . "returned") (:end . 55)\n (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 58) (:start . 56)\n (:id . 51))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 63) (:start . 59)\n (:id . 52))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 73)\n (:start . 64) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 77) (:start . 74)\n (:id . 54))\n ((:tag . "VBN") (:stem . "penalize") (:form . "penalized") (:end . 87)\n (:start . 78) (:id . 55))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 97)\n (:start . 88) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n (:id . 58))\n ((:tag . "NN") (:stem . "complexity") (:form . "complexity") (:end . 115)\n (:start . 105) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 118) (:start . 116)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n (:id . 61))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 128)\n (:start . 123) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.53) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100834@unknown@formal@none@1@S@The resulting ensemble algorithm, SCOPE, has no nuisance parameters and performs significantly better than its component algorithms.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "ensemble") (:form . "ensemble") (:end . 22)\n (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 32)\n (:start . 23) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n (:id . 46))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 39) (:start . 34)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n (:id . 48))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 44) (:start . 41)\n (:id . 49))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 47) (:start . 45)\n (:id . 50))\n ((:tag . "NN") (:stem . "nuisance") (:form . "nuisance") (:end . 56)\n (:start . 48) (:id . 51))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 67)\n (:start . 57) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n (:id . 53))\n ((:tag . "NNS") (:stem . "perform") (:form . "performs") (:end . 80)\n (:start . 72) (:id . 54))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 94) (:start . 81) (:id . 55))\n ((:tag . "RB") (:stem . "better") (:form . "better") (:end . 101)\n (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 106) (:start . 102)\n (:id . 57))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 110) (:start . 107)\n (:id . 58))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 120)\n (:start . 111) (:id . 59))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 131)\n (:start . 121) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n (:id . 61)))@@@1@20@((:ncues ((:id . :x3.54.1) (:span 45 47)))\n (:nscopes ((:id . :x3.54.1) (:span 45 67)))\n (:identifiers (:sid . :s3.54) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100835@unknown@formal@none@1@S@In addition, we find that SCOPE performs favorably compared to a diverse range of existing methods and is robust to the presence of extraneous sequences in its input.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 20) (:start . 16)\n (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n (:id . 47))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 31) (:start . 26)\n (:id . 48))\n ((:tag . "NNS") (:stem . "perform") (:form . "performs") (:end . 40)\n (:start . 32) (:id . 49))\n ((:tag . "RB") (:stem . "favorably") (:form . "favorably") (:end . 50)\n (:start . 41) (:id . 50))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 59)\n (:start . 51) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 62) (:start . 60)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n (:id . 53))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 72)\n (:start . 65) (:id . 54))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 78) (:start . 73)\n (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n (:id . 56))\n ((:tag . "VBG") (:stem . "exist") (:form . "existing") (:end . 90)\n (:start . 82) (:id . 57))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 98)\n (:start . 91) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 105) (:start . 103)\n (:id . 60))\n ((:tag . "JJ") (:stem . "robust") (:form . "robust") (:end . 112)\n (:start . 106) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 115) (:start . 113)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n (:id . 63))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 128)\n (:start . 120) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n (:id . 65))\n ((:tag . "JJ") (:stem . "extraneous") (:form . "extraneous") (:end . 142)\n (:start . 132) (:id . 66))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 152)\n (:start . 143) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 155) (:start . 153)\n (:id . 68))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 159) (:start . 156)\n (:id . 69))\n ((:tag . "NN") (:stem . "input") (:form . "input") (:end . 165)\n (:start . 160) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s3.55) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100836@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s3.56) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011 5100837@unknown@formal@none@1@S@Algorithm@(((:tag . "NNP") (:stem . "Algorithm") (:form . "Algorithm") (:end . 9)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s3.57) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100838@unknown@formal@none@1@S@SCOPE takes as input a set of sequences U that are upstream of a set of genes G that are thought to be coregulated.@(((:tag . "NN") (:stem . "scope") (:form . "SCOPE") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "take") (:form . "takes") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "input") (:form . "input") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n (:id . 46))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 26) (:start . 23)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 48))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 39)\n (:start . 30) (:id . 49))\n ((:tag . "NNP") (:stem . "U") (:form . "U") (:end . 41) (:start . 40)\n (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 46) (:start . 42)\n (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 50) (:start . 47)\n (:id . 52))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 59)\n (:start . 51) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n (:id . 55))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 68) (:start . 65)\n (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n (:id . 57))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 77) (:start . 72)\n (:id . 58))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 79) (:start . 78)\n (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 84) (:start . 80)\n (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 88) (:start . 85)\n (:id . 61))\n ((:tag . "VBN") (:stem . "think") (:form . "thought") (:end . 96)\n (:start . 89) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 99) (:start . 97)\n (:id . 63))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 102) (:start . 100)\n (:id . 64))\n ((:tag . "VBN") (:stem . "coregulate") (:form . "coregulated") (:end . 114)\n (:start . 103) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x3.58.1) (:span 89 96)))\n (:hscopes ((:id . :x3.58.1) (:span 80 114)))\n (:identifiers (:sid . :s3.58) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100840@unknown@formal@none@1@S@In practice, sets of binding sites are represented using a motif.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "practice") (:form . "practice") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 17) (:start . 13)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 46))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 28)\n (:start . 21) (:id . 47))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 34) (:start . 29)\n (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 38) (:start . 35)\n (:id . 49))\n ((:tag . "VBN") (:stem . "represent") (:form . "represented") (:end . 50)\n (:start . 39) (:id . 50))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 56) (:start . 51)\n (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 58) (:start . 57)\n (:id . 52))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 64) (:start . 59)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.60) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100841@unknown@formal@none@1@S@We have found that simple consensus motifs over the full IUPAC alphabet (a 15-letter code consisting of the bases A,T,C,G and all possible combinations) provide enough representational power to adequately describe Û, while still allowing for an efficient search 34.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n (:id . 45))\n ((:tag . "JJ") (:stem . "simple") (:form . "simple") (:end . 25)\n (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 35)\n (:start . 26) (:id . 47))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 42)\n (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 47) (:start . 43)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n (:id . 50))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 56) (:start . 52)\n (:id . 51))\n ((:tag . "NNP") (:stem . "IUPAC") (:form . "IUPAC") (:end . 62) (:start . 57)\n (:id . 52))\n ((:tag . "NN") (:stem . "alphabet") (:form . "alphabet") (:end . 71)\n (:start . 63) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 74) (:start . 73)\n (:id . 55))\n ((:tag . "NN") (:stem . "15-letter") (:form . "15-letter") (:end . 84)\n (:start . 75) (:id . 56))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 89) (:start . 85)\n (:id . 57))\n ((:tag . "VBG") (:stem . "consist") (:form . "consisting") (:end . 100)\n (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n (:id . 60))\n ((:tag . "NNS") (:stem . "base") (:form . "bases") (:end . 113)\n (:start . 108) (:id . 61))\n ((:tag . "NNP") (:stem . "A,T,C,G") (:form . "A,T,C,G") (:end . 121)\n (:start . 114) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n (:id . 63))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 129) (:start . 126)\n (:id . 64))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 138)\n (:start . 130) (:id . 65))\n ((:tag . "NNS") (:stem . "combination") (:form . "combinations") (:end . 151)\n (:start . 139) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n (:id . 67))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 160)\n (:start . 153) (:id . 68))\n ((:tag . "JJ") (:stem . "enough") (:form . "enough") (:end . 167)\n (:start . 161) (:id . 69))\n ((:tag . "JJ") (:stem . "representational") (:form . "representational")\n (:end . 184) (:start . 168) (:id . 70))\n ((:tag . "NN") (:stem . "power") (:form . "power") (:end . 190)\n (:start . 185) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 193) (:start . 191)\n (:id . 72))\n ((:tag . "RB") (:stem . "adequately") (:form . "adequately") (:end . 204)\n (:start . 194) (:id . 73))\n ((:tag . "VB") (:stem . "describe") (:form . "describe") (:end . 213)\n (:start . 205) (:id . 74))\n ((:tag . "NN") (:stem . "û") (:form . "Û") (:end . 215) (:start . 214)\n (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 216) (:start . 215)\n (:id . 76))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 222)\n (:start . 217) (:id . 77))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 228)\n (:start . 223) (:id . 78))\n ((:tag . "VBG") (:stem . "allow") (:form . "allowing") (:end . 237)\n (:start . 229) (:id . 79))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 241) (:start . 238)\n (:id . 80))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 244) (:start . 242)\n (:id . 81))\n ((:tag . "JJ") (:stem . "efficient") (:form . "efficient") (:end . 254)\n (:start . 245) (:id . 82))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 261)\n (:start . 255) (:id . 83))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 264) (:start . 262)\n (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 265) (:start . 264)\n (:id . 85)))@@@1@44@((:identifiers (:sid . :s3.61) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100842@unknown@formal@none@1@S@While alternative representations, such as position weight matrices (PWMs) are more expressive, their heuristic searches are prone to local optima and often do not perform well in practice \s34111213\s.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "alternative") (:form . "alternative") (:end . 17)\n (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "representation") (:form . "representations")\n (:end . 33) (:start . 18) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n (:id . 45))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 39) (:start . 35)\n (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 42) (:start . 40)\n (:id . 47))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 51)\n (:start . 43) (:id . 48))\n ((:tag . "NN") (:stem . "weight") (:form . "weight") (:end . 58)\n (:start . 52) (:id . 49))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 67)\n (:start . 59) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n (:id . 51))\n ((:tag . "NNPS") (:stem . "PWM") (:form . "PWMs") (:end . 73) (:start . 69)\n (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 74) (:start . 73)\n (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 78) (:start . 75)\n (:id . 54))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 83) (:start . 79)\n (:id . 55))\n ((:tag . "JJ") (:stem . "expressive") (:form . "expressive") (:end . 94)\n (:start . 84) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n (:id . 57))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 101)\n (:start . 96) (:id . 58))\n ((:tag . "JJ") (:stem . "heuristic") (:form . "heuristic") (:end . 111)\n (:start . 102) (:id . 59))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 120)\n (:start . 112) (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 124) (:start . 121)\n (:id . 61))\n ((:tag . "JJ") (:stem . "prone") (:form . "prone") (:end . 130)\n (:start . 125) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 133) (:start . 131)\n (:id . 63))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 139)\n (:start . 134) (:id . 64))\n ((:tag . "NNS") (:stem . "optimum") (:form . "optima") (:end . 146)\n (:start . 140) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n (:id . 66))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 156)\n (:start . 151) (:id . 67))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 159) (:start . 157)\n (:id . 68))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 163) (:start . 160)\n (:id . 69))\n ((:tag . "VB") (:stem . "perform") (:form . "perform") (:end . 171)\n (:start . 164) (:id . 70))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 176) (:start . 172)\n (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 179) (:start . 177)\n (:id . 72))\n ((:tag . "NN") (:stem . "practice") (:form . "practice") (:end . 188)\n (:start . 180) (:id . 73))\n ((:tag . "NN") (:stem . "\s") (:form . "\s") (:end . 190) (:start . 189)\n (:id . 74))\n ((:tag . "CD") (:stem . "34111213") (:form . "34111213") (:end . 198)\n (:start . 190) (:id . 75))\n ((:tag . "NN") (:stem . "\s") (:form . "\s") (:end . 199) (:start . 198)\n (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n (:id . 77)))@@@1@36@((:hcues ((:id . :x3.62.2) (:span 125 133)))\n (:ncues ((:id . :x3.62.1) (:span 160 163)))\n (:hscopes ((:id . :x3.62.2) (:span 125 146)))\n (:nscopes ((:id . :x3.62.1) (:span 160 188)))\n (:identifiers (:sid . :s3.62) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100843@unknown@formal@none@1@S@SCOPE has three component algorithms, BEAM, PRISM and SPACER, which search for non-degenerate, short degenerate, and long, highly degenerate and "gapped" motifs, respectively (Figure 1).@(((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 15) (:start . 10)\n (:id . 44))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 25)\n (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 36)\n (:start . 26) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n (:id . 47))\n ((:tag . "NNP") (:stem . "BEAM") (:form . "BEAM") (:end . 42) (:start . 38)\n (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n (:id . 49))\n ((:tag . "NN") (:stem . "prism") (:form . "PRISM") (:end . 49) (:start . 44)\n (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n (:id . 51))\n ((:tag . "NNP") (:stem . "SPACER") (:form . "SPACER") (:end . 60)\n (:start . 54) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 67) (:start . 62)\n (:id . 54))\n ((:tag . "VBP") (:stem . "search") (:form . "search") (:end . 74)\n (:start . 68) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 78) (:start . 75)\n (:id . 56))\n ((:tag . "JJ") (:stem . "non-degenerate") (:form . "non-degenerate")\n (:end . 93) (:start . 79) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n (:id . 58))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 100) (:start . 95)\n (:id . 59))\n ((:tag . "NN") (:stem . "degenerate") (:form . "degenerate") (:end . 111)\n (:start . 101) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n (:id . 62))\n ((:tag . "RB") (:stem . "long") (:form . "long") (:end . 121) (:start . 117)\n (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n (:id . 64))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 129)\n (:start . 123) (:id . 65))\n ((:tag . "VB") (:stem . "degenerate") (:form . "degenerate") (:end . 140)\n (:start . 130) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 144) (:start . 141)\n (:id . 67))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 146) (:start . 145)\n (:id . 68))\n ((:tag . "VBN") (:stem . "gap") (:form . "gapped") (:end . 152)\n (:start . 146) (:id . 69))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 153) (:start . 152)\n (:id . 70))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 160)\n (:start . 154) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n (:id . 72))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 174)\n (:start . 162) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 176) (:start . 175)\n (:id . 74))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 182)\n (:start . 176) (:id . 75))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 184) (:start . 183)\n (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 185) (:start . 184)\n (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n (:id . 78)))@@@1@37@((:identifiers (:sid . :s3.63) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100844@unknown@formal@none@1@S@Each motif is scored considering one or both strands and the motif is marked to indicate which calculation scores higher.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "VBN") (:stem . "score") (:form . "scored") (:end . 20)\n (:start . 14) (:id . 45))\n ((:tag . "VBG") (:stem . "consider") (:form . "considering") (:end . 32)\n (:start . 21) (:id . 46))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 36) (:start . 33)\n (:id . 47))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 39) (:start . 37)\n (:id . 48))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 44) (:start . 40)\n (:id . 49))\n ((:tag . "NNS") (:stem . "strand") (:form . "strands") (:end . 52)\n (:start . 45) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n (:id . 52))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 66) (:start . 61)\n (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 69) (:start . 67)\n (:id . 54))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 76) (:start . 70)\n (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 79) (:start . 77)\n (:id . 56))\n ((:tag . "VB") (:stem . "indicate") (:form . "indicate") (:end . 88)\n (:start . 80) (:id . 57))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 94) (:start . 89)\n (:id . 58))\n ((:tag . "NN") (:stem . "calculation") (:form . "calculation") (:end . 106)\n (:start . 95) (:id . 59))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 113)\n (:start . 107) (:id . 60))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 120)\n (:start . 114) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.64) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100845@unknown@formal@none@1@S@The results of the three algorithms are merged and sorted.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 24) (:start . 19)\n (:id . 46))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 35)\n (:start . 25) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "VBN") (:stem . "merge") (:form . "merged") (:end . 46)\n (:start . 40) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n (:id . 50))\n ((:tag . "VBN") (:stem . "sort") (:form . "sorted") (:end . 57) (:start . 51)\n (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 58) (:start . 57)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s3.65) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100846@unknown@formal@none@1@S@Artifactual motifs, whose significance can be accounted for by higher scoring motifs that they overlap, are identified and removed (for details, see Additional file 1, section S1).@(((:tag . "JJ") (:stem . "artifactual") (:form . "Artifactual") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 18)\n (:start . 12) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n (:id . 44))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 25) (:start . 20)\n (:id . 45))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 38)\n (:start . 26) (:id . 46))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 42) (:start . 39)\n (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 45) (:start . 43)\n (:id . 48))\n ((:tag . "VBN") (:stem . "account") (:form . "accounted") (:end . 55)\n (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 59) (:start . 56)\n (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 62) (:start . 60)\n (:id . 51))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 69) (:start . 63)\n (:id . 52))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 77)\n (:start . 70) (:id . 53))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 84)\n (:start . 78) (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 89) (:start . 85)\n (:id . 55))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 94) (:start . 90)\n (:id . 56))\n ((:tag . "VBP") (:stem . "overlap") (:form . "overlap") (:end . 102)\n (:start . 95) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 107) (:start . 104)\n (:id . 59))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 118)\n (:start . 108) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n (:id . 61))\n ((:tag . "VBN") (:stem . "remove") (:form . "removed") (:end . 130)\n (:start . 123) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 132) (:start . 131)\n (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 135) (:start . 132)\n (:id . 64))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 143)\n (:start . 136) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n (:id . 66))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 148) (:start . 145)\n (:id . 67))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 159)\n (:start . 149) (:id . 68))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 164) (:start . 160)\n (:id . 69))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 166) (:start . 165)\n (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n (:id . 71))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 175)\n (:start . 168) (:id . 72))\n ((:tag . "NN") (:stem . "s1") (:form . "S1") (:end . 178) (:start . 176)\n (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 179) (:start . 178)\n (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s3.66) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100847@unknown@formal@none@1@S@Flow diagram for SCOPE@(((:tag . "NNP") (:stem . "Flow") (:form . "Flow") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "diagram") (:form . "diagram") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 22) (:start . 17)\n (:id . 45)))@@@1@4@((:identifiers (:sid . :s3.67) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5100848@unknown@formal@none@1@S@Flow diagram for SCOPE.@(((:tag . "NNP") (:stem . "Flow") (:form . "Flow") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "diagram") (:form . "diagram") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 22) (:start . 17)\n (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 23) (:start . 22)\n (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.68) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100850@unknown@formal@none@1@S@For yeast (whose upstream regions are standardized to 800 bp), BEAM and PRISM use the overrepresentation-KS objective function (so/ks), while SPACER's slower running time requires the simpler overrepresentation objective function (so).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 11) (:start . 10)\n (:id . 44))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 16) (:start . 11)\n (:id . 45))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 25)\n (:start . 17) (:id . 46))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 33)\n (:start . 26) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 37) (:start . 34)\n (:id . 48))\n ((:tag . "VBN") (:stem . "standardize") (:form . "standardized") (:end . 50)\n (:start . 38) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 53) (:start . 51)\n (:id . 50))\n ((:tag . "CD") (:stem . "800") (:form . "800") (:end . 57) (:start . 54)\n (:id . 51))\n ((:tag . "NN") (:stem . "bp") (:form . "bp") (:end . 60) (:start . 58)\n (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 61) (:start . 60)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n (:id . 54))\n ((:tag . "NNP") (:stem . "BEAM") (:form . "BEAM") (:end . 67) (:start . 63)\n (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n (:id . 56))\n ((:tag . "NN") (:stem . "prism") (:form . "PRISM") (:end . 77) (:start . 72)\n (:id . 57))\n ((:tag . "VBP") (:stem . "use") (:form . "use") (:end . 81) (:start . 78)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n (:id . 59))\n ((:tag . "JJ") (:stem . "overrepresentation-ks")\n (:form . "overrepresentation-KS") (:end . 107) (:start . 86) (:id . 60))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 117)\n (:start . 108) (:id . 61))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 126)\n (:start . 118) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 128) (:start . 127)\n (:id . 63))\n ((:tag . "NNS") (:stem . "so/k") (:form . "so/ks") (:end . 133)\n (:start . 128) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 134) (:start . 133)\n (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n (:id . 66))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 141)\n (:start . 136) (:id . 67))\n ((:tag . "NNP") (:stem . "SPACER") (:form . "SPACER") (:end . 148)\n (:start . 142) (:id . 68))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 150) (:start . 148)\n (:id . 69))\n ((:tag . "JJR") (:stem . "slow") (:form . "slower") (:end . 157)\n (:start . 151) (:id . 70))\n ((:tag . "NN") (:stem . "running") (:form . "running") (:end . 165)\n (:start . 158) (:id . 71))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 170) (:start . 166)\n (:id . 72))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 179)\n (:start . 171) (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 183) (:start . 180)\n (:id . 74))\n ((:tag . "JJR") (:stem . "simple") (:form . "simpler") (:end . 191)\n (:start . 184) (:id . 75))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n (:end . 210) (:start . 192) (:id . 76))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 220)\n (:start . 211) (:id . 77))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 229)\n (:start . 221) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 231) (:start . 230)\n (:id . 79))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 233) (:start . 231)\n (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 234) (:start . 233)\n (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 235) (:start . 234)\n (:id . 82)))@@@1@41@((:identifiers (:sid . :s3.70) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100851@unknown@formal@none@1@S@The top 5 motifs from SPACER are rescored using the combined objective function.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 9) (:start . 8)\n (:id . 44))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 16)\n (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 21) (:start . 17)\n (:id . 46))\n ((:tag . "NNP") (:stem . "SPACER") (:form . "SPACER") (:end . 28)\n (:start . 22) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 32) (:start . 29)\n (:id . 48))\n ((:tag . "VBN") (:stem . "rescore") (:form . "rescored") (:end . 41)\n (:start . 33) (:id . 49))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 47) (:start . 42)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n (:id . 51))\n ((:tag . "JJ") (:stem . "combined") (:form . "combined") (:end . 60)\n (:start . 52) (:id . 52))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 70)\n (:start . 61) (:id . 53))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 79)\n (:start . 71) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.71) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100852@unknown@formal@none@1@S@For bacteria and Drosophila, upstream regions are defined to be the intergenic region upstream of each gene; thus, the KS objective function is not used.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "bacteria") (:form . "bacteria") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 27)\n (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n (:id . 46))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 37)\n (:start . 29) (:id . 47))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 45)\n (:start . 38) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 57)\n (:start . 50) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 63) (:start . 61)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n (:id . 53))\n ((:tag . "JJ") (:stem . "intergenic") (:form . "intergenic") (:end . 78)\n (:start . 68) (:id . 54))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 85)\n (:start . 79) (:id . 55))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 94)\n (:start . 86) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n (:id . 57))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 102) (:start . 98)\n (:id . 58))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 107) (:start . 103)\n (:id . 59))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 108) (:start . 107)\n (:id . 60))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 113) (:start . 109)\n (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n (:id . 63))\n ((:tag . "NNP") (:stem . "KS") (:form . "KS") (:end . 121) (:start . 119)\n (:id . 64))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 131)\n (:start . 122) (:id . 65))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 140)\n (:start . 132) (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 143) (:start . 141)\n (:id . 67))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 147) (:start . 144)\n (:id . 68))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 152) (:start . 148)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n (:id . 70)))@@@1@29@((:ncues ((:id . :x3.72.1) (:span 144 147)))\n (:nscopes ((:id . :x3.72.1) (:span 115 152)))\n (:identifiers (:sid . :s3.72) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100853@unknown@formal@none@1@S@The results of each program are sorted by Sig and lower scoring motifs that substantially overlap higher scoring motifs are removed.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 19) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 27)\n (:start . 20) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 31) (:start . 28)\n (:id . 47))\n ((:tag . "VBN") (:stem . "sort") (:form . "sorted") (:end . 38) (:start . 32)\n (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 41) (:start . 39)\n (:id . 49))\n ((:tag . "NNP") (:stem . "Sig") (:form . "Sig") (:end . 45) (:start . 42)\n (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n (:id . 51))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 55) (:start . 50)\n (:id . 52))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 63)\n (:start . 56) (:id . 53))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 70)\n (:start . 64) (:id . 54))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 75) (:start . 71)\n (:id . 55))\n ((:tag . "RB") (:stem . "substantially") (:form . "substantially")\n (:end . 89) (:start . 76) (:id . 56))\n ((:tag . "VBP") (:stem . "overlap") (:form . "overlap") (:end . 97)\n (:start . 90) (:id . 57))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 104)\n (:start . 98) (:id . 58))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 112)\n (:start . 105) (:id . 59))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 119)\n (:start . 113) (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 123) (:start . 120)\n (:id . 61))\n ((:tag . "VBN") (:stem . "remove") (:form . "removed") (:end . 131)\n (:start . 124) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.73) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100854@unknown@formal@none@1@S@The filtered lists of motifs from the three programs are finally merged by Sig score.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "filter") (:form . "filtered") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "list") (:form . "lists") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 28)\n (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n (:id . 48))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 43) (:start . 38)\n (:id . 49))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 52)\n (:start . 44) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 56) (:start . 53)\n (:id . 51))\n ((:tag . "RB") (:stem . "finally") (:form . "finally") (:end . 64)\n (:start . 57) (:id . 52))\n ((:tag . "VBN") (:stem . "merge") (:form . "merged") (:end . 71)\n (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 74) (:start . 72)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Sig") (:form . "Sig") (:end . 78) (:start . 75)\n (:id . 55))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 84) (:start . 79)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.74) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100855@unknown@formal@none@1@S@Repetitive motifs are identified and removed during all stages.@(((:tag . "JJ") (:stem . "repetitive") (:form . "Repetitive") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 17)\n (:start . 11) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 21) (:start . 18)\n (:id . 44))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 32)\n (:start . 22) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n (:id . 46))\n ((:tag . "VBN") (:stem . "remove") (:form . "removed") (:end . 44)\n (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 51)\n (:start . 45) (:id . 48))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 55) (:start . 52)\n (:id . 49))\n ((:tag . "NNS") (:stem . "stage") (:form . "stages") (:end . 62)\n (:start . 56) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s3.75) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100856@unknown@formal@none@1@S@Each of SCOPE's three component algorithms seeks to maximize the same objective function over a different class of motifs.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 21) (:start . 16)\n (:id . 46))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 31)\n (:start . 22) (:id . 47))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 42)\n (:start . 32) (:id . 48))\n ((:tag . "VBZ") (:stem . "seek") (:form . "seeks") (:end . 48) (:start . 43)\n (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n (:id . 50))\n ((:tag . "VB") (:stem . "maximize") (:form . "maximize") (:end . 60)\n (:start . 52) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n (:id . 52))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 69) (:start . 65)\n (:id . 53))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 79)\n (:start . 70) (:id . 54))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 88)\n (:start . 80) (:id . 55))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 93) (:start . 89)\n (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 95) (:start . 94)\n (:id . 57))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 105)\n (:start . 96) (:id . 58))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 111)\n (:start . 106) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n (:id . 60))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 121)\n (:start . 115) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.76) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100857@unknown@formal@none@1@S@Let M be a random variable over the full space of IUPAC words.@(((:tag . "NN") (:stem . "let") (:form . "Let") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 5) (:start . 4)\n (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 8) (:start . 6)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n (:id . 45))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 17)\n (:start . 11) (:id . 46))\n ((:tag . "NN") (:stem . "variable") (:form . "variable") (:end . 26)\n (:start . 18) (:id . 47))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 31) (:start . 27)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n (:id . 49))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 40) (:start . 36)\n (:id . 50))\n ((:tag . "NN") (:stem . "space") (:form . "space") (:end . 46) (:start . 41)\n (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n (:id . 52))\n ((:tag . "NNP") (:stem . "IUPAC") (:form . "IUPAC") (:end . 55) (:start . 50)\n (:id . 53))\n ((:tag . "NNS") (:stem . "word") (:form . "words") (:end . 61) (:start . 56)\n (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 62) (:start . 61)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.77) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100858@unknown@formal@none@1@S@The statistical significance p(M = m) of a particular word m is determined by the distribution of M over the entire space of upstream sequences in the given species.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 28)\n (:start . 16) (:id . 44))\n ((:tag . "NNP") (:stem . "p(M") (:form . "p(M") (:end . 32) (:start . 29)\n (:id . 45))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 34) (:start . 33)\n (:id . 46))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 36) (:start . 35)\n (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 37) (:start . 36)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 42) (:start . 41)\n (:id . 50))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 53)\n (:start . 43) (:id . 51))\n ((:tag . "NN") (:stem . "word") (:form . "word") (:end . 58) (:start . 54)\n (:id . 52))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 60) (:start . 59)\n (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 63) (:start . 61)\n (:id . 54))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 74)\n (:start . 64) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 77) (:start . 75)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n (:id . 57))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 94)\n (:start . 82) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n (:id . 59))\n ((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 99) (:start . 98)\n (:id . 60))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 104) (:start . 100)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n (:id . 62))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 115)\n (:start . 109) (:id . 63))\n ((:tag . "NN") (:stem . "space") (:form . "space") (:end . 121)\n (:start . 116) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 124) (:start . 122)\n (:id . 65))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 133)\n (:start . 125) (:id . 66))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 143)\n (:start . 134) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 146) (:start . 144)\n (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 150) (:start . 147)\n (:id . 69))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 156)\n (:start . 151) (:id . 70))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 164)\n (:start . 157) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n (:id . 72)))@@@1@31@((:identifiers (:sid . :s3.78) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100860@unknown@formal@none@1@S@All values of M are not, however, equally likely a priori.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 15) (:start . 14)\n (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 19) (:start . 16)\n (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 23) (:start . 20)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n (:id . 48))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 32)\n (:start . 25) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n (:id . 50))\n ((:tag . "RB") (:stem . "equally") (:form . "equally") (:end . 41)\n (:start . 34) (:id . 51))\n ((:tag . "RB") (:stem . "likely") (:form . "likely") (:end . 48)\n (:start . 42) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 50) (:start . 49)\n (:id . 53))\n ((:tag . "NN") (:stem . "priori") (:form . "priori") (:end . 57)\n (:start . 51) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 58) (:start . 57)\n (:id . 55)))@@@1@14@((:hcues ((:id . :x3.80.2) (:span 42 48)))\n (:ncues ((:id . :x3.80.1) (:span 20 23)))\n (:hscopes ((:id . :x3.80.2) (:span 0 57)))\n (:nscopes ((:id . :x3.80.1) (:span 0 57)))\n (:identifiers (:sid . :s3.80) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100861@unknown@formal@none@1@S@For example, it is quite likely that there exists an extremely long sequence that is entirely unique to U.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n (:id . 46))\n ((:tag . "RB") (:stem . "quite") (:form . "quite") (:end . 24) (:start . 19)\n (:id . 47))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 31)\n (:start . 25) (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 36) (:start . 32)\n (:id . 49))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 42) (:start . 37)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "exist") (:form . "exists") (:end . 49)\n (:start . 43) (:id . 51))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 52) (:start . 50)\n (:id . 52))\n ((:tag . "RB") (:stem . "extremely") (:form . "extremely") (:end . 62)\n (:start . 53) (:id . 53))\n ((:tag . "JJ") (:stem . "long") (:form . "long") (:end . 67) (:start . 63)\n (:id . 54))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 76)\n (:start . 68) (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 81) (:start . 77)\n (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 84) (:start . 82)\n (:id . 57))\n ((:tag . "RB") (:stem . "entirely") (:form . "entirely") (:end . 93)\n (:start . 85) (:id . 58))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 100)\n (:start . 94) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 103) (:start . 101)\n (:id . 60))\n ((:tag . "NNP") (:stem . "U") (:form . "U") (:end . 105) (:start . 104)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n (:id . 62)))@@@1@21@((:hcues ((:id . :x3.81.1) (:span 25 31)))\n (:hscopes ((:id . :x3.81.1) (:span 25 105)))\n (:identifiers (:sid . :s3.81) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100862@unknown@formal@none@1@S@Such a unique sequence would appear to be highly significant, until we consider that we have in effect searched all possible sequences until we found one that is unique.@(((:tag . "PDT") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 6) (:start . 5)\n (:id . 43))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 13) (:start . 7)\n (:id . 44))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 22)\n (:start . 14) (:id . 45))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 28) (:start . 23)\n (:id . 46))\n ((:tag . "VB") (:stem . "appear") (:form . "appear") (:end . 35)\n (:start . 29) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 41) (:start . 39)\n (:id . 49))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 48)\n (:start . 42) (:id . 50))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 60)\n (:start . 49) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n (:id . 52))\n ((:tag . "IN") (:stem . "until") (:form . "until") (:end . 67) (:start . 62)\n (:id . 53))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 70) (:start . 68)\n (:id . 54))\n ((:tag . "VBP") (:stem . "consider") (:form . "consider") (:end . 79)\n (:start . 71) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 84) (:start . 80)\n (:id . 56))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 87) (:start . 85)\n (:id . 57))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 92) (:start . 88)\n (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 95) (:start . 93)\n (:id . 59))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 102)\n (:start . 96) (:id . 60))\n ((:tag . "VBD") (:stem . "search") (:form . "searched") (:end . 111)\n (:start . 103) (:id . 61))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 115) (:start . 112)\n (:id . 62))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 124)\n (:start . 116) (:id . 63))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 134)\n (:start . 125) (:id . 64))\n ((:tag . "IN") (:stem . "until") (:form . "until") (:end . 140)\n (:start . 135) (:id . 65))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 143) (:start . 141)\n (:id . 66))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 149)\n (:start . 144) (:id . 67))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 153) (:start . 150)\n (:id . 68))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 158) (:start . 154)\n (:id . 69))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 161) (:start . 159)\n (:id . 70))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 168)\n (:start . 162) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n (:id . 72)))@@@1@31@((:hcues ((:id . :x3.82.1) (:span 116 124))\n ((:id . :x3.82.2) (:span 23 28 29 35)))\n (:hscopes ((:id . :x3.82.1) (:span 116 134)) ((:id . :x3.82.2) (:span 0 60)))\n (:identifiers (:sid . :s3.82) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100863@unknown@formal@none@1@S@To correct for this multiple hypothesis testing problem, van Helden et al. 14 proposed using a Bonferroni correction, in which p(M = m) is penalized by the number of motifs N of length |m|:@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "correct") (:form . "correct") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 19) (:start . 15)\n (:id . 45))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 28)\n (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 39)\n (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "testing") (:form . "testing") (:end . 47)\n (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "problem") (:form . "problem") (:end . 55)\n (:start . 48) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n (:id . 50))\n ((:tag . "NNP") (:stem . "van") (:form . "van") (:end . 60) (:start . 57)\n (:id . 51))\n ((:tag . "NNP") (:stem . "Helden") (:form . "Helden") (:end . 67)\n (:start . 61) (:id . 52))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 70) (:start . 68)\n (:id . 53))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 74) (:start . 71)\n (:id . 54))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 77) (:start . 75)\n (:id . 55))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 86)\n (:start . 78) (:id . 56))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 92) (:start . 87)\n (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 94) (:start . 93)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Bonferroni") (:form . "Bonferroni") (:end . 105)\n (:start . 95) (:id . 59))\n ((:tag . "NN") (:stem . "correction") (:form . "correction") (:end . 116)\n (:start . 106) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 120) (:start . 118)\n (:id . 62))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 126)\n (:start . 121) (:id . 63))\n ((:tag . "NNP") (:stem . "p(M") (:form . "p(M") (:end . 130) (:start . 127)\n (:id . 64))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 132) (:start . 131)\n (:id . 65))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 134) (:start . 133)\n (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 135) (:start . 134)\n (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 138) (:start . 136)\n (:id . 68))\n ((:tag . "VBN") (:stem . "penalize") (:form . "penalized") (:end . 148)\n (:start . 139) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 151) (:start . 149)\n (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n (:id . 71))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 162)\n (:start . 156) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 165) (:start . 163)\n (:id . 73))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 172)\n (:start . 166) (:id . 74))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 174) (:start . 173)\n (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 177) (:start . 175)\n (:id . 76))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 184)\n (:start . 178) (:id . 77))\n ((:tag . "NN") (:stem . "|m|") (:form . "|m|") (:end . 188) (:start . 185)\n (:id . 78))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 189) (:start . 188)\n (:id . 79)))@@@1@38@((:identifiers (:sid . :s3.83) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100864@unknown@formal@none@1@S@Sig = -log(p(M = m)·N).@(((:tag . "NNP") (:stem . "Sig") (:form . "Sig") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 5) (:start . 4)\n (:id . 43))\n ((:tag . "NNP") (:stem . "-log(p(M") (:form . "-log(p(M") (:end . 14)\n (:start . 6) (:id . 44))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 16) (:start . 15)\n (:id . 45))\n ((:tag . "NNP") (:stem . "m)·N") (:form . "m)·N") (:end . 21) (:start . 17)\n (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 22) (:start . 21)\n (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 23) (:start . 22)\n (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.84) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100865@unknown@formal@none@1@S@Thus, if m = "ACGT", N = 44.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 8) (:start . 6)\n (:id . 44))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 10) (:start . 9)\n (:id . 45))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 12) (:start . 11)\n (:id . 46))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 14) (:start . 13)\n (:id . 47))\n ((:tag . "NNP") (:stem . "ACGT") (:form . "ACGT") (:end . 18) (:start . 14)\n (:id . 48))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 19) (:start . 18)\n (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n (:id . 50))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 22) (:start . 21)\n (:id . 51))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 24) (:start . 23)\n (:id . 52))\n ((:tag . "CD") (:stem . "44") (:form . "44") (:end . 27) (:start . 25)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 28) (:start . 27)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.85) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100866@unknown@formal@none@1@S@We employed this same definition of Sig for BEAM, our algorithm that searches for non-degenerate motifs 10.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "employ") (:form . "employed") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 21) (:start . 17)\n (:id . 45))\n ((:tag . "NN") (:stem . "definition") (:form . "definition") (:end . 32)\n (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Sig") (:form . "Sig") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n (:id . 49))\n ((:tag . "NNP") (:stem . "BEAM") (:form . "BEAM") (:end . 48) (:start . 44)\n (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n (:id . 51))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 53) (:start . 50)\n (:id . 52))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 63)\n (:start . 54) (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 68) (:start . 64)\n (:id . 54))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 77)\n (:start . 69) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 81) (:start . 78)\n (:id . 56))\n ((:tag . "JJ") (:stem . "non-degenerate") (:form . "non-degenerate")\n (:end . 96) (:start . 82) (:id . 57))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 103)\n (:start . 97) (:id . 58))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 106) (:start . 104)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.86) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100867@unknown@formal@none@1@S@Defining N for degenerate or bipartite motifs raises a significant conceptual challenge.@(((:tag . "VBG") (:stem . "define") (:form . "Defining") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "JJ") (:stem . "degenerate") (:form . "degenerate") (:end . 25)\n (:start . 15) (:id . 45))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "JJ") (:stem . "bipartite") (:form . "bipartite") (:end . 38)\n (:start . 29) (:id . 47))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 45)\n (:start . 39) (:id . 48))\n ((:tag . "VBZ") (:stem . "raise") (:form . "raises") (:end . 52)\n (:start . 46) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n (:id . 50))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 66)\n (:start . 55) (:id . 51))\n ((:tag . "JJ") (:stem . "conceptual") (:form . "conceptual") (:end . 77)\n (:start . 67) (:id . 52))\n ((:tag . "NN") (:stem . "challenge") (:form . "challenge") (:end . 87)\n (:start . 78) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.87) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100868@unknown@formal@none@1@S@Van Helden et al. 14 chose to use the same definition, but limited their search to a small number of degenerate bases.@(((:tag . "NNP") (:stem . "Van") (:form . "Van") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Helden") (:form . "Helden") (:end . 10)\n (:start . 4) (:id . 43))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 17) (:start . 14)\n (:id . 45))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 20) (:start . 18)\n (:id . 46))\n ((:tag . "VBD") (:stem . "choose") (:form . "chose") (:end . 26)\n (:start . 21) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n (:id . 48))\n ((:tag . "VB") (:stem . "use") (:form . "use") (:end . 33) (:start . 30)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n (:id . 50))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 42) (:start . 38)\n (:id . 51))\n ((:tag . "NN") (:stem . "definition") (:form . "definition") (:end . 53)\n (:start . 43) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n (:id . 53))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 58) (:start . 55)\n (:id . 54))\n ((:tag . "VBD") (:stem . "limit") (:form . "limited") (:end . 66)\n (:start . 59) (:id . 55))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 72)\n (:start . 67) (:id . 56))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 79)\n (:start . 73) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 82) (:start . 80)\n (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 84) (:start . 83)\n (:id . 59))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 90) (:start . 85)\n (:id . 60))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 97)\n (:start . 91) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n (:id . 62))\n ((:tag . "JJ") (:stem . "degenerate") (:form . "degenerate") (:end . 111)\n (:start . 101) (:id . 63))\n ((:tag . "NNS") (:stem . "base") (:form . "bases") (:end . 117)\n (:start . 112) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.88) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100870@unknown@formal@none@1@S@By this logic, ""ACGT"" will not be penalized differently from ""ACNNNNGT"", as both have the same number of bases that contribute any information to protein-DNA binding.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "logic") (:form . "logic") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 45))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 16) (:start . 15)\n (:id . 46))\n ((:tag . "JJ") (:stem . "”ACGT") (:form . "”ACGT") (:end . 21) (:start . 16)\n (:id . 47))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 22) (:start . 21)\n (:id . 48))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 23) (:start . 22)\n (:id . 49))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 28) (:start . 24)\n (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 32) (:start . 29)\n (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 35) (:start . 33)\n (:id . 52))\n ((:tag . "VBN") (:stem . "penalize") (:form . "penalized") (:end . 45)\n (:start . 36) (:id . 53))\n ((:tag . "RB") (:stem . "differently") (:form . "differently") (:end . 57)\n (:start . 46) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 62) (:start . 58)\n (:id . 55))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 64) (:start . 63)\n (:id . 56))\n ((:tag . "JJ") (:stem . "”ACNNNNGT") (:form . "”ACNNNNGT") (:end . 73)\n (:start . 64) (:id . 57))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 74) (:start . 73)\n (:id . 58))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 75) (:start . 74)\n (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 79) (:start . 77)\n (:id . 61))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 84) (:start . 80)\n (:id . 62))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 89) (:start . 85)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n (:id . 64))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 98) (:start . 94)\n (:id . 65))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 105)\n (:start . 99) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 108) (:start . 106)\n (:id . 67))\n ((:tag . "NNS") (:stem . "base") (:form . "bases") (:end . 114)\n (:start . 109) (:id . 68))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 119) (:start . 115)\n (:id . 69))\n ((:tag . "VBP") (:stem . "contribute") (:form . "contribute") (:end . 130)\n (:start . 120) (:id . 70))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 134) (:start . 131)\n (:id . 71))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 146)\n (:start . 135) (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 149) (:start . 147)\n (:id . 73))\n ((:tag . "JJ") (:stem . "protein-dna") (:form . "protein-DNA") (:end . 161)\n (:start . 150) (:id . 74))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 169)\n (:start . 162) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n (:id . 76)))@@@1@35@((:ncues ((:id . :x3.90.1) (:span 29 32)))\n (:nscopes ((:id . :x3.90.1) (:span 16 74)))\n (:identifiers (:sid . :s3.90) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100871@unknown@formal@none@1@S@Building on this intuition, one can argue that the characters ""A"" and ""not-A"" (IUPAC character ""B")" are roughly equivalent, while ""A or G"" (IUPAC character ""R")" is different from ""A"" as there are six ways to define a combination of two bases, while only four ways to define a combination of one base or three bases.@(((:tag . "NNP") (:stem . "Building") (:form . "Building") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 11) (:start . 9)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "intuition") (:form . "intuition") (:end . 26)\n (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n (:id . 46))\n ((:tag . "PRP") (:stem . "one") (:form . "one") (:end . 31) (:start . 28)\n (:id . 47))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 35) (:start . 32)\n (:id . 48))\n ((:tag . "VB") (:stem . "argue") (:form . "argue") (:end . 41) (:start . 36)\n (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 46) (:start . 42)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n (:id . 51))\n ((:tag . "NNS") (:stem . "character") (:form . "characters") (:end . 61)\n (:start . 51) (:id . 52))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 63) (:start . 62)\n (:id . 53))\n ((:tag . "JJ") (:stem . "”A") (:form . "”A") (:end . 65) (:start . 63)\n (:id . 54))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 66) (:start . 65)\n (:id . 55))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 67) (:start . 66)\n (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n (:id . 57))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 73) (:start . 72)\n (:id . 58))\n ((:tag . "JJ") (:stem . "”not-A") (:form . "”not-A") (:end . 79)\n (:start . 73) (:id . 59))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 80) (:start . 79)\n (:id . 60))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 81) (:start . 80)\n (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n (:id . 62))\n ((:tag . "NNP") (:stem . "IUPAC") (:form . "IUPAC") (:end . 88) (:start . 83)\n (:id . 63))\n ((:tag . "NN") (:stem . "character") (:form . "character") (:end . 98)\n (:start . 89) (:id . 64))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 100) (:start . 99)\n (:id . 65))\n ((:tag . "NNP") (:stem . "”B") (:form . "”B") (:end . 102) (:start . 100)\n (:id . 66))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 103) (:start . 102)\n (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n (:id . 68))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 105) (:start . 104)\n (:id . 69))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 109) (:start . 106)\n (:id . 70))\n ((:tag . "RB") (:stem . "roughly") (:form . "roughly") (:end . 117)\n (:start . 110) (:id . 71))\n ((:tag . "JJ") (:stem . "equivalent") (:form . "equivalent") (:end . 128)\n (:start . 118) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n (:id . 73))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 135)\n (:start . 130) (:id . 74))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 137) (:start . 136)\n (:id . 75))\n ((:tag . "NNP") (:stem . "”A") (:form . "”A") (:end . 139) (:start . 137)\n (:id . 76))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 142) (:start . 140)\n (:id . 77))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 144) (:start . 143)\n (:id . 78))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 145) (:start . 144)\n (:id . 79))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 146) (:start . 145)\n (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n (:id . 81))\n ((:tag . "NNP") (:stem . "IUPAC") (:form . "IUPAC") (:end . 153)\n (:start . 148) (:id . 82))\n ((:tag . "NN") (:stem . "character") (:form . "character") (:end . 163)\n (:start . 154) (:id . 83))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 165) (:start . 164)\n (:id . 84))\n ((:tag . "NNP") (:stem . "”R") (:form . "”R") (:end . 167) (:start . 165)\n (:id . 85))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 168) (:start . 167)\n (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n (:id . 87))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 170) (:start . 169)\n (:id . 88))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 173) (:start . 171)\n (:id . 89))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 183)\n (:start . 174) (:id . 90))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 188) (:start . 184)\n (:id . 91))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 190) (:start . 189)\n (:id . 92))\n ((:tag . "JJ") (:stem . "”A") (:form . "”A") (:end . 192) (:start . 190)\n (:id . 93))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 193) (:start . 192)\n (:id . 94))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 194) (:start . 193)\n (:id . 95))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 197) (:start . 195)\n (:id . 96))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 203)\n (:start . 198) (:id . 97))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 207) (:start . 204)\n (:id . 98))\n ((:tag . "CD") (:stem . "six") (:form . "six") (:end . 211) (:start . 208)\n (:id . 99))\n ((:tag . "NNS") (:stem . "way") (:form . "ways") (:end . 216) (:start . 212)\n (:id . 100))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 219) (:start . 217)\n (:id . 101))\n ((:tag . "VB") (:stem . "define") (:form . "define") (:end . 226)\n (:start . 220) (:id . 102))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 228) (:start . 227)\n (:id . 103))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 240)\n (:start . 229) (:id . 104))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 243) (:start . 241)\n (:id . 105))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 247) (:start . 244)\n (:id . 106))\n ((:tag . "NNS") (:stem . "base") (:form . "bases") (:end . 253)\n (:start . 248) (:id . 107))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 254) (:start . 253)\n (:id . 108))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 260)\n (:start . 255) (:id . 109))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 265) (:start . 261)\n (:id . 110))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 270) (:start . 266)\n (:id . 111))\n ((:tag . "NNS") (:stem . "way") (:form . "ways") (:end . 275) (:start . 271)\n (:id . 112))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 278) (:start . 276)\n (:id . 113))\n ((:tag . "VB") (:stem . "define") (:form . "define") (:end . 285)\n (:start . 279) (:id . 114))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 287) (:start . 286)\n (:id . 115))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 299)\n (:start . 288) (:id . 116))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 302) (:start . 300)\n (:id . 117))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 306) (:start . 303)\n (:id . 118))\n ((:tag . "NN") (:stem . "base") (:form . "base") (:end . 311) (:start . 307)\n (:id . 119))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 314) (:start . 312)\n (:id . 120))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 320)\n (:start . 315) (:id . 121))\n ((:tag . "NNS") (:stem . "base") (:form . "bases") (:end . 326)\n (:start . 321) (:id . 122))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 327) (:start . 326)\n (:id . 123)))@@@1@82@((:hcues ((:id . :x3.91.1) (:span 32 35)))\n (:hscopes ((:id . :x3.91.1) (:span 32 193)))\n (:identifiers (:sid . :s3.91) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100872@unknown@formal@none@1@S@For motif m = m1m2...mn, we can therefore define N = ∏ Choose(4, |mi|), where |mi| is the number of DNA bases covered by the IUPAC character mi.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 11) (:start . 10)\n (:id . 44))\n ((:tag . "JJ") (:stem . "=") (:form . "=") (:end . 13) (:start . 12)\n (:id . 45))\n ((:tag . "NN") (:stem . "m1m2") (:form . "m1m2") (:end . 18) (:start . 14)\n (:id . 46))\n ((:tag . ":") (:stem . "…") (:form . "…") (:end . 18) (:start . 18)\n (:id . 47))\n ((:tag . "NN") (:stem . "mn") (:form . "mn") (:end . 23) (:start . 21)\n (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n (:id . 49))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 27) (:start . 25)\n (:id . 50))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 31) (:start . 28)\n (:id . 51))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 41)\n (:start . 32) (:id . 52))\n ((:tag . "VB") (:stem . "define") (:form . "define") (:end . 48)\n (:start . 42) (:id . 53))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 50) (:start . 49)\n (:id . 54))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 52) (:start . 51)\n (:id . 55))\n ((:tag . "NNP") (:stem . "∏") (:form . "∏") (:end . 54) (:start . 53)\n (:id . 56))\n ((:tag . "NNP") (:stem . "Choose(4") (:form . "Choose(4") (:end . 63)\n (:start . 55) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n (:id . 58))\n ((:tag . "NNP") (:stem . "|mi|") (:form . "|mi|") (:end . 69) (:start . 65)\n (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n (:id . 61))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 77) (:start . 72)\n (:id . 62))\n ((:tag . "NNP") (:stem . "|mi|") (:form . "|mi|") (:end . 82) (:start . 78)\n (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 85) (:start . 83)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n (:id . 65))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 96)\n (:start . 90) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n (:id . 67))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 103) (:start . 100)\n (:id . 68))\n ((:tag . "NNS") (:stem . "base") (:form . "bases") (:end . 109)\n (:start . 104) (:id . 69))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 117)\n (:start . 110) (:id . 70))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 120) (:start . 118)\n (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n (:id . 72))\n ((:tag . "NNP") (:stem . "IUPAC") (:form . "IUPAC") (:end . 130)\n (:start . 125) (:id . 73))\n ((:tag . "NN") (:stem . "character") (:form . "character") (:end . 140)\n (:start . 131) (:id . 74))\n ((:tag . "NN") (:stem . "mi") (:form . "mi") (:end . 143) (:start . 141)\n (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s3.92) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100873@unknown@formal@none@1@S@In the case were both orientations of the motif are considered, this number is adjusted to account for palindromes.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 16) (:start . 12)\n (:id . 45))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 21) (:start . 17)\n (:id . 46))\n ((:tag . "NNS") (:stem . "orientation") (:form . "orientations") (:end . 34)\n (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n (:id . 49))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 47) (:start . 42)\n (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 51) (:start . 48)\n (:id . 51))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 62)\n (:start . 52) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n (:id . 53))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 68) (:start . 64)\n (:id . 54))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 75)\n (:start . 69) (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 78) (:start . 76)\n (:id . 56))\n ((:tag . "VBN") (:stem . "adjust") (:form . "adjusted") (:end . 87)\n (:start . 79) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 90) (:start . 88)\n (:id . 58))\n ((:tag . "VB") (:stem . "account") (:form . "account") (:end . 98)\n (:start . 91) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 102) (:start . 99)\n (:id . 60))\n ((:tag . "NNS") (:stem . "palindrome") (:form . "palindromes") (:end . 114)\n (:start . 103) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.93) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100874@unknown@formal@none@1@S@The resulting Sig score thus penalizes motifs based on their length and degeneracy, enabling fair comparisons to be made between different motif classes.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "Sig") (:form . "Sig") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 23) (:start . 18)\n (:id . 45))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 28) (:start . 24)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "penalize") (:form . "penalizes") (:end . 38)\n (:start . 29) (:id . 47))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 45)\n (:start . 39) (:id . 48))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 51) (:start . 46)\n (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 54) (:start . 52)\n (:id . 50))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 60)\n (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 67)\n (:start . 61) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n (:id . 53))\n ((:tag . "NN") (:stem . "degeneracy") (:form . "degeneracy") (:end . 82)\n (:start . 72) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n (:id . 55))\n ((:tag . "VBG") (:stem . "enable") (:form . "enabling") (:end . 92)\n (:start . 84) (:id . 56))\n ((:tag . "JJ") (:stem . "fair") (:form . "fair") (:end . 97) (:start . 93)\n (:id . 57))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 109)\n (:start . 98) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 112) (:start . 110)\n (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 115) (:start . 113)\n (:id . 60))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 120) (:start . 116)\n (:id . 61))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 128)\n (:start . 121) (:id . 62))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 138)\n (:start . 129) (:id . 63))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 144)\n (:start . 139) (:id . 64))\n ((:tag . "NNS") (:stem . "class") (:form . "classes") (:end . 152)\n (:start . 145) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.94) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100875@unknown@formal@none@1@S@Testing@(((:tag . "NNP") (:stem . "Testing") (:form . "Testing") (:end . 7)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s3.95) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100876@unknown@formal@none@1@S@Evaluation of objective functions used by SCOPE@(((:tag . "NN") (:stem . "evaluation") (:form . "Evaluation") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 43))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 23)\n (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 33)\n (:start . 24) (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 38) (:start . 34)\n (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 41) (:start . 39)\n (:id . 47))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 47) (:start . 42)\n (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.96) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5100877@unknown@formal@none@1@S@Each component algorithm in SCOPE efficiently searches its restricted search space, keeping SCOPE's runtime low (average runtime on our datasets were about one minute).@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 14)\n (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 24)\n (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n (:id . 45))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 33) (:start . 28)\n (:id . 46))\n ((:tag . "RB") (:stem . "efficiently") (:form . "efficiently") (:end . 45)\n (:start . 34) (:id . 47))\n ((:tag . "VBZ") (:stem . "search") (:form . "searches") (:end . 54)\n (:start . 46) (:id . 48))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 58) (:start . 55)\n (:id . 49))\n ((:tag . "JJ") (:stem . "restricted") (:form . "restricted") (:end . 69)\n (:start . 59) (:id . 50))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 76)\n (:start . 70) (:id . 51))\n ((:tag . "NN") (:stem . "space") (:form . "space") (:end . 82) (:start . 77)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n (:id . 53))\n ((:tag . "VBG") (:stem . "keep") (:form . "keeping") (:end . 91)\n (:start . 84) (:id . 54))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 97) (:start . 92)\n (:id . 55))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 99) (:start . 97)\n (:id . 56))\n ((:tag . "NN") (:stem . "runtime") (:form . "runtime") (:end . 107)\n (:start . 100) (:id . 57))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 111) (:start . 108)\n (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 113) (:start . 112)\n (:id . 59))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 120)\n (:start . 113) (:id . 60))\n ((:tag . "NN") (:stem . "runtime") (:form . "runtime") (:end . 128)\n (:start . 121) (:id . 61))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 131) (:start . 129)\n (:id . 62))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 135) (:start . 132)\n (:id . 63))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 144)\n (:start . 136) (:id . 64))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 149) (:start . 145)\n (:id . 65))\n ((:tag . "RB") (:stem . "about") (:form . "about") (:end . 155)\n (:start . 150) (:id . 66))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 159) (:start . 156)\n (:id . 67))\n ((:tag . "NN") (:stem . "minute") (:form . "minute") (:end . 166)\n (:start . 160) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s3.97) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100878@unknown@formal@none@1@S@This efficiency allowed us to explore several objective functions for scoring the statistical significance p(M = m) of motifs.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "efficiency") (:form . "efficiency") (:end . 15)\n (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "allow") (:form . "allowed") (:end . 23)\n (:start . 16) (:id . 44))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 26) (:start . 24)\n (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "VB") (:stem . "explore") (:form . "explore") (:end . 37)\n (:start . 30) (:id . 47))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 45)\n (:start . 38) (:id . 48))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 55)\n (:start . 46) (:id . 49))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 65)\n (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 69) (:start . 66)\n (:id . 51))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 77)\n (:start . 70) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n (:id . 53))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 93)\n (:start . 82) (:id . 54))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 106)\n (:start . 94) (:id . 55))\n ((:tag . "NNP") (:stem . "p(M") (:form . "p(M") (:end . 110) (:start . 107)\n (:id . 56))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 112) (:start . 111)\n (:id . 57))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 114) (:start . 113)\n (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 118) (:start . 116)\n (:id . 60))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 125)\n (:start . 119) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.98) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100880@unknown@formal@none@1@S@For precise definitions, see Methods.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "precise") (:form . "precise") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "definition") (:form . "definitions") (:end . 23)\n (:start . 12) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n (:id . 45))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Methods") (:form . "Methods") (:end . 36)\n (:start . 29) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 37) (:start . 36)\n (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.100) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100881@unknown@formal@none@1@S@To establish which objective function (or combination of functions) was most suitable, we tested each objective function independently of SCOPE, using a subset of the S. cerevisiae dataset.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "establish") (:form . "establish") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 28)\n (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 37)\n (:start . 29) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 39) (:start . 38)\n (:id . 47))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 41) (:start . 39)\n (:id . 48))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 53)\n (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n (:id . 50))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 66)\n (:start . 57) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 71) (:start . 68)\n (:id . 53))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 76) (:start . 72)\n (:id . 54))\n ((:tag . "JJ") (:stem . "suitable") (:form . "suitable") (:end . 85)\n (:start . 77) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n (:id . 56))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 89) (:start . 87)\n (:id . 57))\n ((:tag . "VBD") (:stem . "test") (:form . "tested") (:end . 96) (:start . 90)\n (:id . 58))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 101) (:start . 97)\n (:id . 59))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 111)\n (:start . 102) (:id . 60))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 120)\n (:start . 112) (:id . 61))\n ((:tag . "RB") (:stem . "independently") (:form . "independently")\n (:end . 134) (:start . 121) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n (:id . 63))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 143)\n (:start . 138) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n (:id . 65))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 150) (:start . 145)\n (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 152) (:start . 151)\n (:id . 67))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 159)\n (:start . 153) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 162) (:start . 160)\n (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n (:id . 70))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 169) (:start . 167)\n (:id . 71))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 180)\n (:start . 170) (:id . 72))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 188)\n (:start . 181) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.101) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100882@unknown@formal@none@1@S@The measure used to assess the biological relevance of a motif was accuracy, a measure of the nucleotide level overlap between a motif and the known binding sites (for details see Methods).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "measure") (:form . "measure") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . "VB") (:stem . "assess") (:form . "assess") (:end . 26)\n (:start . 20) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n (:id . 47))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 41)\n (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "relevance") (:form . "relevance") (:end . 51)\n (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 56) (:start . 55)\n (:id . 51))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 62) (:start . 57)\n (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 66) (:start . 63)\n (:id . 53))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 75)\n (:start . 67) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 78) (:start . 77)\n (:id . 56))\n ((:tag . "NN") (:stem . "measure") (:form . "measure") (:end . 86)\n (:start . 79) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n (:id . 59))\n ((:tag . "NN") (:stem . "nucleotide") (:form . "nucleotide") (:end . 104)\n (:start . 94) (:id . 60))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 110)\n (:start . 105) (:id . 61))\n ((:tag . "NN") (:stem . "overlap") (:form . "overlap") (:end . 118)\n (:start . 111) (:id . 62))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 126)\n (:start . 119) (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 128) (:start . 127)\n (:id . 64))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 134)\n (:start . 129) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 138) (:start . 135)\n (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 142) (:start . 139)\n (:id . 67))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 148)\n (:start . 143) (:id . 68))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 156)\n (:start . 149) (:id . 69))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 162)\n (:start . 157) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 164) (:start . 163)\n (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 167) (:start . 164)\n (:id . 72))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 175)\n (:start . 168) (:id . 73))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 179) (:start . 176)\n (:id . 74))\n ((:tag . "NNP") (:stem . "Method") (:form . "Methods") (:end . 187)\n (:start . 180) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s3.102) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100883@unknown@formal@none@1@S@From each regulon from the SCPD database 15 we selected ten six-mers at random from the upstream sequences and ten six-mers at random from the collection of known binding sites for that regulon.@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "regulon") (:form . "regulon") (:end . 17)\n (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 22) (:start . 18)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "NNP") (:stem . "SCPD") (:form . "SCPD") (:end . 31) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 40)\n (:start . 32) (:id . 48))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 43) (:start . 41)\n (:id . 49))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 46) (:start . 44)\n (:id . 50))\n ((:tag . "VBD") (:stem . "select") (:form . "selected") (:end . 55)\n (:start . 47) (:id . 51))\n ((:tag . "CD") (:stem . "ten") (:form . "ten") (:end . 59) (:start . 56)\n (:id . 52))\n ((:tag . "NNS") (:stem . "six-mer") (:form . "six-mers") (:end . 68)\n (:start . 60) (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 71) (:start . 69)\n (:id . 54))\n ((:tag . "NN") (:stem . "random") (:form . "random") (:end . 78)\n (:start . 72) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 83) (:start . 79)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n (:id . 57))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 96)\n (:start . 88) (:id . 58))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 106)\n (:start . 97) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n (:id . 60))\n ((:tag . "CD") (:stem . "ten") (:form . "ten") (:end . 114) (:start . 111)\n (:id . 61))\n ((:tag . "NNS") (:stem . "six-mer") (:form . "six-mers") (:end . 123)\n (:start . 115) (:id . 62))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 126) (:start . 124)\n (:id . 63))\n ((:tag . "NN") (:stem . "random") (:form . "random") (:end . 133)\n (:start . 127) (:id . 64))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 138) (:start . 134)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 142) (:start . 139)\n (:id . 66))\n ((:tag . "NN") (:stem . "collection") (:form . "collection") (:end . 153)\n (:start . 143) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 156) (:start . 154)\n (:id . 68))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 162)\n (:start . 157) (:id . 69))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 170)\n (:start . 163) (:id . 70))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 176)\n (:start . 171) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 180) (:start . 177)\n (:id . 72))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 185) (:start . 181)\n (:id . 73))\n ((:tag . "NN") (:stem . "regulon") (:form . "regulon") (:end . 193)\n (:start . 186) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s3.103) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100884@unknown@formal@none@1@S@For each of these sampled six-mers, we calculated accuracy with respect to the known binding sites.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 17) (:start . 12)\n (:id . 45))\n ((:tag . "VBN") (:stem . "sample") (:form . "sampled") (:end . 25)\n (:start . 18) (:id . 46))\n ((:tag . "NNS") (:stem . "six-mer") (:form . "six-mers") (:end . 34)\n (:start . 26) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 38) (:start . 36)\n (:id . 49))\n ((:tag . "VBD") (:stem . "calculate") (:form . "calculated") (:end . 49)\n (:start . 39) (:id . 50))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 58)\n (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 63) (:start . 59)\n (:id . 52))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 71)\n (:start . 64) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 74) (:start . 72)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n (:id . 55))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 84) (:start . 79)\n (:id . 56))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 92)\n (:start . 85) (:id . 57))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 98) (:start . 93)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.104) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100885@unknown@formal@none@1@S@We also calculated the Sig score for each six-mer, using four objective functions (KS, overrepresentation, coverage and combined KS-overrepresentation).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "calculate") (:form . "calculated") (:end . 18)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Sig") (:form . "Sig") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 32) (:start . 27)\n (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 36) (:start . 33)\n (:id . 48))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 41) (:start . 37)\n (:id . 49))\n ((:tag . "NN") (:stem . "six-mer") (:form . "six-mer") (:end . 49)\n (:start . 42) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n (:id . 51))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 56) (:start . 51)\n (:id . 52))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 61) (:start . 57)\n (:id . 53))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 71)\n (:start . 62) (:id . 54))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 81)\n (:start . 72) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n (:id . 56))\n ((:tag . "NNP") (:stem . "KS") (:form . "KS") (:end . 85) (:start . 83)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n (:id . 58))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n (:end . 105) (:start . 87) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n (:id . 60))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 115)\n (:start . 107) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 119) (:start . 116)\n (:id . 62))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 128)\n (:start . 120) (:id . 63))\n ((:tag . "NN") (:stem . "ks-overrepresentation")\n (:form . "KS-overrepresentation") (:end . 150) (:start . 129) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.105) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100886@unknown@formal@none@1@S@We then plotted Sig versus accuracy for each objective function, to determine which objective functions correlated most strongly with biological relevance (Figure 2).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "plot") (:form . "plotted") (:end . 15) (:start . 8)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Sig") (:form . "Sig") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "CC") (:stem . "versus") (:form . "versus") (:end . 26)\n (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 35)\n (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 44) (:start . 40)\n (:id . 49))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 54)\n (:start . 45) (:id . 50))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 63)\n (:start . 55) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n (:id . 53))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 77)\n (:start . 68) (:id . 54))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 83) (:start . 78)\n (:id . 55))\n ((:tag . "NN") (:stem . "objective") (:form . "objective") (:end . 93)\n (:start . 84) (:id . 56))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 103)\n (:start . 94) (:id . 57))\n ((:tag . "VBD") (:stem . "correlate") (:form . "correlated") (:end . 114)\n (:start . 104) (:id . 58))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 119) (:start . 115)\n (:id . 59))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 128)\n (:start . 120) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 133) (:start . 129)\n (:id . 61))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 144)\n (:start . 134) (:id . 62))\n ((:tag . "NN") (:stem . "relevance") (:form . "relevance") (:end . 154)\n (:start . 145) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 156) (:start . 155)\n (:id . 64))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 162)\n (:start . 156) (:id . 65))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 164) (:start . 163)\n (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 165) (:start . 164)\n (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s3.106) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100887@unknown@formal@none@1@S@Correlation between accuracy and Sig scores@(((:tag . "NN") (:stem . "correlation") (:form . "Correlation") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 19)\n (:start . 12) (:id . 43))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 28)\n (:start . 20) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n (:id . 45))\n ((:tag . "NN") (:stem . "sig") (:form . "Sig") (:end . 36) (:start . 33)\n (:id . 46))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 43)\n (:start . 37) (:id . 47)))@@@1@6@((:identifiers (:sid . :s3.107) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|FigureLegend|)))@oe@9-2-2011 5100888@unknown@formal@none@1@S@Correlation between accuracy and Sig scores.@(((:tag . "NN") (:stem . "correlation") (:form . "Correlation") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 19)\n (:start . 12) (:id . 43))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 28)\n (:start . 20) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n (:id . 45))\n ((:tag . "NN") (:stem . "sig") (:form . "Sig") (:end . 36) (:start . 33)\n (:id . 46))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 43)\n (:start . 37) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 44) (:start . 43)\n (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.108) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100890@unknown@formal@none@1@S@The 6-mers were randomly sampled from both the upstream regions and the known binding sites to ensure coverage or a wide range of accuracy.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "6-mer") (:form . "6-mers") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 24)\n (:start . 16) (:id . 45))\n ((:tag . "VBN") (:stem . "sample") (:form . "sampled") (:end . 32)\n (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 37) (:start . 33)\n (:id . 47))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 42) (:start . 38)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n (:id . 49))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 55)\n (:start . 47) (:id . 50))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 63)\n (:start . 56) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n (:id . 53))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 77) (:start . 72)\n (:id . 54))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 85)\n (:start . 78) (:id . 55))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 91) (:start . 86)\n (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n (:id . 57))\n ((:tag . "VB") (:stem . "ensure") (:form . "ensure") (:end . 101)\n (:start . 95) (:id . 58))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 110)\n (:start . 102) (:id . 59))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 113) (:start . 111)\n (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 115) (:start . 114)\n (:id . 61))\n ((:tag . "JJ") (:stem . "wide") (:form . "wide") (:end . 120) (:start . 116)\n (:id . 62))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 126)\n (:start . 121) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n (:id . 64))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 138)\n (:start . 130) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.110) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100891@unknown@formal@none@1@S@The x-axis plots the Bonferroni-corrected and log2 transformed Sig score for each metric.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "x-axis") (:form . "x-axis") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "plot") (:form . "plots") (:end . 16) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "JJ") (:stem . "bonferroni-corrected")\n (:form . "Bonferroni-corrected") (:end . 41) (:start . 21) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n (:id . 47))\n ((:tag . "NN") (:stem . "log2") (:form . "log2") (:end . 50) (:start . 46)\n (:id . 48))\n ((:tag . "VBN") (:stem . "transform") (:form . "transformed") (:end . 62)\n (:start . 51) (:id . 49))\n ((:tag . "NNP") (:stem . "Sig") (:form . "Sig") (:end . 66) (:start . 63)\n (:id . 50))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 72) (:start . 67)\n (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 76) (:start . 73)\n (:id . 52))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 81) (:start . 77)\n (:id . 53))\n ((:tag . "NN") (:stem . "metric") (:form . "metric") (:end . 88)\n (:start . 82) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.111) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100892@unknown@formal@none@1@S@The red lines indicate the 95th Sig percentile.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 22)\n (:start . 14) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "JJ") (:stem . "95th") (:form . "95th") (:end . 31) (:start . 27)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Sig") (:form . "Sig") (:end . 35) (:start . 32)\n (:id . 48))\n ((:tag . "NN") (:stem . "percentile") (:form . "percentile") (:end . 46)\n (:start . 36) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 47) (:start . 46)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s3.112) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100893@unknown@formal@none@1@S@These plots demonstrate that overrepresentation is a closer approximation to biological relevance than coverage or KS alone.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "plot") (:form . "plots") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 23)\n (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n (:id . 45))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n (:end . 47) (:start . 29) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 50) (:start . 48)\n (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n (:id . 48))\n ((:tag . "JJR") (:stem . "close") (:form . "closer") (:end . 59)\n (:start . 53) (:id . 49))\n ((:tag . "NN") (:stem . "approximation") (:form . "approximation")\n (:end . 73) (:start . 60) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 76) (:start . 74)\n (:id . 51))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 87)\n (:start . 77) (:id . 52))\n ((:tag . "NN") (:stem . "relevance") (:form . "relevance") (:end . 97)\n (:start . 88) (:id . 53))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 102) (:start . 98)\n (:id . 54))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 111)\n (:start . 103) (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 114) (:start . 112)\n (:id . 56))\n ((:tag . "NN") (:stem . "ks") (:form . "KS") (:end . 117) (:start . 115)\n (:id . 57))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 123)\n (:start . 118) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.113) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100894@unknown@formal@none@1@S@Adding KS to overrepresentation modestly improved the correlation by 13% (as compared to overrepresentation alone) to R2 = 0.28.@(((:tag . "VBG") (:stem . "add") (:form . "Adding") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "ks") (:form . "KS") (:end . 9) (:start . 7)\n (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 12) (:start . 10)\n (:id . 44))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n (:end . 31) (:start . 13) (:id . 45))\n ((:tag . "RB") (:stem . "modestly") (:form . "modestly") (:end . 40)\n (:start . 32) (:id . 46))\n ((:tag . "VBD") (:stem . "improve") (:form . "improved") (:end . 49)\n (:start . 41) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n (:id . 48))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 65)\n (:start . 54) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 68) (:start . 66)\n (:id . 50))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 71) (:start . 69)\n (:id . 51))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 72) (:start . 71)\n (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 74) (:start . 73)\n (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 76) (:start . 74)\n (:id . 54))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 85)\n (:start . 77) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n (:id . 56))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n (:end . 107) (:start . 89) (:id . 57))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 113)\n (:start . 108) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 117) (:start . 115)\n (:id . 60))\n ((:tag . "NN") (:stem . "r2") (:form . "R2") (:end . 120) (:start . 118)\n (:id . 61))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 122) (:start . 121)\n (:id . 62))\n ((:tag . "CD") (:stem . "0.28") (:form . "0.28") (:end . 127) (:start . 123)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.114) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100895@unknown@formal@none@1@S@To assess the degree of class separation achieved by the two objective functions, we ranked the sampled six-mers by Sig score, and calculated the percentage of motifs with high Sig scores (in the 95th percentile and above) that possessed a reasonable degree of overlap with the known binding sites (accuracy ≥ 0.10).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "assess") (:form . "assess") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 20)\n (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 46))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 29) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 40)\n (:start . 30) (:id . 48))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 49)\n (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 52) (:start . 50)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n (:id . 51))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 60) (:start . 57)\n (:id . 52))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 70)\n (:start . 61) (:id . 53))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 80)\n (:start . 71) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n (:id . 55))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 84) (:start . 82)\n (:id . 56))\n ((:tag . "VBD") (:stem . "rank") (:form . "ranked") (:end . 91) (:start . 85)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n (:id . 58))\n ((:tag . "VBN") (:stem . "sample") (:form . "sampled") (:end . 103)\n (:start . 96) (:id . 59))\n ((:tag . "NNS") (:stem . "six-mer") (:form . "six-mers") (:end . 112)\n (:start . 104) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 115) (:start . 113)\n (:id . 61))\n ((:tag . "NNP") (:stem . "Sig") (:form . "Sig") (:end . 119) (:start . 116)\n (:id . 62))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 125)\n (:start . 120) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n (:id . 65))\n ((:tag . "VBD") (:stem . "calculate") (:form . "calculated") (:end . 141)\n (:start . 131) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n (:id . 67))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 156)\n (:start . 146) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 159) (:start . 157)\n (:id . 69))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 166)\n (:start . 160) (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 171) (:start . 167)\n (:id . 71))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 176) (:start . 172)\n (:id . 72))\n ((:tag . "NNP") (:stem . "Sig") (:form . "Sig") (:end . 180) (:start . 177)\n (:id . 73))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 187)\n (:start . 181) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 189) (:start . 188)\n (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 191) (:start . 189)\n (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 195) (:start . 192)\n (:id . 77))\n ((:tag . "JJ") (:stem . "95th") (:form . "95th") (:end . 200) (:start . 196)\n (:id . 78))\n ((:tag . "NN") (:stem . "percentile") (:form . "percentile") (:end . 211)\n (:start . 201) (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 215) (:start . 212)\n (:id . 80))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 221)\n (:start . 216) (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 222) (:start . 221)\n (:id . 82))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 227) (:start . 223)\n (:id . 83))\n ((:tag . "VBD") (:stem . "possess") (:form . "possessed") (:end . 237)\n (:start . 228) (:id . 84))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 239) (:start . 238)\n (:id . 85))\n ((:tag . "JJ") (:stem . "reasonable") (:form . "reasonable") (:end . 250)\n (:start . 240) (:id . 86))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 257)\n (:start . 251) (:id . 87))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 260) (:start . 258)\n (:id . 88))\n ((:tag . "NN") (:stem . "overlap") (:form . "overlap") (:end . 268)\n (:start . 261) (:id . 89))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 273) (:start . 269)\n (:id . 90))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 277) (:start . 274)\n (:id . 91))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 283)\n (:start . 278) (:id . 92))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 291)\n (:start . 284) (:id . 93))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 297)\n (:start . 292) (:id . 94))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 299) (:start . 298)\n (:id . 95))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 307)\n (:start . 299) (:id . 96))\n ((:tag . "NN") (:stem . "≥") (:form . "≥") (:end . 309) (:start . 308)\n (:id . 97))\n ((:tag . "CD") (:stem . "0.10") (:form . "0.10") (:end . 314) (:start . 310)\n (:id . 98))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 315) (:start . 314)\n (:id . 99))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 316) (:start . 315)\n (:id . 100)))@@@1@59@((:identifiers (:sid . :s3.115) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100896@unknown@formal@none@1@S@By the overrepresentation measure, 74.4% of high scoring motifs had accuracy = 0.10, while 79.1% of high scoring motifs by KS-overrepresentation had accuracy ≥ 0.10.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n (:end . 25) (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "measure") (:form . "measure") (:end . 33)\n (:start . 26) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n (:id . 46))\n ((:tag . "CD") (:stem . "74.4") (:form . "74.4") (:end . 39) (:start . 35)\n (:id . 47))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 40) (:start . 39)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n (:id . 49))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 48) (:start . 44)\n (:id . 50))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 56)\n (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 63)\n (:start . 57) (:id . 52))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 67) (:start . 64)\n (:id . 53))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 76)\n (:start . 68) (:id . 54))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 78) (:start . 77)\n (:id . 55))\n ((:tag . "CD") (:stem . "0.10") (:form . "0.10") (:end . 83) (:start . 79)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n (:id . 57))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 90) (:start . 85)\n (:id . 58))\n ((:tag . "CD") (:stem . "79.1") (:form . "79.1") (:end . 95) (:start . 91)\n (:id . 59))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 96) (:start . 95)\n (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n (:id . 61))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 104) (:start . 100)\n (:id . 62))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 112)\n (:start . 105) (:id . 63))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 119)\n (:start . 113) (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 122) (:start . 120)\n (:id . 65))\n ((:tag . "NNP") (:stem . "KS-overrepresentation")\n (:form . "KS-overrepresentation") (:end . 144) (:start . 123) (:id . 66))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 148) (:start . 145)\n (:id . 67))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 157)\n (:start . 149) (:id . 68))\n ((:tag . "NNP") (:stem . "≥") (:form . "≥") (:end . 159) (:start . 158)\n (:id . 69))\n ((:tag . "CD") (:stem . "0.10") (:form . "0.10") (:end . 164) (:start . 160)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s3.116) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100897@unknown@formal@none@1@S@This analysis suggests that more complex objective functions may provide a better estimate of biological significance than the overrepresentation objective functions commonly used.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 22)\n (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 27) (:start . 23)\n (:id . 45))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 32) (:start . 28)\n (:id . 46))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 40)\n (:start . 33) (:id . 47))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 50)\n (:start . 41) (:id . 48))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 60)\n (:start . 51) (:id . 49))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 64) (:start . 61)\n (:id . 50))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 72)\n (:start . 65) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 74) (:start . 73)\n (:id . 52))\n ((:tag . "JJR") (:stem . "good") (:form . "better") (:end . 81) (:start . 75)\n (:id . 53))\n ((:tag . "NN") (:stem . "estimate") (:form . "estimate") (:end . 90)\n (:start . 82) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n (:id . 55))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 104)\n (:start . 94) (:id . 56))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 117)\n (:start . 105) (:id . 57))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 122) (:start . 118)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n (:id . 59))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n (:end . 145) (:start . 127) (:id . 60))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 155)\n (:start . 146) (:id . 61))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 165)\n (:start . 156) (:id . 62))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 174)\n (:start . 166) (:id . 63))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 179) (:start . 175)\n (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n (:id . 65)))@@@1@24@((:hcues ((:id . :x3.117.1) (:span 61 64)) ((:id . :x3.117.2) (:span 14 22)))\n (:hscopes ((:id . :x3.117.1) (:span 61 179))\n ((:id . :x3.117.2) (:span 14 179)))\n (:identifiers (:sid . :s3.117) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100898@unknown@formal@none@1@S@We thus chose to run SCOPE using the overrepresentation-KS combined objective function on the S. cerevisiae dataset, in which the upstream regions are of fixed length.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "choose") (:form . "chose") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "VB") (:stem . "run") (:form . "run") (:end . 20) (:start . 17)\n (:id . 46))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 26) (:start . 21)\n (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 32) (:start . 27)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n (:id . 49))\n ((:tag . "JJ") (:stem . "overrepresentation-ks")\n (:form . "overrepresentation-KS") (:end . 58) (:start . 37) (:id . 50))\n ((:tag . "JJ") (:stem . "combined") (:form . "combined") (:end . 67)\n (:start . 59) (:id . 51))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 77)\n (:start . 68) (:id . 52))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 86)\n (:start . 78) (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 89) (:start . 87)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n (:id . 55))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 96) (:start . 94)\n (:id . 56))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 107)\n (:start . 97) (:id . 57))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 115)\n (:start . 108) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 119) (:start . 117)\n (:id . 60))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 125)\n (:start . 120) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n (:id . 62))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 138)\n (:start . 130) (:id . 63))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 146)\n (:start . 139) (:id . 64))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 150) (:start . 147)\n (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 153) (:start . 151)\n (:id . 66))\n ((:tag . "VBN") (:stem . "fix") (:form . "fixed") (:end . 159) (:start . 154)\n (:id . 67))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 166)\n (:start . 160) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s3.118) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100900@unknown@formal@none@1@S@Because identifying the genomic positions of highly degenerate bipartite motifs is prohibitively slow, initial rankings of motifs for SPACER were computed using the overrepresentation objective function, and the overrepresentation-KS objective function was used only to produce the final ordering and scores.@(((:tag . "IN") (:stem . "because") (:form . 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")") (:form . ")") (:end . 137) (:start . 136)\n (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s3.126) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100907@unknown@formal@none@1@S@SCOPE performed well on the synthetic datasets, correctly identifying 92% of planted motifs that are over-represented relative to background (those motifs with a Sig score of greater than 5; Figure 3).@(((:tag . "NN") (:stem . "scope") (:form . "SCOPE") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "perform") (:form . "performed") (:end . 15)\n (:start . 6) (:id . 43))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 20) (:start . 16)\n (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 23) (:start . 21)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n (:id . 46))\n ((:tag . "JJ") (:stem . "synthetic") (:form . "synthetic") (:end . 37)\n (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 46)\n (:start . 38) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n (:id . 49))\n ((:tag . "RB") (:stem . "correctly") (:form . "correctly") (:end . 57)\n (:start . 48) (:id . 50))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 69)\n (:start . 58) (:id . 51))\n ((:tag . "CD") (:stem . "92") (:form . "92") (:end . 72) (:start . 70)\n (:id . 52))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 73) (:start . 72)\n (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n (:id . 54))\n ((:tag . "VBN") (:stem . "plant") (:form . "planted") (:end . 84)\n (:start . 77) (:id . 55))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 91)\n (:start . 85) (:id . 56))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 96) (:start . 92)\n (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 100) (:start . 97)\n (:id . 58))\n ((:tag . "JJ") (:stem . "over-represented") (:form . "over-represented")\n (:end . 117) (:start . 101) (:id . 59))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 126)\n (:start . 118) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 129) (:start . 127)\n (:id . 61))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 140)\n (:start . 130) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n (:id . 63))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 147)\n (:start . 142) (:id . 64))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 154)\n (:start . 148) (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 159) (:start . 155)\n (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 161) (:start . 160)\n (:id . 67))\n ((:tag . "NNP") (:stem . "Sig") (:form . "Sig") (:end . 165) (:start . 162)\n (:id . 68))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 171)\n (:start . 166) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 174) (:start . 172)\n (:id . 70))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 182)\n (:start . 175) (:id . 71))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 187) (:start . 183)\n (:id . 72))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 189) (:start . 188)\n (:id . 73))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 190) (:start . 189)\n (:id . 74))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 197)\n (:start . 191) (:id . 75))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 199) (:start . 198)\n (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 200) (:start . 199)\n (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n (:id . 78)))@@@1@37@((:identifiers (:sid . :s3.127) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100908@unknown@formal@none@1@S@Performance at different overrepresentation Sig values on synthetic data@(((:tag . "NNP") (:stem . "Performance") (:form . "Performance") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 14) (:start . 12)\n (:id . 43))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 24)\n (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n (:end . 43) (:start . 25) (:id . 45))\n ((:tag . "NN") (:stem . "sig") (:form . "Sig") (:end . 47) (:start . 44)\n (:id . 46))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 54)\n (:start . 48) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 57) (:start . 55)\n (:id . 48))\n ((:tag . "JJ") (:stem . "synthetic") (:form . "synthetic") (:end . 67)\n (:start . 58) (:id . 49))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 72) (:start . 68)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s3.128) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|FigureLegend|)))@oe@9-2-2011 5100910@unknown@formal@none@1@S@A motif was "found" if the top scoring motif returned by SCOPE overlapped the planted motif by at least 50%.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 7) (:start . 2)\n (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 11) (:start . 8)\n (:id . 44))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 13) (:start . 12)\n (:id . 45))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 18) (:start . 13)\n (:id . 46))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 19) (:start . 18)\n (:id . 47))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 22) (:start . 20)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 49))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 30) (:start . 27)\n (:id . 50))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 38)\n (:start . 31) (:id . 51))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 44) (:start . 39)\n (:id . 52))\n ((:tag . "VBN") (:stem . "return") (:form . "returned") (:end . 53)\n (:start . 45) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 56) (:start . 54)\n (:id . 54))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 62) (:start . 57)\n (:id . 55))\n ((:tag . "VBD") (:stem . "overlap") (:form . "overlapped") (:end . 73)\n (:start . 63) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n (:id . 57))\n ((:tag . "VBN") (:stem . "plant") (:form . "planted") (:end . 85)\n (:start . 78) (:id . 58))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 91) (:start . 86)\n (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 94) (:start . 92)\n (:id . 60))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 97) (:start . 95)\n (:id . 61))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 103)\n (:start . 98) (:id . 62))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 106) (:start . 104)\n (:id . 63))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 107) (:start . 106)\n (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.130) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100911@unknown@formal@none@1@S@Different Sig values were achieved by varying the number of upstream regions, the number of motifs per upstream region, and the number of extraneous upstream regions without planted motifs.@(((:tag . "JJ") (:stem . "different") (:form . "Different") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Sig") (:form . "Sig") (:end . 13) (:start . 10)\n (:id . 43))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 20)\n (:start . 14) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 25) (:start . 21)\n (:id . 45))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 34)\n (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 37) (:start . 35)\n (:id . 47))\n ((:tag . "VBG") (:stem . "vary") (:form . "varying") (:end . 45)\n (:start . 38) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 56)\n (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n (:id . 51))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 68)\n (:start . 60) (:id . 52))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 76)\n (:start . 69) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n (:id . 55))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 88)\n (:start . 82) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n (:id . 57))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 98)\n (:start . 92) (:id . 58))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 102) (:start . 99)\n (:id . 59))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 111)\n (:start . 103) (:id . 60))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 118)\n (:start . 112) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n (:id . 64))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 134)\n (:start . 128) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n (:id . 66))\n ((:tag . "JJ") (:stem . "extraneous") (:form . "extraneous") (:end . 148)\n (:start . 138) (:id . 67))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 157)\n (:start . 149) (:id . 68))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 165)\n (:start . 158) (:id . 69))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 173)\n (:start . 166) (:id . 70))\n ((:tag . "VBN") (:stem . "plant") (:form . "planted") (:end . 181)\n (:start . 174) (:id . 71))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 188)\n (:start . 182) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n (:id . 73)))@@@1@32@((:ncues ((:id . :x3.131.1) (:span 166 173)))\n (:nscopes ((:id . :x3.131.1) (:span 166 188)))\n (:identifiers (:sid . :s3.131) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100912@unknown@formal@none@1@S@A Sig value of 0 implies that one motif of that significance is expected by chance.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Sig") (:form . "Sig") (:end . 5) (:start . 2)\n (:id . 43))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 11) (:start . 6)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 45))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 16) (:start . 15)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "imply") (:form . "implies") (:end . 24)\n (:start . 17) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 29) (:start . 25)\n (:id . 48))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 33) (:start . 30)\n (:id . 49))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 39) (:start . 34)\n (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n (:id . 51))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 47) (:start . 43)\n (:id . 52))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 60)\n (:start . 48) (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 63) (:start . 61)\n (:id . 54))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 72)\n (:start . 64) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 75) (:start . 73)\n (:id . 56))\n ((:tag . "NN") (:stem . "chance") (:form . "chance") (:end . 82)\n (:start . 76) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.132) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100913@unknown@formal@none@1@S@While synthetic test sets are useful in algorithmic development and initial testing, the results of such tests must be taken with a grain of salt, as they are highly dependent on the model used to generate the test sets 6.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "synthetic") (:form . "synthetic") (:end . 15)\n (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 20) (:start . 16)\n (:id . 44))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 25) (:start . 21)\n (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n (:id . 46))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 36)\n (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n (:id . 48))\n ((:tag . "JJ") (:stem . "algorithmic") (:form . "algorithmic") (:end . 51)\n (:start . 40) (:id . 49))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 63)\n (:start . 52) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n (:id . 51))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 75)\n (:start . 68) (:id . 52))\n ((:tag . "NN") (:stem . "testing") (:form . "testing") (:end . 83)\n (:start . 76) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n (:id . 55))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 96)\n (:start . 89) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n (:id . 57))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 104) (:start . 100)\n (:id . 58))\n ((:tag . "NNS") (:stem . "test") (:form . "tests") (:end . 110)\n (:start . 105) (:id . 59))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 115) (:start . 111)\n (:id . 60))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 118) (:start . 116)\n (:id . 61))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 124)\n (:start . 119) (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 129) (:start . 125)\n (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 131) (:start . 130)\n (:id . 64))\n ((:tag . "NN") (:stem . "grain") (:form . "grain") (:end . 137)\n (:start . 132) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 140) (:start . 138)\n (:id . 66))\n ((:tag . "NN") (:stem . "salt") (:form . "salt") (:end . 145) (:start . 141)\n (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n (:id . 68))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 149) (:start . 147)\n (:id . 69))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 154) (:start . 150)\n (:id . 70))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 158) (:start . 155)\n (:id . 71))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 165)\n (:start . 159) (:id . 72))\n ((:tag . "JJ") (:stem . "dependent") (:form . "dependent") (:end . 175)\n (:start . 166) (:id . 73))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 178) (:start . 176)\n (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 182) (:start . 179)\n (:id . 75))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 188)\n (:start . 183) (:id . 76))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 193) (:start . 189)\n (:id . 77))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 196) (:start . 194)\n (:id . 78))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 205)\n (:start . 197) (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 209) (:start . 206)\n (:id . 80))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 214) (:start . 210)\n (:id . 81))\n ((:tag . "VBZ") (:stem . "set") (:form . "sets") (:end . 219) (:start . 215)\n (:id . 82))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 221) (:start . 220)\n (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n (:id . 84)))@@@1@43@((:identifiers (:sid . :s3.133) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100914@unknown@formal@none@1@S@We therefore tested SCOPE on an extensive array of regulons with known binding sites (for details of datasets, see Additional file 1, section S3).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . "VBD") (:stem . "test") (:form . "tested") (:end . 19) (:start . 13)\n (:id . 44))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 25) (:start . 20)\n (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 31) (:start . 29)\n (:id . 47))\n ((:tag . "JJ") (:stem . "extensive") (:form . "extensive") (:end . 41)\n (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "array") (:form . "array") (:end . 47) (:start . 42)\n (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n (:id . 50))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 59)\n (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 64) (:start . 60)\n (:id . 52))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 70) (:start . 65)\n (:id . 53))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 78)\n (:start . 71) (:id . 54))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 84) (:start . 79)\n (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 89) (:start . 86)\n (:id . 57))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 97)\n (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n (:id . 59))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 109)\n (:start . 101) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n (:id . 61))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 114) (:start . 111)\n (:id . 62))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 125)\n (:start . 115) (:id . 63))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 130) (:start . 126)\n (:id . 64))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 132) (:start . 131)\n (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n (:id . 66))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 141)\n (:start . 134) (:id . 67))\n ((:tag . "NN") (:stem . "s3") (:form . "S3") (:end . 144) (:start . 142)\n (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 145) (:start . 144)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s3.134) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100915@unknown@formal@none@1@S@We ran SCOPE on each regulon and, following the scoring methodology used by Sinha and Tompa 6, we computed the accuracy for each of the top three motifs reported by SCOPE against the known binding sites.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "run") (:form . "ran") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 12) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 20) (:start . 16)\n (:id . 46))\n ((:tag . "NN") (:stem . "regulon") (:form . "regulon") (:end . 28)\n (:start . 21) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n (:id . 49))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 43)\n (:start . 34) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n (:id . 51))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 55)\n (:start . 48) (:id . 52))\n ((:tag . "NN") (:stem . "methodology") (:form . "methodology") (:end . 67)\n (:start . 56) (:id . 53))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 72) (:start . 68)\n (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 75) (:start . 73)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Sinha") (:form . "Sinha") (:end . 81) (:start . 76)\n (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n (:id . 57))\n ((:tag . "NNP") (:stem . "Tompa") (:form . "Tompa") (:end . 91) (:start . 86)\n (:id . 58))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 93) (:start . 92)\n (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n (:id . 60))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 97) (:start . 95)\n (:id . 61))\n ((:tag . "VBD") (:stem . "compute") (:form . "computed") (:end . 106)\n (:start . 98) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n (:id . 63))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 119)\n (:start . 111) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 123) (:start . 120)\n (:id . 65))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 128) (:start . 124)\n (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 135) (:start . 132)\n (:id . 68))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 139) (:start . 136)\n (:id . 69))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 145)\n (:start . 140) (:id . 70))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 152)\n (:start . 146) (:id . 71))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 161)\n (:start . 153) (:id . 72))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 164) (:start . 162)\n (:id . 73))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 170)\n (:start . 165) (:id . 74))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 178)\n (:start . 171) (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 182) (:start . 179)\n (:id . 76))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 188)\n (:start . 183) (:id . 77))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 196)\n (:start . 189) (:id . 78))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 202)\n (:start . 197) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n (:id . 80)))@@@1@39@((:identifiers (:sid . :s3.135) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100916@unknown@formal@none@1@S@The motifs reported by SCOPE overlap to a large extent with the published cis-regulatory elements (as discussed in Additional file 1, section S3, a difference of one base pair length between the reported motif and the published cis-regulatory element results in an expected accuracy of about 0.25).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 19)\n (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 22) (:start . 20)\n (:id . 45))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 28) (:start . 23)\n (:id . 46))\n ((:tag . "NN") (:stem . "overlap") (:form . "overlap") (:end . 36)\n (:start . 29) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 41) (:start . 40)\n (:id . 49))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 47) (:start . 42)\n (:id . 50))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 54)\n (:start . 48) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 59) (:start . 55)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n (:id . 53))\n ((:tag . "VBN") (:stem . "publish") (:form . "published") (:end . 73)\n (:start . 64) (:id . 54))\n ((:tag . "JJ") (:stem . "cis-regulatory") (:form . "cis-regulatory")\n (:end . 88) (:start . 74) (:id . 55))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 97)\n (:start . 89) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 99) (:start . 98)\n (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 101) (:start . 99)\n (:id . 58))\n ((:tag . "VBN") (:stem . "discuss") (:form . "discussed") (:end . 111)\n (:start . 102) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n (:id . 60))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 125)\n (:start . 115) (:id . 61))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 130) (:start . 126)\n (:id . 62))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 132) (:start . 131)\n (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n (:id . 64))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 141)\n (:start . 134) (:id . 65))\n ((:tag . "NN") (:stem . "s3") (:form . "S3") (:end . 144) (:start . 142)\n (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 147) (:start . 146)\n (:id . 68))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 158)\n (:start . 148) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 161) (:start . 159)\n (:id . 70))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 165) (:start . 162)\n (:id . 71))\n ((:tag . "NN") (:stem . "base") (:form . "base") (:end . 170) (:start . 166)\n (:id . 72))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 175) (:start . 171)\n (:id . 73))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 182)\n (:start . 176) (:id . 74))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 190)\n (:start . 183) (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 194) (:start . 191)\n (:id . 76))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 203)\n (:start . 195) (:id . 77))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 209)\n (:start . 204) (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 213) (:start . 210)\n (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 217) (:start . 214)\n (:id . 80))\n ((:tag . "VBN") (:stem . "publish") (:form . "published") (:end . 227)\n (:start . 218) (:id . 81))\n ((:tag . "JJ") (:stem . "cis-regulatory") (:form . "cis-regulatory")\n (:end . 242) (:start . 228) (:id . 82))\n ((:tag . "NN") (:stem . "element") (:form . "element") (:end . 250)\n (:start . 243) (:id . 83))\n ((:tag . "VBZ") (:stem . "result") (:form . "results") (:end . 258)\n (:start . 251) (:id . 84))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 261) (:start . 259)\n (:id . 85))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 264) (:start . 262)\n (:id . 86))\n ((:tag . "JJ") (:stem . "expected") (:form . "expected") (:end . 273)\n (:start . 265) (:id . 87))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 282)\n (:start . 274) (:id . 88))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 285) (:start . 283)\n (:id . 89))\n ((:tag . "RB") (:stem . "about") (:form . "about") (:end . 291)\n (:start . 286) (:id . 90))\n ((:tag . "CD") (:stem . "0.25") (:form . "0.25") (:end . 296) (:start . 292)\n (:id . 91))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 297) (:start . 296)\n (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 298) (:start . 297)\n (:id . 93)))@@@1@52@((:identifiers (:sid . :s3.136) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100917@unknown@formal@none@1@S@SCOPE was run on 78 regulons from S. cerevisiae, B. subtilis, E. coli and D. melanogaster.@(((:tag . "NN") (:stem . "scope") (:form . "SCOPE") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "VBN") (:stem . "run") (:form . "run") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "CD") (:stem . "78") (:form . "78") (:end . 19) (:start . 17)\n (:id . 46))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 28)\n (:start . 20) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 33) (:start . 29)\n (:id . 48))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 36) (:start . 34)\n (:id . 49))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 47)\n (:start . 37) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n (:id . 51))\n ((:tag . "NNP") (:stem . "B.") (:form . "B.") (:end . 51) (:start . 49)\n (:id . 52))\n ((:tag . "NNP") (:stem . "subtilis") (:form . "subtilis") (:end . 60)\n (:start . 52) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n (:id . 54))\n ((:tag . "NNP") (:stem . "E.") (:form . "E.") (:end . 64) (:start . 62)\n (:id . 55))\n ((:tag . "NNP") (:stem . "coli") (:form . "coli") (:end . 69) (:start . 65)\n (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n (:id . 57))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 76) (:start . 74)\n (:id . 58))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 89)\n (:start . 77) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.137) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100918@unknown@formal@none@1@S@On these datasets, SCOPE's average accuracy was 0.28, 0.29, 0.16, and 0.08 respectively.@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 17)\n (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n (:id . 45))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 24) (:start . 19)\n (:id . 46))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 26) (:start . 24)\n (:id . 47))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 34)\n (:start . 27) (:id . 48))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 43)\n (:start . 35) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 47) (:start . 44)\n (:id . 50))\n ((:tag . "CD") (:stem . "0.28") (:form . "0.28") (:end . 52) (:start . 48)\n (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n (:id . 52))\n ((:tag . "CD") (:stem . "0.29") (:form . "0.29") (:end . 58) (:start . 54)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n (:id . 54))\n ((:tag . "CD") (:stem . "0.16") (:form . "0.16") (:end . 64) (:start . 60)\n (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n (:id . 57))\n ((:tag . "CD") (:stem . "0.08") (:form . "0.08") (:end . 74) (:start . 70)\n (:id . 58))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 87)\n (:start . 75) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.138) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100920@unknown@formal@none@1@S@Indeed, we found that SCOPE increased accuracy by 31–44% over BEAM, PRISM or SPACER alone.@(((:tag . "RB") (:stem . "indeed") (:form . "Indeed") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 10) (:start . 8)\n (:id . 44))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 16) (:start . 11)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n (:id . 46))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 27) (:start . 22)\n (:id . 47))\n ((:tag . "VBD") (:stem . "increase") (:form . "increased") (:end . 37)\n (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 46)\n (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 49) (:start . 47)\n (:id . 50))\n ((:tag . "CD") (:stem . "31–44") (:form . "31–44") (:end . 55) (:start . 50)\n (:id . 51))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 56) (:start . 55)\n (:id . 52))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 61) (:start . 57)\n (:id . 53))\n ((:tag . "NNP") (:stem . "BEAM") (:form . "BEAM") (:end . 66) (:start . 62)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n (:id . 55))\n ((:tag . "NN") (:stem . "prism") (:form . "PRISM") (:end . 73) (:start . 68)\n (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 76) (:start . 74)\n (:id . 57))\n ((:tag . "NN") (:stem . "spacer") (:form . "SPACER") (:end . 83)\n (:start . 77) (:id . 58))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 89) (:start . 84)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.140) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100921@unknown@formal@none@1@S@This improvement was achieved by combining BEAM's high positive predictive value (PPV) with PRISM's high sensitivity (Figure 4).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "improvement") (:form . "improvement") (:end . 16)\n (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 20) (:start . 17)\n (:id . 44))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 29)\n (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 32) (:start . 30)\n (:id . 46))\n ((:tag . "VBG") (:stem . "combine") (:form . "combining") (:end . 42)\n (:start . 33) (:id . 47))\n ((:tag . "NNP") (:stem . 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(:end . 128) (:start . 127)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.141) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100922@unknown@formal@none@1@S@Sensitivity is defined here as the fraction of the known binding sites (at the nucleotide level) predicted by the motif finder, and PPV is defined as the fraction of nucleotides predicted by the motif finder that correspond to the known binding sites (see Methods for details).@(((:tag . "NN") (:stem . "sensitivity") (:form . "Sensitivity") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n (:id . 43))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 22)\n (:start . 15) (:id . 44))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 27) (:start . 23)\n (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . 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",") (:end . 87) (:start . 86)\n (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 90) (:start . 88)\n (:id . 54))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 94) (:start . 91)\n (:id . 55))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 103)\n (:start . 95) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.143) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|TableLegend|)))@oe@9-2-2011 5100924@unknown@formal@none@1@S@A "Win" is a regulon for which a program had the highest accuracy and that accuracy was at least 0.10.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 3) (:start . 2)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Win") (:form . "Win") (:end . 6) (:start . 3)\n (:id . 44))\n ((:tag . "''") (:stem . 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(:end . 102) (:start . 101)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.144) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100925@unknown@formal@none@1@S@Programs in a two-way tie are credited with 0.5 wins each, so by construction, SCOPE can at best share a win with one of the other programs.@(((:tag . "NNS") (:stem . "program") (:form . "Programs") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n (:id . 44))\n ((:tag . "JJ") (:stem . "two-way") (:form . "two-way") (:end . 21)\n (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "tie") (:form . "tie") (:end . 25) (:start . 22)\n (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n (:id . 47))\n ((:tag . "VBN") (:stem . "credit") (:form . 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"program") (:form . "programs") (:end . 139)\n (:start . 131) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s3.145) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100926@unknown@formal@none@1@S@A perfect winner-take-all ensemble method would have the same number of wins as all the component algorithms combined.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "perfect") (:form . "perfect") (:end . 9)\n (:start . 2) (:id . 43))\n ((:tag . "JJ") (:stem . "winner-take-all") (:form . "winner-take-all")\n (:end . 25) (:start . 10) (:id . 44))\n ((:tag . "JJ") (:stem . "ensemble") (:form . "ensemble") (:end . 34)\n (:start . 26) (:id . 45))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 41)\n (:start . 35) (:id . 46))\n ((:tag . "MD") (:stem . 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"NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 108)\n (:start . 98) (:id . 58))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 117)\n (:start . 109) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n (:id . 60)))@@@1@19@((:hcues ((:id . :x3.146.1) (:span 42 47)))\n (:hscopes ((:id . :x3.146.1) (:span 42 117)))\n (:identifiers (:sid . :s3.146) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100927@unknown@formal@none@1@S@A "clear win (loss)" is a regulon for which SCOPE's accuracy was at least 0.10 higher (lower) than the other program.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 3) (:start . 2)\n (:id . 43))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 8) (:start . 3)\n (:id . 44))\n ((:tag . "NN") (:stem . "win") (:form . 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"the") (:end . 102) (:start . 99)\n (:id . 67))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 108)\n (:start . 103) (:id . 68))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 116)\n (:start . 109) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s3.147) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100928@unknown@formal@none@1@S@The p-value reported for the paired t-test was Bonferroni-corrected to account for multiple (three) comparisons.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "p-value") (:form . "p-value") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 20)\n (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . 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"(") (:end . 93) (:start . 92)\n (:id . 55))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 98) (:start . 93)\n (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n (:id . 57))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 111)\n (:start . 100) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.148) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100930@unknown@formal@none@1@S@Average and standard error of sensitivity and PPV for the component algorithms of SCOPE on all 78 regulons.@(((:tag . "JJ") (:stem . "average") (:form . "Average") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n (:id . 43))\n ((:tag . "JJ") (:stem . "standard") (:form . 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"NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 87) (:start . 82)\n (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 90) (:start . 88)\n (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 94) (:start . 91)\n (:id . 57))\n ((:tag . "CD") (:stem . "78") (:form . "78") (:end . 97) (:start . 95)\n (:id . 58))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 106)\n (:start . 98) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.150) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100931@unknown@formal@none@1@S@Bars represent standard error.@(((:tag . "NNS") (:stem . "bar") (:form . "Bars") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 14)\n (:start . 5) (:id . 43))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 23)\n (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 29) (:start . 24)\n (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 30) (:start . 29)\n (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.151) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100932@unknown@formal@none@1@S@An ensemble motif finder with a learning rule that is no better than random will provide an accuracy that is equal to the average of its three component algorithms.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "ensemble") (:form . "ensemble") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 17) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "finder") (:form . "finder") (:end . 24)\n (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . 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"its") (:end . 136) (:start . 133)\n (:id . 67))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 142)\n (:start . 137) (:id . 68))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 152)\n (:start . 143) (:id . 69))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 163)\n (:start . 153) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n (:id . 71)))@@@1@30@((:ncues ((:id . :x3.152.1) (:span 54 56)))\n (:nscopes ((:id . :x3.152.1) (:span 54 75)))\n (:identifiers (:sid . :s3.152) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100933@unknown@formal@none@1@S@To provide a basis for evaluating the performance of SCOPE's learning rule, we constructed an ensemble learning method (referred to here as BASELINE) from the results of BEAM, PRISM and SPACER, by randomly selecting one of the accuracies from these three programs for each regulon.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "basis") (:form . "basis") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "IN") (:stem . 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"NNP") (:stem . "SPACER") (:form . "SPACER") (:end . 192)\n (:start . 186) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 193) (:start . 192)\n (:id . 78))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 196) (:start . 194)\n (:id . 79))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 205)\n (:start . 197) (:id . 80))\n ((:tag . "VBG") (:stem . "select") (:form . "selecting") (:end . 215)\n (:start . 206) (:id . 81))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 219) (:start . 216)\n (:id . 82))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 222) (:start . 220)\n (:id . 83))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 226) (:start . 223)\n (:id . 84))\n ((:tag . "NNS") (:stem . "accuracy") (:form . "accuracies") (:end . 237)\n (:start . 227) (:id . 85))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 242) (:start . 238)\n (:id . 86))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 248)\n (:start . 243) (:id . 87))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 254)\n (:start . 249) (:id . 88))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 263)\n (:start . 255) (:id . 89))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 267) (:start . 264)\n (:id . 90))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 272) (:start . 268)\n (:id . 91))\n ((:tag . "NN") (:stem . "regulon") (:form . "regulon") (:end . 280)\n (:start . 273) (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 281) (:start . 280)\n (:id . 93)))@@@1@52@((:identifiers (:sid . :s3.153) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100934@unknown@formal@none@1@S@Over 120,000 trials, BASELINE's average performance on this dataset was 0.176 with a standard deviation of 0.013.@(((:tag . "IN") (:stem . "over") (:form . "Over") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "120,000") (:form . "120,000") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "NNS") (:stem . "trial") (:form . "trials") (:end . 19)\n (:start . 13) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n (:id . 45))\n ((:tag . "NNP") (:stem . "BASELINE") (:form . "BASELINE") (:end . 29)\n (:start . 21) (:id . 46))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 31) (:start . 29)\n (:id . 47))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 39)\n (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 51)\n (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 54) (:start . 52)\n (:id . 50))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 59) (:start . 55)\n (:id . 51))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 67)\n (:start . 60) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 71) (:start . 68)\n (:id . 53))\n ((:tag . "CD") (:stem . "0.176") (:form . "0.176") (:end . 77) (:start . 72)\n (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 82) (:start . 78)\n (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 84) (:start . 83)\n (:id . 56))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 93)\n (:start . 85) (:id . 57))\n ((:tag . "NN") (:stem . "deviation") (:form . "deviation") (:end . 103)\n (:start . 94) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n (:id . 59))\n ((:tag . "CD") (:stem . "0.013") (:form . "0.013") (:end . 112)\n (:start . 107) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s3.154) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100935@unknown@formal@none@1@S@BASELINE's average score never exceeded that of SCOPE (p < 8.25 × 10-6).@(((:tag . "NN") (:stem . "baseline") (:form . "BASELINE") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 10) (:start . 8)\n (:id . 43))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 18)\n (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 24) (:start . 19)\n (:id . 45))\n ((:tag . "RB") (:stem . "never") (:form . "never") (:end . 30) (:start . 25)\n (:id . 46))\n ((:tag . "VBD") (:stem . "exceed") (:form . "exceeded") (:end . 39)\n (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 44) (:start . 40)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 53) (:start . 48)\n (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n (:id . 51))\n ((:tag . "NN") (:stem . "p") (:form . "p") (:end . 56) (:start . 55)\n (:id . 52))\n ((:tag . "JJR") (:stem . "<") (:form . "<") (:end . 58) (:start . 57)\n (:id . 53))\n ((:tag . "CD") (:stem . "8.25") (:form . "8.25") (:end . 63) (:start . 59)\n (:id . 54))\n ((:tag . "CC") (:stem . "×") (:form . "×") (:end . 65) (:start . 64)\n (:id . 55))\n ((:tag . "CD") (:stem . "10-6") (:form . "10-6") (:end . 70) (:start . 66)\n (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 71) (:start . 70)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.155) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100936@unknown@formal@none@1@S@When compared to its component algorithms, SCOPE picked the highest accuracy motif in 66% of the cases (as opposed to 33% for a random selection between three algorithms).@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 16) (:start . 14)\n (:id . 44))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 30)\n (:start . 21) (:id . 46))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 41)\n (:start . 31) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n (:id . 48))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 48) (:start . 43)\n (:id . 49))\n ((:tag . "VBD") (:stem . "pick") (:form . "picked") (:end . 55) (:start . 49)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n (:id . 51))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 67)\n (:start . 60) (:id . 52))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 76)\n (:start . 68) (:id . 53))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 82) (:start . 77)\n (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 85) (:start . 83)\n (:id . 55))\n ((:tag . "CD") (:stem . "66") (:form . "66") (:end . 88) (:start . 86)\n (:id . 56))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 89) (:start . 88)\n (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n (:id . 59))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 102) (:start . 97)\n (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 106) (:start . 104)\n (:id . 62))\n ((:tag . "VBN") (:stem . "oppose") (:form . "opposed") (:end . 114)\n (:start . 107) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 117) (:start . 115)\n (:id . 64))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 120) (:start . 118)\n (:id . 65))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 121) (:start . 120)\n (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 125) (:start . 122)\n (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 127) (:start . 126)\n (:id . 68))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 134)\n (:start . 128) (:id . 69))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 144)\n (:start . 135) (:id . 70))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 152)\n (:start . 145) (:id . 71))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 158)\n (:start . 153) (:id . 72))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 169)\n (:start . 159) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 170) (:start . 169)\n (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s3.156) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100937@unknown@formal@none@1@S@These results suggest that SCOPE's learning rule is highly effective, though it may certainly be improved further.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 13)\n (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 21)\n (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n (:id . 45))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 32) (:start . 27)\n (:id . 46))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 34) (:start . 32)\n (:id . 47))\n ((:tag . "NN") (:stem . "learning") (:form . "learning") (:end . 43)\n (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "rule") (:form . "rule") (:end . 48) (:start . 44)\n (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 51) (:start . 49)\n (:id . 50))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 58)\n (:start . 52) (:id . 51))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 68)\n (:start . 59) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n (:id . 53))\n ((:tag . "IN") (:stem . "though") (:form . "though") (:end . 76)\n (:start . 70) (:id . 54))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 79) (:start . 77)\n (:id . 55))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 83) (:start . 80)\n (:id . 56))\n ((:tag . "RB") (:stem . "certainly") (:form . "certainly") (:end . 93)\n (:start . 84) (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 96) (:start . 94)\n (:id . 58))\n ((:tag . "VBN") (:stem . "improve") (:form . "improved") (:end . 105)\n (:start . 97) (:id . 59))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 113)\n (:start . 106) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n (:id . 61)))@@@1@20@((:hcues ((:id . :x3.157.1) (:span 80 83)) ((:id . :x3.157.2) (:span 14 21)))\n (:hscopes ((:id . :x3.157.1) (:span 77 113))\n ((:id . :x3.157.2) (:span 14 113)))\n (:identifiers (:sid . :s3.157) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100938@unknown@formal@none@1@S@Of course, SCOPE's learning rule is extremely simple, and more complex learning rules may allow SCOPE to approach its theoretical upper bound.@(((:tag . "IN") (:stem . "of") (:form . "Of") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "course") (:form . "course") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 44))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 16) (:start . 11)\n (:id . 45))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 18) (:start . 16)\n (:id . 46))\n ((:tag . "NN") (:stem . "learning") (:form . "learning") (:end . 27)\n (:start . 19) (:id . 47))\n ((:tag . "NN") (:stem . "rule") (:form . "rule") (:end . 32) (:start . 28)\n (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 35) (:start . 33)\n (:id . 49))\n ((:tag . "RB") (:stem . "extremely") (:form . "extremely") (:end . 45)\n (:start . 36) (:id . 50))\n ((:tag . "JJ") (:stem . "simple") (:form . "simple") (:end . 52)\n (:start . 46) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n (:id . 53))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 62) (:start . 58)\n (:id . 54))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 70)\n (:start . 63) (:id . 55))\n ((:tag . "VBG") (:stem . "learn") (:form . "learning") (:end . 79)\n (:start . 71) (:id . 56))\n ((:tag . "NNS") (:stem . "rule") (:form . "rules") (:end . 85) (:start . 80)\n (:id . 57))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 89) (:start . 86)\n (:id . 58))\n ((:tag . "VB") (:stem . "allow") (:form . "allow") (:end . 95) (:start . 90)\n (:id . 59))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 101)\n (:start . 96) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 104) (:start . 102)\n (:id . 61))\n ((:tag . "VB") (:stem . "approach") (:form . "approach") (:end . 113)\n (:start . 105) (:id . 62))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 117) (:start . 114)\n (:id . 63))\n ((:tag . "JJ") (:stem . "theoretical") (:form . "theoretical") (:end . 129)\n (:start . 118) (:id . 64))\n ((:tag . "JJ") (:stem . "upper") (:form . "upper") (:end . 135)\n (:start . 130) (:id . 65))\n ((:tag . "NN") (:stem . "bound") (:form . "bound") (:end . 141)\n (:start . 136) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n (:id . 67)))@@@1@26@((:hcues ((:id . :x3.158.1) (:span 86 89)))\n (:hscopes ((:id . :x3.158.1) (:span 86 141)))\n (:identifiers (:sid . :s3.158) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100940@unknown@formal@none@1@S@The training of a more complex learning rule must, however, be performed in a cross-validation framework, and the size of the available dataset of regulons will place a practical limit on the complexity of the learning rule that can be devised.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 22) (:start . 18)\n (:id . 46))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 30)\n (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "learning") (:form . "learning") (:end . 39)\n (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "rule") (:form . "rule") (:end . 44) (:start . 40)\n (:id . 49))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 49) (:start . 45)\n (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n (:id . 51))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 58)\n (:start . 51) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 62) (:start . 60)\n (:id . 54))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 72)\n (:start . 63) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 75) (:start . 73)\n (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 77) (:start . 76)\n (:id . 57))\n ((:tag . "NN") (:stem . "cross-validation") (:form . "cross-validation")\n (:end . 94) (:start . 78) (:id . 58))\n ((:tag . "NN") (:stem . "framework") (:form . "framework") (:end . 104)\n (:start . 95) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n (:id . 62))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 118) (:start . 114)\n (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n (:id . 65))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 135)\n (:start . 126) (:id . 66))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 143)\n (:start . 136) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 146) (:start . 144)\n (:id . 68))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 155)\n (:start . 147) (:id . 69))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 160) (:start . 156)\n (:id . 70))\n ((:tag . "VB") (:stem . "place") (:form . "place") (:end . 166)\n (:start . 161) (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 168) (:start . 167)\n (:id . 72))\n ((:tag . "JJ") (:stem . "practical") (:form . "practical") (:end . 178)\n (:start . 169) (:id . 73))\n ((:tag . "NN") (:stem . "limit") (:form . "limit") (:end . 184)\n (:start . 179) (:id . 74))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 187) (:start . 185)\n (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 191) (:start . 188)\n (:id . 76))\n ((:tag . "NN") (:stem . "complexity") (:form . "complexity") (:end . 202)\n (:start . 192) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 205) (:start . 203)\n (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 209) (:start . 206)\n (:id . 79))\n ((:tag . "NN") (:stem . "learning") (:form . "learning") (:end . 218)\n (:start . 210) (:id . 80))\n ((:tag . "NN") (:stem . "rule") (:form . "rule") (:end . 223) (:start . 219)\n (:id . 81))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 228) (:start . 224)\n (:id . 82))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 232) (:start . 229)\n (:id . 83))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 235) (:start . 233)\n (:id . 84))\n ((:tag . "VBN") (:stem . "devise") (:form . "devised") (:end . 243)\n (:start . 236) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 244) (:start . 243)\n (:id . 86)))@@@1@45@((:identifiers (:sid . :s3.160) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100941@unknown@formal@none@1@S@Comparison with other motif finding programs@(((:tag . "NN") (:stem . "comparison") (:form . "Comparison") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 15) (:start . 11)\n (:id . 43))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 21) (:start . 16)\n (:id . 44))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 27) (:start . 22)\n (:id . 45))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 35)\n (:start . 28) (:id . 46))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 44)\n (:start . 36) (:id . 47)))@@@1@6@((:identifiers (:sid . :s3.161) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5100942@unknown@formal@none@1@S@To provide a frame of reference for SCOPE's performance, we ran ten other popular motif finders on these datasets (for details and references see Table 2).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 46))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 31)\n (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 35) (:start . 32)\n (:id . 48))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 41) (:start . 36)\n (:id . 49))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 43) (:start . 41)\n (:id . 50))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 55)\n (:start . 44) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 59) (:start . 57)\n (:id . 53))\n ((:tag . "VBD") (:stem . "run") (:form . "ran") (:end . 63) (:start . 60)\n (:id . 54))\n ((:tag . "CD") (:stem . "ten") (:form . "ten") (:end . 67) (:start . 64)\n (:id . 55))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 73) (:start . 68)\n (:id . 56))\n ((:tag . "JJ") (:stem . "popular") (:form . "popular") (:end . 81)\n (:start . 74) (:id . 57))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 87) (:start . 82)\n (:id . 58))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 95)\n (:start . 88) (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 98) (:start . 96)\n (:id . 60))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 104) (:start . 99)\n (:id . 61))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 113)\n (:start . 105) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 118) (:start . 115)\n (:id . 64))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 126)\n (:start . 119) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n (:id . 66))\n ((:tag . "NNS") (:stem . "reference") (:form . "references") (:end . 141)\n (:start . 131) (:id . 67))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 145) (:start . 142)\n (:id . 68))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 151)\n (:start . 146) (:id . 69))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 153) (:start . 152)\n (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 154) (:start . 153)\n (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n (:id . 72)))@@@1@31@((:identifiers (:sid . :s3.162) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100943@unknown@formal@none@1@S@We ran all programs directly from their websites, leaving all parameters at their defaults.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "run") (:form . "ran") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 10) (:start . 7)\n (:id . 44))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 19)\n (:start . 11) (:id . 45))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 28)\n (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 39)\n (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "website") (:form . "websites") (:end . 48)\n (:start . 40) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n (:id . 50))\n ((:tag . "VBG") (:stem . "leave") (:form . "leaving") (:end . 57)\n (:start . 50) (:id . 51))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 61) (:start . 58)\n (:id . 52))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 72)\n (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 75) (:start . 73)\n (:id . 54))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 81)\n (:start . 76) (:id . 55))\n ((:tag . "NNS") (:stem . "default") (:form . "defaults") (:end . 90)\n (:start . 82) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.163) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100944@unknown@formal@none@1@S@The only parameter that we specified (where available) was the species from which the background sequences were derived.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "only") (:form . "only") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "parameter") (:form . "parameter") (:end . 18)\n (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "VBD") (:stem . "specify") (:form . "specified") (:end . 36)\n (:start . 27) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 38) (:start . 37)\n (:id . 48))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 43) (:start . 38)\n (:id . 49))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 53)\n (:start . 44) (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 54) (:start . 53)\n (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 58) (:start . 55)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n (:id . 53))\n ((:tag . "NN") (:stem . "species") (:form . "species") (:end . 70)\n (:start . 63) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 75) (:start . 71)\n (:id . 55))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 81) (:start . 76)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n (:id . 57))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 96)\n (:start . 86) (:id . 58))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 106)\n (:start . 97) (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 111) (:start . 107)\n (:id . 60))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 119)\n (:start . 112) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.164) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100945@unknown@formal@none@1@S@Thus, the results of this performance comparison may be interpreted as a comparison against other motif finders when those motif finders are run using their default values.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 17)\n (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 25) (:start . 21)\n (:id . 47))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 37)\n (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 48)\n (:start . 38) (:id . 49))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 52) (:start . 49)\n (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 55) (:start . 53)\n (:id . 51))\n ((:tag . "VBN") (:stem . "interpret") (:form . "interpreted") (:end . 67)\n (:start . 56) (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 70) (:start . 68)\n (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 72) (:start . 71)\n (:id . 54))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 83)\n (:start . 73) (:id . 55))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 91)\n (:start . 84) (:id . 56))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 97) (:start . 92)\n (:id . 57))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 103) (:start . 98)\n (:id . 58))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 111)\n (:start . 104) (:id . 59))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 116) (:start . 112)\n (:id . 60))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 122)\n (:start . 117) (:id . 61))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 128)\n (:start . 123) (:id . 62))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 136)\n (:start . 129) (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 140) (:start . 137)\n (:id . 64))\n ((:tag . "VBN") (:stem . "run") (:form . "run") (:end . 144) (:start . 141)\n (:id . 65))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 150) (:start . 145)\n (:id . 66))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 156)\n (:start . 151) (:id . 67))\n ((:tag . "NN") (:stem . "default") (:form . "default") (:end . 164)\n (:start . 157) (:id . 68))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 171)\n (:start . 165) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x3.165.1) (:span 49 52)))\n (:hscopes ((:id . :x3.165.1) (:span 6 171)))\n (:identifiers (:sid . :s3.165) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100946@unknown@formal@none@1@S@Motif discovery algorithms used in the performance comparison.@(((:tag . "NN") (:stem . "motif") (:form . "Motif") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "discovery") (:form . "discovery") (:end . 15)\n (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 26)\n (:start . 16) (:id . 44))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 31) (:start . 27)\n (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n (:id . 47))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 50)\n (:start . 39) (:id . 48))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 61)\n (:start . 51) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 62) (:start . 61)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s3.166) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|TableLegend|)))@oe@9-2-2011 5100947@unknown@formal@none@1@S@Nuisance parameters are parameters that cannot be precisely defined without knowledge of the true binding sites (such as motif length, number of occurrences and orientation).@(((:tag . "NN") (:stem . "nuisance") (:form . "Nuisance") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 19)\n (:start . 9) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 23) (:start . 20)\n (:id . 44))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 34)\n (:start . 24) (:id . 45))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 39) (:start . 35)\n (:id . 46))\n ((:tag . "NN") (:stem . "cannot") (:form . "cannot") (:end . 46)\n (:start . 40) (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 49) (:start . 47)\n (:id . 48))\n ((:tag . "RB") (:stem . "precisely") (:form . "precisely") (:end . 59)\n (:start . 50) (:id . 49))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 67)\n (:start . 60) (:id . 50))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 75)\n (:start . 68) (:id . 51))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 85)\n (:start . 76) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n (:id . 54))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 97) (:start . 93)\n (:id . 55))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 105)\n (:start . 98) (:id . 56))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 111)\n (:start . 106) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 113) (:start . 112)\n (:id . 58))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 117) (:start . 113)\n (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 120) (:start . 118)\n (:id . 60))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 126)\n (:start . 121) (:id . 61))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 133)\n (:start . 127) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n (:id . 63))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 141)\n (:start . 135) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n (:id . 65))\n ((:tag . "NNS") (:stem . "occurrence") (:form . "occurrences") (:end . 156)\n (:start . 145) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n (:id . 67))\n ((:tag . "NN") (:stem . "orientation") (:form . "orientation") (:end . 172)\n (:start . 161) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 173) (:start . 172)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x3.167.2) (:span 40 46)))\n (:ncues ((:id . :x3.167.1) (:span 68 75)))\n (:hscopes ((:id . :x3.167.2) (:span 40 173)))\n (:nscopes ((:id . :x3.167.1) (:span 68 173)))\n (:identifiers (:sid . :s3.167) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100948@unknown@formal@none@1@S@For MotifSampler and wConsensus, the lower part of the range indicates required parameters, while the upper part indicates the total number of parameters, including "power user" parameters that the program authors stress should typically be left as default.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "MotifSampler") (:form . "MotifSampler") (:end . 16)\n (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n (:id . 44))\n ((:tag . "NNP") (:stem . "wConsensus") (:form . "wConsensus") (:end . 31)\n (:start . 21) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n (:id . 47))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 42) (:start . 37)\n (:id . 48))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 47) (:start . 43)\n (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n (:id . 51))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 60) (:start . 55)\n (:id . 52))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 70)\n (:start . 61) (:id . 53))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 79)\n (:start . 71) (:id . 54))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 90)\n (:start . 80) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n (:id . 56))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 97) (:start . 92)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n (:id . 58))\n ((:tag . "JJ") (:stem . "upper") (:form . "upper") (:end . 107)\n (:start . 102) (:id . 59))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 112) (:start . 108)\n (:id . 60))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 122)\n (:start . 113) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n (:id . 62))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 132)\n (:start . 127) (:id . 63))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 139)\n (:start . 133) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n (:id . 65))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 153)\n (:start . 143) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 154) (:start . 153)\n (:id . 67))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 164)\n (:start . 155) (:id . 68))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 166) (:start . 165)\n (:id . 69))\n ((:tag . "NN") (:stem . "power") (:form . "power") (:end . 171)\n (:start . 166) (:id . 70))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 176) (:start . 172)\n (:id . 71))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 177) (:start . 176)\n (:id . 72))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 188)\n (:start . 178) (:id . 73))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 193) (:start . 189)\n (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 197) (:start . 194)\n (:id . 75))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 205)\n (:start . 198) (:id . 76))\n ((:tag . "NNS") (:stem . "author") (:form . "authors") (:end . 213)\n (:start . 206) (:id . 77))\n ((:tag . "NN") (:stem . "stress") (:form . "stress") (:end . 220)\n (:start . 214) (:id . 78))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 227)\n (:start . 221) (:id . 79))\n ((:tag . "RB") (:stem . "typically") (:form . "typically") (:end . 237)\n (:start . 228) (:id . 80))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 240) (:start . 238)\n (:id . 81))\n ((:tag . "VBN") (:stem . "leave") (:form . "left") (:end . 245)\n (:start . 241) (:id . 82))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 248) (:start . 246)\n (:id . 83))\n ((:tag . "NN") (:stem . "default") (:form . "default") (:end . 256)\n (:start . 249) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 257) (:start . 256)\n (:id . 85)))@@@1@44@((:hcues ((:id . :x3.168.1) (:span 221 227)))\n (:hscopes ((:id . :x3.168.1) (:span 194 256)))\n (:identifiers (:sid . :s3.168) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100950@unknown@formal@none@1@S@SCOPE has no user-adjustable parameters, although its component algorithms do contain a number of internal parameters "("hyperparameters")" that govern their search over common nuisance parameters.@(((:tag . "NN") (:stem . "scope") (:form . "SCOPE") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 12) (:start . 10)\n (:id . 44))\n ((:tag . "JJ") (:stem . "user-adjustable") (:form . "user-adjustable")\n (:end . 28) (:start . 13) (:id . 45))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 39)\n (:start . 29) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n (:id . 47))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 49)\n (:start . 41) (:id . 48))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 53) (:start . 50)\n (:id . 49))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 63)\n (:start . 54) (:id . 50))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 74)\n (:start . 64) (:id . 51))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 77) (:start . 75)\n (:id . 52))\n ((:tag . "VB") (:stem . "contain") (:form . "contain") (:end . 85)\n (:start . 78) (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 87) (:start . 86)\n (:id . 54))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 94)\n (:start . 88) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n (:id . 56))\n ((:tag . "JJ") (:stem . "internal") (:form . "internal") (:end . 106)\n (:start . 98) (:id . 57))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 117)\n (:start . 107) (:id . 58))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 119) (:start . 118)\n (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 120) (:start . 119)\n (:id . 60))\n ((:tag . "NNS") (:stem . "”hyperparameters") (:form . "”hyperparameters")\n (:end . 136) (:start . 120) (:id . 61))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 137) (:start . 136)\n (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n (:id . 63))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 139) (:start . 138)\n (:id . 64))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 144) (:start . 140)\n (:id . 65))\n ((:tag . "VBP") (:stem . "govern") (:form . "govern") (:end . 151)\n (:start . 145) (:id . 66))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 157)\n (:start . 152) (:id . 67))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 164)\n (:start . 158) (:id . 68))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 169) (:start . 165)\n (:id . 69))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 176)\n (:start . 170) (:id . 70))\n ((:tag . "NN") (:stem . "nuisance") (:form . "nuisance") (:end . 185)\n (:start . 177) (:id . 71))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 196)\n (:start . 186) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n (:id . 73)))@@@1@32@((:ncues ((:id . :x3.170.1) (:span 10 12)))\n (:nscopes ((:id . :x3.170.1) (:span 10 39)))\n (:identifiers (:sid . :s3.170) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100951@unknown@formal@none@1@S@On synthetic datasets, we found SCOPE's component algorithms to be quite robust to the settings of these hyperparameters.@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "synthetic") (:form . "synthetic") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 21)\n (:start . 13) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 25) (:start . 23)\n (:id . 46))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 31) (:start . 26)\n (:id . 47))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 37) (:start . 32)\n (:id . 48))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 39) (:start . 37)\n (:id . 49))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 49)\n (:start . 40) (:id . 50))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 60)\n (:start . 50) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 66) (:start . 64)\n (:id . 53))\n ((:tag . "RB") (:stem . "quite") (:form . "quite") (:end . 72) (:start . 67)\n (:id . 54))\n ((:tag . "JJ") (:stem . "robust") (:form . "robust") (:end . 79)\n (:start . 73) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 82) (:start . 80)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n (:id . 57))\n ((:tag . "NNS") (:stem . "setting") (:form . "settings") (:end . 95)\n (:start . 87) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n (:id . 59))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 104) (:start . 99)\n (:id . 60))\n ((:tag . "NNS") (:stem . "hyperparameter") (:form . "hyperparameters")\n (:end . 120) (:start . 105) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.171) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100952@unknown@formal@none@1@S@We have therefore fixed those parameters to reasonable values and do not expose them to the user 101112.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 17)\n (:start . 8) (:id . 44))\n ((:tag . "VBN") (:stem . "fix") (:form . "fixed") (:end . 23) (:start . 18)\n (:id . 45))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 29) (:start . 24)\n (:id . 46))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 40)\n (:start . 30) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 43) (:start . 41)\n (:id . 48))\n ((:tag . "JJ") (:stem . "reasonable") (:form . "reasonable") (:end . 54)\n (:start . 44) (:id . 49))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 61)\n (:start . 55) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n (:id . 51))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 68) (:start . 66)\n (:id . 52))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 72) (:start . 69)\n (:id . 53))\n ((:tag . "VB") (:stem . "expose") (:form . "expose") (:end . 79)\n (:start . 73) (:id . 54))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 84) (:start . 80)\n (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 87) (:start . 85)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n (:id . 57))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 96) (:start . 92)\n (:id . 58))\n ((:tag . "CD") (:stem . "101112") (:form . "101112") (:end . 103)\n (:start . 97) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n (:id . 60)))@@@1@19@((:ncues ((:id . :x3.172.1) (:span 69 72)))\n (:nscopes ((:id . :x3.172.1) (:span 69 96)))\n (:identifiers (:sid . :s3.172) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100953@unknown@formal@none@1@S@This construction means that SCOPE can only run in a default configuration.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "construction") (:form . "construction") (:end . 17)\n (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "mean") (:form . "means") (:end . 23) (:start . 18)\n (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n (:id . 45))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 34) (:start . 29)\n (:id . 46))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 38) (:start . 35)\n (:id . 47))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 43) (:start . 39)\n (:id . 48))\n ((:tag . "VB") (:stem . "run") (:form . "run") (:end . 47) (:start . 44)\n (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n (:id . 51))\n ((:tag . "NN") (:stem . "default") (:form . "default") (:end . 60)\n (:start . 53) (:id . 52))\n ((:tag . "NN") (:stem . "configuration") (:form . "configuration")\n (:end . 74) (:start . 61) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.173) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100954@unknown@formal@none@1@S@We compared the motif finding programs using the criteria set forth in Sinha and Tompa, including average accuracy and the number of total wins (highest accuracy on a regulon, where that accuracy is at least 0.1) 6.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "compare") (:form . "compared") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 21) (:start . 16)\n (:id . 45))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 29)\n (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 38)\n (:start . 30) (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 44) (:start . 39)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n (:id . 49))\n ((:tag . "NNS") (:stem . "criterion") (:form . "criteria") (:end . 57)\n (:start . 49) (:id . 50))\n ((:tag . "VBD") (:stem . "set") (:form . "set") (:end . 61) (:start . 58)\n (:id . 51))\n ((:tag . "RB") (:stem . "forth") (:form . "forth") (:end . 67) (:start . 62)\n (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 70) (:start . 68)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Sinha") (:form . "Sinha") (:end . 76) (:start . 71)\n (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Tompa") (:form . "Tompa") (:end . 86) (:start . 81)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n (:id . 57))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 97)\n (:start . 88) (:id . 58))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 105)\n (:start . 98) (:id . 59))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 114)\n (:start . 106) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n (:id . 62))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 129)\n (:start . 123) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n (:id . 64))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 138)\n (:start . 133) (:id . 65))\n ((:tag . "NNS") (:stem . "win") (:form . "wins") (:end . 143) (:start . 139)\n (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 145) (:start . 144)\n (:id . 67))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 152)\n (:start . 145) (:id . 68))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 161)\n (:start . 153) (:id . 69))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 164) (:start . 162)\n (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 166) (:start . 165)\n (:id . 71))\n ((:tag . "NN") (:stem . "regulon") (:form . "regulon") (:end . 174)\n (:start . 167) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n (:id . 73))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 181)\n (:start . 176) (:id . 74))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 186) (:start . 182)\n (:id . 75))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 195)\n (:start . 187) (:id . 76))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 198) (:start . 196)\n (:id . 77))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 201) (:start . 199)\n (:id . 78))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 207)\n (:start . 202) (:id . 79))\n ((:tag . "CD") (:stem . "0.1") (:form . "0.1") (:end . 211) (:start . 208)\n (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 212) (:start . 211)\n (:id . 81))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 214) (:start . 213)\n (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n (:id . 83)))@@@1@42@((:identifiers (:sid . :s3.174) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100955@unknown@formal@none@1@S@On this dataset, SCOPE had the highest score by both criteria (Figure 5a).@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 15)\n (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n (:id . 45))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 22) (:start . 17)\n (:id . 46))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 26) (:start . 23)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n (:id . 48))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 38)\n (:start . 31) (:id . 49))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 44) (:start . 39)\n (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 47) (:start . 45)\n (:id . 51))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 52) (:start . 48)\n (:id . 52))\n ((:tag . "NNS") (:stem . "criterion") (:form . "criteria") (:end . 61)\n (:start . 53) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 69)\n (:start . 63) (:id . 55))\n ((:tag . "NN") (:stem . "5a") (:form . "5a") (:end . 72) (:start . 70)\n (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 73) (:start . 72)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.175) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100956@unknown@formal@none@1@S@The cumulative distribution of accuracy shows that SCOPE had the most high-scoring motifs at every level (Figure 5b).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "cumulative") (:form . "cumulative") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 27)\n (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 45))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 39)\n (:start . 31) (:id . 46))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 45) (:start . 40)\n (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 50) (:start . 46)\n (:id . 48))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 56) (:start . 51)\n (:id . 49))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 60) (:start . 57)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n (:id . 51))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 69) (:start . 65)\n (:id . 52))\n ((:tag . "JJ") (:stem . "high-scoring") (:form . "high-scoring") (:end . 82)\n (:start . 70) (:id . 53))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 89)\n (:start . 83) (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 92) (:start . 90)\n (:id . 55))\n ((:tag . "DT") (:stem . "every") (:form . "every") (:end . 98) (:start . 93)\n (:id . 56))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 104) (:start . 99)\n (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 112)\n (:start . 106) (:id . 59))\n ((:tag . "NN") (:stem . "5b") (:form . "5b") (:end . 115) (:start . 113)\n (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.176) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100957@unknown@formal@none@1@S@When we looked at the number of clear head-to-head wins (such a win is taken to occur when the difference in accuracy between SCOPE and another motif finder is greater than 0.1 6), we found that SCOPE scored a clear majority (82%) of clear head-to-head wins (Figure 5c).@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "VBD") (:stem . "look") (:form . "looked") (:end . 14) (:start . 8)\n (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 17) (:start . 15)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 28)\n (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n (:id . 48))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 37) (:start . 32)\n (:id . 49))\n ((:tag . "JJ") (:stem . "head-to-head") (:form . "head-to-head") (:end . 50)\n (:start . 38) (:id . 50))\n ((:tag . "NNS") (:stem . "win") (:form . "wins") (:end . 55) (:start . 51)\n (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n (:id . 52))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 61) (:start . 57)\n (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 63) (:start . 62)\n (:id . 54))\n ((:tag . "NN") (:stem . "win") (:form . "win") (:end . 67) (:start . 64)\n (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 70) (:start . 68)\n (:id . 56))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 76) (:start . 71)\n (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 79) (:start . 77)\n (:id . 58))\n ((:tag . "VB") (:stem . "occur") (:form . "occur") (:end . 85) (:start . 80)\n (:id . 59))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 90) (:start . 86)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n (:id . 61))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 105)\n (:start . 95) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n (:id . 63))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 117)\n (:start . 109) (:id . 64))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 125)\n (:start . 118) (:id . 65))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 131)\n (:start . 126) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 135) (:start . 132)\n (:id . 67))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 143)\n (:start . 136) (:id . 68))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 149)\n (:start . 144) (:id . 69))\n ((:tag . "NN") (:stem . "finder") (:form . "finder") (:end . 156)\n (:start . 150) (:id . 70))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 159) (:start . 157)\n (:id . 71))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 167)\n (:start . 160) (:id . 72))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 172) (:start . 168)\n (:id . 73))\n ((:tag . "CD") (:stem . "0.1") (:form . "0.1") (:end . 176) (:start . 173)\n (:id . 74))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 178) (:start . 177)\n (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 179) (:start . 178)\n (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 180) (:start . 179)\n (:id . 77))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 183) (:start . 181)\n (:id . 78))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 189)\n (:start . 184) (:id . 79))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 194) (:start . 190)\n (:id . 80))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 200)\n (:start . 195) (:id . 81))\n ((:tag . "VBD") (:stem . "score") (:form . "scored") (:end . 207)\n (:start . 201) (:id . 82))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 209) (:start . 208)\n (:id . 83))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 215)\n (:start . 210) (:id . 84))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 224)\n (:start . 216) (:id . 85))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 226) (:start . 225)\n (:id . 86))\n ((:tag . "CD") (:stem . "82") (:form . "82") (:end . 228) (:start . 226)\n (:id . 87))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 229) (:start . 228)\n (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 230) (:start . 229)\n (:id . 89))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 233) (:start . 231)\n (:id . 90))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 239)\n (:start . 234) (:id . 91))\n ((:tag . "JJ") (:stem . "head-to-head") (:form . "head-to-head") (:end . 252)\n (:start . 240) (:id . 92))\n ((:tag . "NNS") (:stem . "win") (:form . "wins") (:end . 257) (:start . 253)\n (:id . 93))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 259) (:start . 258)\n (:id . 94))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 265)\n (:start . 259) (:id . 95))\n ((:tag . "NNP") (:stem . "5c") (:form . "5c") (:end . 268) (:start . 266)\n (:id . 96))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 269) (:start . 268)\n (:id . 97))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 270) (:start . 269)\n (:id . 98)))@@@1@57@((:identifiers (:sid . :s3.177) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100958@unknown@formal@none@1@S@The average accuracies of BEAM, PRISM and SPACER on this dataset were similar to those of the ten other programs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "accuracy") (:form . "accuracies") (:end . 22)\n (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n (:id . 45))\n ((:tag . "NNP") (:stem . "BEAM") (:form . "BEAM") (:end . 30) (:start . 26)\n (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n (:id . 47))\n ((:tag . "NN") (:stem . "prism") (:form . "PRISM") (:end . 37) (:start . 32)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n (:id . 49))\n ((:tag . "NN") (:stem . "spacer") (:form . "SPACER") (:end . 48)\n (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 51) (:start . 49)\n (:id . 51))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 56) (:start . 52)\n (:id . 52))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 64)\n (:start . 57) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 69) (:start . 65)\n (:id . 54))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 77)\n (:start . 70) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 80) (:start . 78)\n (:id . 56))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 86) (:start . 81)\n (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n (:id . 59))\n ((:tag . "CD") (:stem . "ten") (:form . "ten") (:end . 97) (:start . 94)\n (:id . 60))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 103) (:start . 98)\n (:id . 61))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 112)\n (:start . 104) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.178) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100960@unknown@formal@none@1@S@Performance comparisons.@(((:tag . "NNP") (:stem . "Performance") (:form . "Performance") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 23)\n (:start . 12) (:id . 43))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 24) (:start . 23)\n (:id . 44)))@@@1@3@((:identifiers (:sid . :s3.180) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100961@unknown@formal@none@1@S@(a) Mean and standard error of accuracy for each of 78 regulons.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "LS") (:stem . "a") (:form . "a") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "mean") (:form . "Mean") (:end . 8) (:start . 4)\n (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 12) (:start . 9)\n (:id . 46))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 21)\n (:start . 13) (:id . 47))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 27) (:start . 22)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 49))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 39)\n (:start . 31) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n (:id . 51))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 48) (:start . 44)\n (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n (:id . 53))\n ((:tag . "CD") (:stem . "78") (:form . "78") (:end . 54) (:start . 52)\n (:id . 54))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 63)\n (:start . 55) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 64) (:start . 63)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s3.181) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100962@unknown@formal@none@1@S@(b) Cumulative distribution of accuracy for each program.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "b") (:form . "b") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "cumulative") (:form . "Cumulative") (:end . 14)\n (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 27)\n (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 47))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 39)\n (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n (:id . 49))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 48) (:start . 44)\n (:id . 50))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 56)\n (:start . 49) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 57) (:start . 56)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s3.182) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100963@unknown@formal@none@1@S@(c) Fraction of regulons with a clear outcome (margin of difference in accuracy between two programs was greater than 0.10) won by SCOPE.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "c") (:form . "c") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "fraction") (:form . "Fraction") (:end . 12)\n (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 46))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 24)\n (:start . 16) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 29) (:start . 25)\n (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 31) (:start . 30)\n (:id . 49))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 37) (:start . 32)\n (:id . 50))\n ((:tag . "NN") (:stem . "outcome") (:form . "outcome") (:end . 45)\n (:start . 38) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 47) (:start . 46)\n (:id . 52))\n ((:tag . "NN") (:stem . "margin") (:form . "margin") (:end . 53)\n (:start . 47) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n (:id . 54))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 67)\n (:start . 57) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 70) (:start . 68)\n (:id . 56))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 79)\n (:start . 71) (:id . 57))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 87)\n (:start . 80) (:id . 58))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 91) (:start . 88)\n (:id . 59))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 100)\n (:start . 92) (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 104) (:start . 101)\n (:id . 61))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 112)\n (:start . 105) (:id . 62))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 117) (:start . 113)\n (:id . 63))\n ((:tag . "CD") (:stem . "0.10") (:form . "0.10") (:end . 122) (:start . 118)\n (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 123) (:start . 122)\n (:id . 65))\n ((:tag . "VBN") (:stem . "win") (:form . "won") (:end . 127) (:start . 124)\n (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 130) (:start . 128)\n (:id . 67))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 136)\n (:start . 131) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s3.183) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100964@unknown@formal@none@1@S@Program abbreviations and details in Table 2; performance details in tables S1 and S2 in Additional file 1.@(((:tag . "NN") (:stem . "program") (:form . "Program") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "abbreviation") (:form . "abbreviations")\n (:end . 21) (:start . 8) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 25) (:start . 22)\n (:id . 44))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 33)\n (:start . 26) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n (:id . 46))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 42) (:start . 37)\n (:id . 47))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 44) (:start . 43)\n (:id . 48))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 45) (:start . 44)\n (:id . 49))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 57)\n (:start . 46) (:id . 50))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 65)\n (:start . 58) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n (:id . 52))\n ((:tag . "NNS") (:stem . "table") (:form . "tables") (:end . 75)\n (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "s1") (:form . "S1") (:end . 78) (:start . 76)\n (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n (:id . 55))\n ((:tag . "NN") (:stem . "s2") (:form . "S2") (:end . 85) (:start . 83)\n (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n (:id . 57))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 99)\n (:start . 89) (:id . 58))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 104) (:start . 100)\n (:id . 59))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 106) (:start . 105)\n (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s3.184) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100965@unknown@formal@none@1@S@A formal statistical analysis found that SCOPE's performance margin over the other motif finders run on this dataset was statistically significant at p < 10-5 (for details, see Additional file 1, section S3).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "formal") (:form . "formal") (:end . 8) (:start . 2)\n (:id . 43))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 20)\n (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 29)\n (:start . 21) (:id . 45))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 35) (:start . 30)\n (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 40) (:start . 36)\n (:id . 47))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 46) (:start . 41)\n (:id . 48))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 48) (:start . 46)\n (:id . 49))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 60)\n (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "margin") (:form . "margin") (:end . 67)\n (:start . 61) (:id . 51))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 72) (:start . 68)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n (:id . 53))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 82) (:start . 77)\n (:id . 54))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 88) (:start . 83)\n (:id . 55))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 96)\n (:start . 89) (:id . 56))\n ((:tag . "VBP") (:stem . "run") (:form . "run") (:end . 100) (:start . 97)\n (:id . 57))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 103) (:start . 101)\n (:id . 58))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 108) (:start . 104)\n (:id . 59))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 116)\n (:start . 109) (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 120) (:start . 117)\n (:id . 61))\n ((:tag . "RB") (:stem . "statistically") (:form . "statistically")\n (:end . 134) (:start . 121) (:id . 62))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 146)\n (:start . 135) (:id . 63))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 149) (:start . 147)\n (:id . 64))\n ((:tag . "NN") (:stem . "p") (:form . "p") (:end . 151) (:start . 150)\n (:id . 65))\n ((:tag . "SYM") (:stem . "<") (:form . "<") (:end . 153) (:start . 152)\n (:id . 66))\n ((:tag . "CD") (:stem . "10-5") (:form . "10-5") (:end . 158) (:start . 154)\n (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 160) (:start . 159)\n (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 163) (:start . 160)\n (:id . 69))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 171)\n (:start . 164) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 172) (:start . 171)\n (:id . 71))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 176) (:start . 173)\n (:id . 72))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 187)\n (:start . 177) (:id . 73))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 192) (:start . 188)\n (:id . 74))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 194) (:start . 193)\n (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 195) (:start . 194)\n (:id . 76))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 203)\n (:start . 196) (:id . 77))\n ((:tag . "NN") (:stem . "s3") (:form . "S3") (:end . 206) (:start . 204)\n (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 207) (:start . 206)\n (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n (:id . 80)))@@@1@39@((:identifiers (:sid . :s3.185) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100966@unknown@formal@none@1@S@Corroborating the results of previously published performance comparisons \s14567\s, none of the other programs showed a statistically significant difference relative to the other nine.@(((:tag . "VBG") (:stem . "corroborate") (:form . "Corroborating") (:end . 13)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 43))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 25)\n (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n (:id . 45))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 39)\n (:start . 29) (:id . 46))\n ((:tag . "VBN") (:stem . "publish") (:form . "published") (:end . 49)\n (:start . 40) (:id . 47))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 61)\n (:start . 50) (:id . 48))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 73)\n (:start . 62) (:id . 49))\n ((:tag . "VBP") (:stem . "\s") (:form . "\s") (:end . 75) (:start . 74)\n (:id . 50))\n ((:tag . "CD") (:stem . "14567") (:form . "14567") (:end . 80) (:start . 75)\n (:id . 51))\n ((:tag . "NN") (:stem . "\s") (:form . "\s") (:end . 81) (:start . 80)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n (:id . 53))\n ((:tag . "NN") (:stem . "none") (:form . "none") (:end . 87) (:start . 83)\n (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n (:id . 56))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 100) (:start . 95)\n (:id . 57))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 109)\n (:start . 101) (:id . 58))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 116)\n (:start . 110) (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 118) (:start . 117)\n (:id . 60))\n ((:tag . "RB") (:stem . "statistically") (:form . "statistically")\n (:end . 132) (:start . 119) (:id . 61))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 144)\n (:start . 133) (:id . 62))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 155)\n (:start . 145) (:id . 63))\n ((:tag . "JJ") (:stem . "relative") (:form . 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"CD") (:stem . "ten") (:form . "ten") (:end . 74) (:start . 71)\n (:id . 53))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 83)\n (:start . 75) (:id . 54))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 86) (:start . 84)\n (:id . 55))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 91) (:start . 87)\n (:id . 56))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 99)\n (:start . 92) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 102) (:start . 100)\n (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 104) (:start . 103)\n (:id . 59))\n ((:tag . "RB") (:stem . "statistically") (:form . "statistically")\n (:end . 118) (:start . 105) (:id . 60))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 130)\n (:start . 119) (:id . 61))\n ((:tag . "NN") (:stem . "margin") (:form . "margin") (:end . 137)\n (:start . 131) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n (:id . 63)))@@@1@22@((:ncues ((:id . :x3.187.1) (:span 11 15)))\n (:nscopes ((:id . :x3.187.1) (:span 11 137)))\n (:identifiers (:sid . :s3.187) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100968@unknown@formal@none@1@S@SCOPE's high accuracy was a reflection of both high PPV and high sensitivity (Figure 6a; see Methods for a precise definition).@(((:tag . "NN") (:stem . "scope") (:form . "SCOPE") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 21)\n (:start . 13) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . 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(:end . 127) (:start . 126)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s3.188) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100970@unknown@formal@none@1@S@In contrast, none of the other motif finders that performed well by one criterion performed well by the other, as shown by the average ranks for each motif finder over both sensitivity and PPV (Figure 6b).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "none") (:form . "none") (:end . 17) (:start . 13)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n (:id . 47))\n ((:tag . 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"well") (:end . 96) (:start . 92)\n (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 99) (:start . 97)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n (:id . 60))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 109)\n (:start . 104) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n (:id . 62))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 113) (:start . 111)\n (:id . 63))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 119)\n (:start . 114) (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 122) (:start . 120)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n (:id . 66))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 134)\n (:start . 127) (:id . 67))\n ((:tag . "NNS") (:stem . "rank") (:form . "ranks") (:end . 140)\n (:start . 135) (:id . 68))\n ((:tag . "IN") (:stem . 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"IN") (:stem . "on") (:form . "on") (:end . 73) (:start . 71)\n (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 77) (:start . 74)\n (:id . 57))\n ((:tag . "CD") (:stem . "78") (:form . "78") (:end . 80) (:start . 78)\n (:id . 58))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 89)\n (:start . 81) (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.191) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|FigureLegend|)))@oe@9-2-2011 5100972@unknown@formal@none@1@S@(a) Average and standard error of sensitivity and PPV for each program on all 78 regulons.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "LS") (:stem . "a") (:form . "a") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "average") (:form . "Average") (:end . 11)\n (:start . 4) (:id . 45))\n ((:tag . 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"on") (:end . 73) (:start . 71)\n (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 77) (:start . 74)\n (:id . 57))\n ((:tag . "CD") (:stem . "78") (:form . "78") (:end . 80) (:start . 78)\n (:id . 58))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 89)\n (:start . 81) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.192) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100973@unknown@formal@none@1@S@In cases where the program failed to return a result, the sensitivity is 0 and the PPV is undefined.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . 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"case") (:form . "Cases") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 21)\n (:start . 14) (:id . 45))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 25) (:start . 22)\n (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 29) (:start . 26)\n (:id . 47))\n ((:tag . "VB") (:stem . "support") (:form . "support") (:end . 37)\n (:start . 30) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n (:id . 49))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 49)\n (:start . 42) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 54) (:start . 50)\n (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 58) (:start . 55)\n (:id . 52))\n ((:tag . "VBN") (:stem . "include") (:form . "included") (:end . 67)\n (:start . 59) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n (:id . 54)))@@@1@13@((:ncues ((:id . :x3.194.2) (:span 55 58)) ((:id . :x3.194.1) (:span 26 29)))\n (:nscopes ((:id . :x3.194.1) (:span 26 49)) ((:id . :x3.194.2) (:span 0 67)))\n (:identifiers (:sid . :s3.194) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100975@unknown@formal@none@1@S@(b) Ranks on this plot were computed by taking the average of sensitivity and PPV ranks for each program.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "LS") (:stem . "b") (:form . "b") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNS") (:stem . "rank") (:form . "Ranks") (:end . 9) (:start . 4)\n (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 12) (:start . 10)\n (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 17) (:start . 13)\n (:id . 47))\n ((:tag . "NN") (:stem . "plot") (:form . "plot") (:end . 22) (:start . 18)\n (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 27) (:start . 23)\n (:id . 49))\n ((:tag . "VBN") (:stem . "compute") (:form . "computed") (:end . 36)\n (:start . 28) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 39) (:start . 37)\n (:id . 51))\n ((:tag . "VBG") (:stem . "take") (:form . "taking") (:end . 46) (:start . 40)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n (:id . 53))\n ((:tag . "NN") (:stem . "average") (:form . "average") (:end . 58)\n (:start . 51) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n (:id . 55))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 73)\n (:start . 62) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n (:id . 57))\n ((:tag . "NNP") (:stem . "PPV") (:form . "PPV") (:end . 81) (:start . 78)\n (:id . 58))\n ((:tag . "NNS") (:stem . "rank") (:form . "ranks") (:end . 87) (:start . 82)\n (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 91) (:start . 88)\n (:id . 60))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 96) (:start . 92)\n (:id . 61))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 104)\n (:start . 97) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.195) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100976@unknown@formal@none@1@S@Performance in the presence of extraneous upstream sequences@(((:tag . "NNP") (:stem . "Performance") (:form . "Performance") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 14) (:start . 12)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 44))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 27)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "JJ") (:stem . "extraneous") (:form . "extraneous") (:end . 41)\n (:start . 31) (:id . 47))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 50)\n (:start . 42) (:id . 48))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 60)\n (:start . 51) (:id . 49)))@@@1@8@((:identifiers (:sid . :s3.196) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5100977@unknown@formal@none@1@S@In practice, microarray co-expression data are often used to identify genes in a particular regulon.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "practice") (:form . "practice") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "microarray") (:form . "microarray") (:end . 23)\n (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "co-expression") (:form . "co-expression")\n (:end . 37) (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 42) (:start . 38)\n (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 46) (:start . 43)\n (:id . 48))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 52) (:start . 47)\n (:id . 49))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 57) (:start . 53)\n (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n (:id . 51))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 69)\n (:start . 61) (:id . 52))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 75) (:start . 70)\n (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 80) (:start . 79)\n (:id . 55))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 91)\n (:start . 81) (:id . 56))\n ((:tag . "NN") (:stem . "regulon") (:form . "regulon") (:end . 99)\n (:start . 92) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.197) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100978@unknown@formal@none@1@S@This approach identifies genes that are either directly or indirectly regulated by the transcription factor of interest.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "identify") (:form . "identifies") (:end . 24)\n (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 30) (:start . 25)\n (:id . 45))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 35) (:start . 31)\n (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 39) (:start . 36)\n (:id . 47))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 46)\n (:start . 40) (:id . 48))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 55)\n (:start . 47) (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 58) (:start . 56)\n (:id . 50))\n ((:tag . "RB") (:stem . "indirectly") (:form . "indirectly") (:end . 69)\n (:start . 59) (:id . 51))\n ((:tag . "VBN") (:stem . "regulate") (:form . "regulated") (:end . 79)\n (:start . 70) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 82) (:start . 80)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n (:id . 54))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n (:end . 100) (:start . 87) (:id . 55))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 107)\n (:start . 101) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n (:id . 57))\n ((:tag . "NN") (:stem . "interest") (:form . "interest") (:end . 119)\n (:start . 111) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.198) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100980@unknown@formal@none@1@S@Adding sequences that do not contain binding sites decreases the signal-to-noise ratio, making motif finding more difficult 4.@(((:tag . "VBG") (:stem . "add") (:form . "Adding") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 16)\n (:start . 7) (:id . 43))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n (:id . 44))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 24) (:start . 22)\n (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "VB") (:stem . "contain") (:form . "contain") (:end . 36)\n (:start . 29) (:id . 47))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 44)\n (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 50) (:start . 45)\n (:id . 49))\n ((:tag . "VBZ") (:stem . "decrease") (:form . "decreases") (:end . 60)\n (:start . 51) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n (:id . 51))\n ((:tag . "JJ") (:stem . "signal-to-noise") (:form . "signal-to-noise")\n (:end . 80) (:start . 65) (:id . 52))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 86) (:start . 81)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n (:id . 54))\n ((:tag . "VBG") (:stem . "make") (:form . "making") (:end . 94) (:start . 88)\n (:id . 55))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 100) (:start . 95)\n (:id . 56))\n ((:tag . "VBG") (:stem . "find") (:form . "finding") (:end . 108)\n (:start . 101) (:id . 57))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 113) (:start . 109)\n (:id . 58))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 123)\n (:start . 114) (:id . 59))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 125) (:start . 124)\n (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n (:id . 61)))@@@1@20@((:ncues ((:id . :x3.200.1) (:span 25 28)))\n (:nscopes ((:id . :x3.200.1) (:span 25 50)))\n (:identifiers (:sid . :s3.200) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100981@unknown@formal@none@1@S@We thus tested SCOPE's performance on regulons containing additional extraneous upstream sequences.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "test") (:form . "tested") (:end . 14) (:start . 8)\n (:id . 44))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 22) (:start . 20)\n (:id . 46))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 34)\n (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 37) (:start . 35)\n (:id . 48))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 46)\n (:start . 38) (:id . 49))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 57)\n (:start . 47) (:id . 50))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 68)\n (:start . 58) (:id . 51))\n ((:tag . "JJ") (:stem . "extraneous") (:form . "extraneous") (:end . 79)\n (:start . 69) (:id . 52))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 88)\n (:start . 80) (:id . 53))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 98)\n (:start . 89) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.201) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100982@unknown@formal@none@1@S@For all 33 regulons in the SCPD dataset, we added randomly selected upstream S. cerevisiae sequences such that the total number of extraneous sequences was between 0.5 and 4 times the number of true upstream sequences in the regulon.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 10) (:start . 8)\n (:id . 44))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 19)\n (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 22) (:start . 20)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 47))\n ((:tag . "NNP") (:stem . "SCPD") (:form . "SCPD") (:end . 31) (:start . 27)\n (:id . 48))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 39)\n (:start . 32) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 43) (:start . 41)\n (:id . 51))\n ((:tag . "VBD") (:stem . "add") (:form . "added") (:end . 49) (:start . 44)\n (:id . 52))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 58)\n (:start . 50) (:id . 53))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 67)\n (:start . 59) (:id . 54))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 76)\n (:start . 68) (:id . 55))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 79) (:start . 77)\n (:id . 56))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 90)\n (:start . 80) (:id . 57))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 100)\n (:start . 91) (:id . 58))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 105) (:start . 101)\n (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 110) (:start . 106)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n (:id . 61))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 120)\n (:start . 115) (:id . 62))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 127)\n (:start . 121) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 130) (:start . 128)\n (:id . 64))\n ((:tag . "JJ") (:stem . "extraneous") (:form . "extraneous") (:end . 141)\n (:start . 131) (:id . 65))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 151)\n (:start . 142) (:id . 66))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 155) (:start . 152)\n (:id . 67))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 163)\n (:start . 156) (:id . 68))\n ((:tag . "CD") (:stem . "0.5") (:form . "0.5") (:end . 167) (:start . 164)\n (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 171) (:start . 168)\n (:id . 70))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 173) (:start . 172)\n (:id . 71))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 179)\n (:start . 174) (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 183) (:start . 180)\n (:id . 73))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 190)\n (:start . 184) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 193) (:start . 191)\n (:id . 75))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 198) (:start . 194)\n (:id . 76))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 207)\n (:start . 199) (:id . 77))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 217)\n (:start . 208) (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 220) (:start . 218)\n (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 224) (:start . 221)\n (:id . 80))\n ((:tag . "NN") (:stem . "regulon") (:form . "regulon") (:end . 232)\n (:start . 225) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 233) (:start . 232)\n (:id . 82)))@@@1@41@((:identifiers (:sid . :s3.202) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100983@unknown@formal@none@1@S@SCOPE's accuracy on this dataset was remarkably stable in the presence of extraneous sequences.@(((:tag . "NN") (:stem . "scope") (:form . "SCOPE") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 16)\n (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 24) (:start . 20)\n (:id . 46))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 32)\n (:start . 25) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 36) (:start . 33)\n (:id . 48))\n ((:tag . "RB") (:stem . "remarkably") (:form . "remarkably") (:end . 47)\n (:start . 37) (:id . 49))\n ((:tag . "JJ") (:stem . "stable") (:form . "stable") (:end . 54)\n (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n (:id . 52))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 70)\n (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n (:id . 54))\n ((:tag . "JJ") (:stem . "extraneous") (:form . "extraneous") (:end . 84)\n (:start . 74) (:id . 55))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 94)\n (:start . 85) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.203) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100984@unknown@formal@none@1@S@Figure 7 shows the aggregate results of this test, with the SCPD regulons divided into three groups based on SCOPE's accuracy on the true regulon.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 8) (:start . 7)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . 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(:end . 163) (:start . 162)\n (:id . 63)))@@@1@22@((:ncues ((:id . :x3.215.1) (:span 108 112)))\n (:nscopes ((:id . :x3.215.1) (:span 108 162)))\n (:identifiers (:sid . :s3.215) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100996@unknown@formal@none@1@S@A brief survey of the per-regulon results of these performance comparisons yields two key observations: (1) there are many regulons for which a large number of programs find a small portion of the binding sites (though not necessarily the same portion); and (2) every program has a respectable number of "wins" (i.e. every program is the best existing program on some handful of regulons 145678.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "brief") (:form . "brief") (:end . 7) (:start . 2)\n (:id . 43))\n ((:tag . "NN") (:stem . "survey") (:form . 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"145678") (:end . 394)\n (:start . 388) (:id . 117))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 395) (:start . 394)\n (:id . 118)))@@@1@77@((:identifiers (:sid . :s3.216) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100997@unknown@formal@none@1@S@Such observations are common in many machine learning applications, and are the direct result of complex search spaces that force restrictions on either the search strategy or the representation of the solution space (in this case, the motif model used to represent the motifs).@(((:tag . "JJ") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "observation") (:form . "observations") (:end . 17)\n (:start . 5) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 21) (:start . 18)\n (:id . 44))\n ((:tag . "JJ") (:stem . "common") (:form . 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(:end . 247) (:start . 246)\n (:id . 85)))@@@1@44@((:identifiers (:sid . :s3.218) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101000@unknown@formal@none@1@S@The HLK ensemble method 4 successfully exploits the first key observation above.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "HLK") (:form . "HLK") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "ensemble") (:form . "ensemble") (:end . 16)\n (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 23)\n (:start . 17) (:id . 45))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 25) (:start . 24)\n (:id . 46))\n ((:tag . "RB") (:stem . "successfully") (:form . "successfully") (:end . 38)\n (:start . 26) (:id . 47))\n ((:tag . "VBZ") (:stem . "exploit") (:form . "exploits") (:end . 47)\n (:start . 39) (:id . 48))\n ((:tag . 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"4") (:end . 157) (:start . 156)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x3.222.1) (:span 94 97)) ((:id . :x3.222.2) (:span 65 73)))\n (:hscopes ((:id . :x3.222.1) (:span 94 155))\n ((:id . :x3.222.2) (:span 65 155)))\n (:identifiers (:sid . :s3.222) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101003@unknown@formal@none@1@S@The limitation arises, however, in regulons where only one program has a high accuracy and the others fail to find any portion of the binding sites.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "limitation") (:form . "limitation") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "arise") (:form . "arises") (:end . 21)\n (:start . 15) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . 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(:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n (:id . 65)))@@@1@24@((:hcues ((:id . :x3.224.1) (:span 21 27)))\n (:hscopes ((:id . :x3.224.1) (:span 21 117)))\n (:identifiers (:sid . :s3.224) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101005@unknown@formal@none@1@S@The second observation, that all motif finders win some number of regulons and often perform roughly the same on average, is broadly consistent with a theorem in the Machine Learning field referred to as the No Free Lunch Theorem 1819.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 22)\n (:start . 11) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n (:id . 45))\n ((:tag . "IN") (:stem . 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"as") (:end . 203) (:start . 201)\n (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 207) (:start . 204)\n (:id . 78))\n ((:tag . "NNP") (:stem . "No") (:form . "No") (:end . 210) (:start . 208)\n (:id . 79))\n ((:tag . "NNP") (:stem . "Free") (:form . "Free") (:end . 215) (:start . 211)\n (:id . 80))\n ((:tag . "NNP") (:stem . "Lunch") (:form . "Lunch") (:end . 221)\n (:start . 216) (:id . 81))\n ((:tag . "NNP") (:stem . "Theorem") (:form . "Theorem") (:end . 229)\n (:start . 222) (:id . 82))\n ((:tag . "CD") (:stem . "1819") (:form . "1819") (:end . 234) (:start . 230)\n (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 235) (:start . 234)\n (:id . 84)))@@@1@43@((:identifiers (:sid . :s3.225) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101006@unknown@formal@none@1@S@Briefly, this theorem states that, averaged over all datasets, the performance of all search algorithms are exactly the same, with the corollary that two algorithms will have the exact same number of wins in relation to each other.@(((:tag . "NNP") (:stem . "Briefly") (:form . "Briefly") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "theorem") (:form . "theorem") (:end . 21)\n (:start . 14) (:id . 45))\n ((:tag . "VBZ") (:stem . "state") (:form . "states") (:end . 28)\n (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n (:id . 48))\n ((:tag . "VBD") (:stem . "average") (:form . "averaged") (:end . 43)\n (:start . 35) (:id . 49))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 48) (:start . 44)\n (:id . 50))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 52) (:start . 49)\n (:id . 51))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 61)\n (:start . 53) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n (:id . 54))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 78)\n (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 85) (:start . 82)\n (:id . 57))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 92)\n (:start . 86) (:id . 58))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 103)\n (:start . 93) (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 107) (:start . 104)\n (:id . 60))\n ((:tag . "RB") (:stem . "exactly") (:form . "exactly") (:end . 115)\n (:start . 108) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n (:id . 62))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 124) (:start . 120)\n (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 130) (:start . 126)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n (:id . 66))\n ((:tag . "NN") (:stem . "corollary") (:form . "corollary") (:end . 144)\n (:start . 135) (:id . 67))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 149) (:start . 145)\n (:id . 68))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 153) (:start . 150)\n (:id . 69))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 164)\n (:start . 154) (:id . 70))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 169) (:start . 165)\n (:id . 71))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 174) (:start . 170)\n (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 178) (:start . 175)\n (:id . 73))\n ((:tag . "JJ") (:stem . "exact") (:form . "exact") (:end . 184)\n (:start . 179) (:id . 74))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 189) (:start . 185)\n (:id . 75))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 196)\n (:start . 190) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 199) (:start . 197)\n (:id . 77))\n ((:tag . "NNS") (:stem . "win") (:form . "wins") (:end . 204) (:start . 200)\n (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 207) (:start . 205)\n (:id . 79))\n ((:tag . "NN") (:stem . "relation") (:form . "relation") (:end . 216)\n (:start . 208) (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 219) (:start . 217)\n (:id . 81))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 224) (:start . 220)\n (:id . 82))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 230)\n (:start . 225) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 231) (:start . 230)\n (:id . 84)))@@@1@43@((:identifiers (:sid . :s3.226) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101007@unknown@formal@none@1@S@In practice, this theorem argues for the use of specialized domain knowledge 20, where available, and may suggest that similar average performance across a diversity of approaches is an indication of the diversity of the datasets themselves.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "practice") (:form . "practice") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 17) (:start . 13)\n (:id . 45))\n ((:tag . "NN") (:stem . "theorem") (:form . "theorem") (:end . 25)\n (:start . 18) (:id . 46))\n ((:tag . "VBZ") (:stem . "argue") (:form . "argues") (:end . 32)\n (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 36) (:start . 33)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n (:id . 49))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 44) (:start . 41)\n (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n (:id . 51))\n ((:tag . "VBN") (:stem . "specialize") (:form . "specialized") (:end . 59)\n (:start . 48) (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 66)\n (:start . 60) (:id . 53))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 76)\n (:start . 67) (:id . 54))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 79) (:start . 77)\n (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n (:id . 56))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 86) (:start . 81)\n (:id . 57))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 96)\n (:start . 87) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n (:id . 60))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 105) (:start . 102)\n (:id . 61))\n ((:tag . "VB") (:stem . "suggest") (:form . "suggest") (:end . 113)\n (:start . 106) (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 118) (:start . 114)\n (:id . 63))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 126)\n (:start . 119) (:id . 64))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 134)\n (:start . 127) (:id . 65))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 146)\n (:start . 135) (:id . 66))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 153)\n (:start . 147) (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 155) (:start . 154)\n (:id . 68))\n ((:tag . "NN") (:stem . "diversity") (:form . "diversity") (:end . 165)\n (:start . 156) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 168) (:start . 166)\n (:id . 70))\n ((:tag . "NNS") (:stem . "approach") (:form . "approaches") (:end . 179)\n (:start . 169) (:id . 71))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 182) (:start . 180)\n (:id . 72))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 185) (:start . 183)\n (:id . 73))\n ((:tag . "NN") (:stem . "indication") (:form . "indication") (:end . 196)\n (:start . 186) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 199) (:start . 197)\n (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 203) (:start . 200)\n (:id . 76))\n ((:tag . "NN") (:stem . "diversity") (:form . "diversity") (:end . 213)\n (:start . 204) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 216) (:start . 214)\n (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 220) (:start . 217)\n (:id . 79))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 229)\n (:start . 221) (:id . 80))\n ((:tag . "PRP") (:stem . "themselves") (:form . "themselves") (:end . 240)\n (:start . 230) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 241) (:start . 240)\n (:id . 82)))@@@1@41@((:hcues ((:id . :x3.227.1) (:span 186 196))\n ((:id . :x3.227.2) (:span 106 113)) ((:id . :x3.227.3) (:span 102 105)))\n (:hscopes ((:id . :x3.227.1) (:span 186 240))\n ((:id . :x3.227.2) (:span 106 240)) ((:id . :x3.227.3) (:span 102 240)))\n (:identifiers (:sid . :s3.227) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101008@unknown@formal@none@1@S@Thus, motif finders designed for one class of motifs will win on regulons containing those motifs, but will perform poorly on other regulons, while more general motif finders will tend to have more consistently mediocre performance.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 11) (:start . 6)\n (:id . 44))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 19)\n (:start . 12) (:id . 45))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 28)\n (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 32) (:start . 29)\n (:id . 47))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 36) (:start . 33)\n (:id . 48))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 42) (:start . 37)\n (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n (:id . 50))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 52)\n (:start . 46) (:id . 51))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 57) (:start . 53)\n (:id . 52))\n ((:tag . "VB") (:stem . "win") (:form . "win") (:end . 61) (:start . 58)\n (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 64) (:start . 62)\n (:id . 54))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 73)\n (:start . 65) (:id . 55))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 84)\n (:start . 74) (:id . 56))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 90) (:start . 85)\n (:id . 57))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 97)\n (:start . 91) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n (:id . 59))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 102) (:start . 99)\n (:id . 60))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 107) (:start . 103)\n (:id . 61))\n ((:tag . "VB") (:stem . "perform") (:form . "perform") (:end . 115)\n (:start . 108) (:id . 62))\n ((:tag . "RB") (:stem . "poorly") (:form . "poorly") (:end . 122)\n (:start . 116) (:id . 63))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 125) (:start . 123)\n (:id . 64))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 131)\n (:start . 126) (:id . 65))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 140)\n (:start . 132) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n (:id . 67))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 147)\n (:start . 142) (:id . 68))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 152) (:start . 148)\n (:id . 69))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 160)\n (:start . 153) (:id . 70))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 166)\n (:start . 161) (:id . 71))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 174)\n (:start . 167) (:id . 72))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 179) (:start . 175)\n (:id . 73))\n ((:tag . "VB") (:stem . "tend") (:form . "tend") (:end . 184) (:start . 180)\n (:id . 74))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 187) (:start . 185)\n (:id . 75))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 192) (:start . 188)\n (:id . 76))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 197) (:start . 193)\n (:id . 77))\n ((:tag . "RB") (:stem . "consistently") (:form . "consistently") (:end . 210)\n (:start . 198) (:id . 78))\n ((:tag . "JJ") (:stem . "mediocre") (:form . "mediocre") (:end . 219)\n (:start . 211) (:id . 79))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 231)\n (:start . 220) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n (:id . 81)))@@@1@40@((:hcues ((:id . :x3.228.1) (:span 180 184)))\n (:hscopes ((:id . :x3.228.1) (:span 180 231)))\n (:identifiers (:sid . :s3.228) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101010@unknown@formal@none@1@S@The working hypothesis is, in effect, that the local maxima are predictable (corresponding to one of three motif classes) and exploitable (we can find the local maxima in each class and choose whichever is higher).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBG") (:stem . "work") (:form . "working") (:end . 11) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 22)\n (:start . 12) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 36)\n (:start . 30) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 42) (:start . 38)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n (:id . 51))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 52) (:start . 47)\n (:id . 52))\n ((:tag . "NNS") (:stem . "maximum") (:form . "maxima") (:end . 59)\n (:start . 53) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 63) (:start . 60)\n (:id . 54))\n ((:tag . "JJ") (:stem . "predictable") (:form . "predictable") (:end . 75)\n (:start . 64) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 77) (:start . 76)\n (:id . 56))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 90)\n (:start . 77) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 93) (:start . 91)\n (:id . 58))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 97) (:start . 94)\n (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n (:id . 60))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 106)\n (:start . 101) (:id . 61))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 112)\n (:start . 107) (:id . 62))\n ((:tag . "NNS") (:stem . "class") (:form . "classes") (:end . 120)\n (:start . 113) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 121) (:start . 120)\n (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n (:id . 65))\n ((:tag . "JJ") (:stem . "exploitable") (:form . "exploitable") (:end . 137)\n (:start . 126) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n (:id . 67))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 141) (:start . 139)\n (:id . 68))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 145) (:start . 142)\n (:id . 69))\n ((:tag . "VB") (:stem . "find") (:form . "find") (:end . 150) (:start . 146)\n (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n (:id . 71))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 160)\n (:start . 155) (:id . 72))\n ((:tag . "NNS") (:stem . "maximum") (:form . "maxima") (:end . 167)\n (:start . 161) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 170) (:start . 168)\n (:id . 74))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 175) (:start . 171)\n (:id . 75))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 181)\n (:start . 176) (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 185) (:start . 182)\n (:id . 77))\n ((:tag . "NN") (:stem . "choose") (:form . "choose") (:end . 192)\n (:start . 186) (:id . 78))\n ((:tag . "WDT") (:stem . "whichever") (:form . "whichever") (:end . 202)\n (:start . 193) (:id . 79))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 205) (:start . 203)\n (:id . 80))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 212)\n (:start . 206) (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 213) (:start . 212)\n (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n (:id . 83)))@@@1@42@((:hcues ((:id . :x3.230.1) (:span 12 22)))\n (:hscopes ((:id . :x3.230.1) (:span 12 137)))\n (:identifiers (:sid . :s3.230) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101011@unknown@formal@none@1@S@Consistent with this hypothesis, there was very little overlap among the component algorithms of SCOPE (each wins about 20 of the 78 regulons, with very few ties) and, by taking the maximum score from those three local maxima, SCOPE tended to choose the motif with the highest accuracy in a clear majority of the cases (66%, compared to 33% for a random learning rule).@(((:tag . "JJ") (:stem . "consistent") (:form . "Consistent") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 15) (:start . 11)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 20) (:start . 16)\n (:id . 44))\n ((:tag . 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"result") (:form . "results") (:end . 129)\n (:start . 122) (:id . 69))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 137)\n (:start . 130) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n (:id . 71))\n ((:tag . "NN") (:stem . "generalizability") (:form . "generalizability")\n (:end . 158) (:start . 142) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 161) (:start . 159)\n (:id . 73))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 167)\n (:start . 162) (:id . 74))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 169) (:start . 167)\n (:id . 75))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 173) (:start . 170)\n (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 176) (:start . 174)\n (:id . 77))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 183)\n (:start . 177) (:id . 78))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 193)\n (:start . 184) (:id . 79))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 196) (:start . 194)\n (:id . 80))\n ((:tag . "RB") (:stem . "biologically") (:form . "biologically") (:end . 209)\n (:start . 197) (:id . 81))\n ((:tag . "JJ") (:stem . "relevant") (:form . "relevant") (:end . 218)\n (:start . 210) (:id . 82))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 227)\n (:start . 219) (:id . 83))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 232) (:start . 228)\n (:id . 84))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 238)\n (:start . 233) (:id . 85))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 246)\n (:start . 239) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 247) (:start . 246)\n (:id . 87)))@@@1@46@((:hcues ((:id . :x3.235.1) (:span 130 137)))\n (:hscopes ((:id . :x3.235.1) (:span 130 246)))\n (:identifiers (:sid . :s3.235) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101016@unknown@formal@none@1@S@These observations are not offered as definitive proof that there are only three classes of motifs; rather, they show that power can be gained by identifying distinct motif classes and combining specialized algorithms with a unified scoring rule.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "observation") (:form . "observations") (:end . 18)\n (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 22) (:start . 19)\n (:id . 44))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 26) (:start . 23)\n (:id . 45))\n ((:tag . "VBN") (:stem . "offer") (:form . "offered") (:end . 34)\n (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 37) (:start . 35)\n (:id . 47))\n ((:tag . "JJ") (:stem . "definitive") (:form . "definitive") (:end . 48)\n (:start . 38) (:id . 48))\n ((:tag . "NN") (:stem . "proof") (:form . "proof") (:end . 54) (:start . 49)\n (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 59) (:start . 55)\n (:id . 50))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 65) (:start . 60)\n (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 69) (:start . 66)\n (:id . 52))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 74) (:start . 70)\n (:id . 53))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 80) (:start . 75)\n (:id . 54))\n ((:tag . "NNS") (:stem . "class") (:form . "classes") (:end . 88)\n (:start . 81) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n (:id . 56))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 98)\n (:start . 92) (:id . 57))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 99) (:start . 98)\n (:id . 58))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 106)\n (:start . 100) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n (:id . 60))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 112) (:start . 108)\n (:id . 61))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 117) (:start . 113)\n (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 122) (:start . 118)\n (:id . 63))\n ((:tag . "NN") (:stem . "power") (:form . "power") (:end . 128)\n (:start . 123) (:id . 64))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 132) (:start . 129)\n (:id . 65))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 135) (:start . 133)\n (:id . 66))\n ((:tag . "VBN") (:stem . "gain") (:form . "gained") (:end . 142)\n (:start . 136) (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 145) (:start . 143)\n (:id . 68))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 157)\n (:start . 146) (:id . 69))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 166)\n (:start . 158) (:id . 70))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 172)\n (:start . 167) (:id . 71))\n ((:tag . "NNS") (:stem . "class") (:form . "classes") (:end . 180)\n (:start . 173) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 184) (:start . 181)\n (:id . 73))\n ((:tag . "VBG") (:stem . "combine") (:form . "combining") (:end . 194)\n (:start . 185) (:id . 74))\n ((:tag . "VBN") (:stem . "specialize") (:form . "specialized") (:end . 206)\n (:start . 195) (:id . 75))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 217)\n (:start . 207) (:id . 76))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 222) (:start . 218)\n (:id . 77))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 224) (:start . 223)\n (:id . 78))\n ((:tag . "JJ") (:stem . "unified") (:form . "unified") (:end . 232)\n (:start . 225) (:id . 79))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 240)\n (:start . 233) (:id . 80))\n ((:tag . "NN") (:stem . "rule") (:form . "rule") (:end . 245) (:start . 241)\n (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 246) (:start . 245)\n (:id . 82)))@@@1@41@((:ncues ((:id . :x3.236.1) (:span 23 26)))\n (:nscopes ((:id . :x3.236.1) (:span 0 98)))\n (:identifiers (:sid . :s3.236) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101017@unknown@formal@none@1@S@It is possible that more power could be gained by identifying other distinct motif classes and adding algorithms that explicitly search for those classes.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 14)\n (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n (:id . 45))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 24) (:start . 20)\n (:id . 46))\n ((:tag . "NN") (:stem . "power") (:form . "power") (:end . 30) (:start . 25)\n (:id . 47))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 36) (:start . 31)\n (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 39) (:start . 37)\n (:id . 49))\n ((:tag . "VBN") (:stem . "gain") (:form . "gained") (:end . 46) (:start . 40)\n (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 49) (:start . 47)\n (:id . 51))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 61)\n (:start . 50) (:id . 52))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 67) (:start . 62)\n (:id . 53))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 76)\n (:start . 68) (:id . 54))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 82) (:start . 77)\n (:id . 55))\n ((:tag . "NNS") (:stem . "class") (:form . "classes") (:end . 90)\n (:start . 83) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n (:id . 57))\n ((:tag . "VBG") (:stem . "add") (:form . "adding") (:end . 101) (:start . 95)\n (:id . 58))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 112)\n (:start . 102) (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 117) (:start . 113)\n (:id . 60))\n ((:tag . "RB") (:stem . "explicitly") (:form . "explicitly") (:end . 128)\n (:start . 118) (:id . 61))\n ((:tag . "VBP") (:stem . "search") (:form . "search") (:end . 135)\n (:start . 129) (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 139) (:start . 136)\n (:id . 63))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 145)\n (:start . 140) (:id . 64))\n ((:tag . "NNS") (:stem . "class") (:form . "classes") (:end . 153)\n (:start . 146) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x3.237.1) (:span 31 36)) ((:id . :x3.237.2) (:span 6 14)))\n (:hscopes ((:id . :x3.237.1) (:span 20 153))\n ((:id . :x3.237.2) (:span 6 153)))\n (:identifiers (:sid . :s3.237) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101018@unknown@formal@none@1@S@For example, Zinc finger transcription factors have been demonstrated to bind three triplets of nucleotides which overlap at their third base positions 21.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Zinc") (:form . "Zinc") (:end . 17) (:start . 13)\n (:id . 45))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 24)\n (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n (:end . 38) (:start . 25) (:id . 47))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 46)\n (:start . 39) (:id . 48))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 51) (:start . 47)\n (:id . 49))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 56) (:start . 52)\n (:id . 50))\n ((:tag . "VBN") (:stem . "demonstrate") (:form . "demonstrated") (:end . 69)\n (:start . 57) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n (:id . 52))\n ((:tag . "VB") (:stem . "bind") (:form . "bind") (:end . 77) (:start . 73)\n (:id . 53))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 83) (:start . 78)\n (:id . 54))\n ((:tag . "NNS") (:stem . "triplet") (:form . "triplets") (:end . 92)\n (:start . 84) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n (:id . 56))\n ((:tag . "NNS") (:stem . "nucleotide") (:form . "nucleotides") (:end . 107)\n (:start . 96) (:id . 57))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 113)\n (:start . 108) (:id . 58))\n ((:tag . "VBP") (:stem . "overlap") (:form . "overlap") (:end . 121)\n (:start . 114) (:id . 59))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 124) (:start . 122)\n (:id . 60))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 130)\n (:start . 125) (:id . 61))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 136)\n (:start . 131) (:id . 62))\n ((:tag . "NN") (:stem . "base") (:form . "base") (:end . 141) (:start . 137)\n (:id . 63))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 151)\n (:start . 142) (:id . 64))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 154) (:start . 152)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.238) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101020@unknown@formal@none@1@S@Thus, all nondegenerate triplets in a set of upstream regions could be scored and the highest-scoring triplets combined into a single five-mer with a two-base degeneracy (corresponding to the IUPAC characters R,Y, W, S, K or M) at the middle position.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 9) (:start . 6)\n (:id . 44))\n ((:tag . "JJ") (:stem . "nondegenerate") (:form . "nondegenerate")\n (:end . 23) (:start . 10) (:id . 45))\n ((:tag . "NNS") (:stem . "triplet") (:form . "triplets") (:end . 32)\n (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n (:id . 48))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 41) (:start . 38)\n (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n (:id . 50))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 53)\n (:start . 45) (:id . 51))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 61)\n (:start . 54) (:id . 52))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 67) (:start . 62)\n (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 70) (:start . 68)\n (:id . 54))\n ((:tag . "VBN") (:stem . "score") (:form . "scored") (:end . 77)\n (:start . 71) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n (:id . 57))\n ((:tag . "JJ") (:stem . "highest-scoring") (:form . "highest-scoring")\n (:end . 101) (:start . 86) (:id . 58))\n ((:tag . "NNS") (:stem . "triplet") (:form . "triplets") (:end . 110)\n (:start . 102) (:id . 59))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 119)\n (:start . 111) (:id . 60))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 124) (:start . 120)\n (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 126) (:start . 125)\n (:id . 62))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 133)\n (:start . 127) (:id . 63))\n ((:tag . "NN") (:stem . "five-mer") (:form . "five-mer") (:end . 142)\n (:start . 134) (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 147) (:start . 143)\n (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 149) (:start . 148)\n (:id . 66))\n ((:tag . "JJ") (:stem . "two-base") (:form . "two-base") (:end . 158)\n (:start . 150) (:id . 67))\n ((:tag . "NN") (:stem . "degeneracy") (:form . "degeneracy") (:end . 169)\n (:start . 159) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 171) (:start . 170)\n (:id . 69))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 184)\n (:start . 171) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 187) (:start . 185)\n (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 191) (:start . 188)\n (:id . 72))\n ((:tag . "NNP") (:stem . "IUPAC") (:form . "IUPAC") (:end . 197)\n (:start . 192) (:id . 73))\n ((:tag . "NNS") (:stem . "character") (:form . "characters") (:end . 208)\n (:start . 198) (:id . 74))\n ((:tag . "NNP") (:stem . "R,Y") (:form . "R,Y") (:end . 212) (:start . 209)\n (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 213) (:start . 212)\n (:id . 76))\n ((:tag . "NNP") (:stem . "W") (:form . "W") (:end . 215) (:start . 214)\n (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 216) (:start . 215)\n (:id . 78))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 218) (:start . 217)\n (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 219) (:start . 218)\n (:id . 80))\n ((:tag . "NNP") (:stem . "K") (:form . "K") (:end . 221) (:start . 220)\n (:id . 81))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 224) (:start . 222)\n (:id . 82))\n ((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 226) (:start . 225)\n (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 227) (:start . 226)\n (:id . 84))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 230) (:start . 228)\n (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 234) (:start . 231)\n (:id . 86))\n ((:tag . "JJ") (:stem . "middle") (:form . "middle") (:end . 241)\n (:start . 235) (:id . 87))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 250)\n (:start . 242) (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 251) (:start . 250)\n (:id . 89)))@@@1@48@((:hcues ((:id . :x3.240.1) (:span 62 67)))\n (:hscopes ((:id . :x3.240.1) (:span 6 77)))\n (:identifiers (:sid . :s3.240) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101021@unknown@formal@none@1@S@The highest-scoring five-mers could then be combined with the highest scoring triplets to generate a seven-mer with two-base degeneracies at positions three and five.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "highest-scoring") (:form . "highest-scoring")\n (:end . 19) (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "five-mer") (:form . "five-mers") (:end . 29)\n (:start . 20) (:id . 44))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 35) (:start . 30)\n (:id . 45))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 40) (:start . 36)\n (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 43) (:start . 41)\n (:id . 47))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 52)\n (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 57) (:start . 53)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n (:id . 50))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 69)\n (:start . 62) (:id . 51))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 77)\n (:start . 70) (:id . 52))\n ((:tag . "NNS") (:stem . "triplet") (:form . "triplets") (:end . 86)\n (:start . 78) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n (:id . 54))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 98)\n (:start . 90) (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 100) (:start . 99)\n (:id . 56))\n ((:tag . "NN") (:stem . "seven-mer") (:form . "seven-mer") (:end . 110)\n (:start . 101) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 115) (:start . 111)\n (:id . 58))\n ((:tag . "JJ") (:stem . "two-base") (:form . "two-base") (:end . 124)\n (:start . 116) (:id . 59))\n ((:tag . "NNS") (:stem . "degeneracy") (:form . "degeneracies") (:end . 137)\n (:start . 125) (:id . 60))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 140) (:start . 138)\n (:id . 61))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 150)\n (:start . 141) (:id . 62))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 156)\n (:start . 151) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n (:id . 64))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 165) (:start . 161)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x3.241.1) (:span 30 35)))\n (:hscopes ((:id . :x3.241.1) (:span 0 165)))\n (:identifiers (:sid . :s3.241) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101022@unknown@formal@none@1@S@Provided the appropriate Bonferroni correction is applied for this new class of motifs, these motifs may be easily compared with the results from BEAM, PRISM and SPACER, thereby extending the SCOPE ensemble to include a fourth class of motifs.@(((:tag . "VBN") (:stem . "provide") (:form . "Provided") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 43))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 24)\n (:start . 13) (:id . 44))\n ((:tag . "NNP") (:stem . "Bonferroni") (:form . "Bonferroni") (:end . 35)\n (:start . 25) (:id . 45))\n ((:tag . "NN") (:stem . "correction") (:form . "correction") (:end . 46)\n (:start . 36) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 49) (:start . 47)\n (:id . 47))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 57)\n (:start . 50) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 61) (:start . 58)\n (:id . 49))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 66) (:start . 62)\n (:id . 50))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 70) (:start . 67)\n (:id . 51))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 76) (:start . 71)\n (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n (:id . 53))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 86)\n (:start . 80) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n (:id . 55))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 93) (:start . 88)\n (:id . 56))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 100)\n (:start . 94) (:id . 57))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 104) (:start . 101)\n (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 107) (:start . 105)\n (:id . 59))\n ((:tag . "RB") (:stem . "easily") (:form . "easily") (:end . 114)\n (:start . 108) (:id . 60))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 123)\n (:start . 115) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 128) (:start . 124)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n (:id . 63))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 140)\n (:start . 133) (:id . 64))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 145) (:start . 141)\n (:id . 65))\n ((:tag . "NNP") (:stem . "BEAM") (:form . "BEAM") (:end . 150) (:start . 146)\n (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 151) (:start . 150)\n (:id . 67))\n ((:tag . "NN") (:stem . "prism") (:form . "PRISM") (:end . 157)\n (:start . 152) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 161) (:start . 158)\n (:id . 69))\n ((:tag . "NNP") (:stem . "SPACER") (:form . "SPACER") (:end . 168)\n (:start . 162) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 169) (:start . 168)\n (:id . 71))\n ((:tag . "RB") (:stem . "thereby") (:form . "thereby") (:end . 177)\n (:start . 170) (:id . 72))\n ((:tag . "VBG") (:stem . "extend") (:form . "extending") (:end . 187)\n (:start . 178) (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 191) (:start . 188)\n (:id . 74))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 197)\n (:start . 192) (:id . 75))\n ((:tag . "VB") (:stem . "ensemble") (:form . "ensemble") (:end . 206)\n (:start . 198) (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 209) (:start . 207)\n (:id . 77))\n ((:tag . "VB") (:stem . "include") (:form . "include") (:end . 217)\n (:start . 210) (:id . 78))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 219) (:start . 218)\n (:id . 79))\n ((:tag . "JJ") (:stem . "fourth") (:form . "fourth") (:end . 226)\n (:start . 220) (:id . 80))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 232)\n (:start . 227) (:id . 81))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 235) (:start . 233)\n (:id . 82))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 242)\n (:start . 236) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 243) (:start . 242)\n (:id . 84)))@@@1@43@((:hcues ((:id . :x3.242.1) (:span 101 104)))\n (:hscopes ((:id . :x3.242.1) (:span 88 168)))\n (:identifiers (:sid . :s3.242) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101023@unknown@formal@none@1@S@We note, however, that as more methods are added to SCOPE, it will be increasingly difficult to devise a scoring metric that can accurately choose the best result from among the components.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "note") (:form . "note") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 16)\n (:start . 9) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 25) (:start . 23)\n (:id . 48))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 30) (:start . 26)\n (:id . 49))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 38)\n (:start . 31) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 42) (:start . 39)\n (:id . 51))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 48) (:start . 43)\n (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n (:id . 53))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 57) (:start . 52)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n (:id . 55))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 61) (:start . 59)\n (:id . 56))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 66) (:start . 62)\n (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 69) (:start . 67)\n (:id . 58))\n ((:tag . "RB") (:stem . "increasingly") (:form . "increasingly") (:end . 82)\n (:start . 70) (:id . 59))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 92)\n (:start . 83) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 95) (:start . 93)\n (:id . 61))\n ((:tag . "VB") (:stem . "devise") (:form . "devise") (:end . 102)\n (:start . 96) (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 104) (:start . 103)\n (:id . 63))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 112)\n (:start . 105) (:id . 64))\n ((:tag . "NN") (:stem . "metric") (:form . "metric") (:end . 119)\n (:start . 113) (:id . 65))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 124) (:start . 120)\n (:id . 66))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 128) (:start . 125)\n (:id . 67))\n ((:tag . "RB") (:stem . "accurately") (:form . "accurately") (:end . 139)\n (:start . 129) (:id . 68))\n ((:tag . "VB") (:stem . "choose") (:form . "choose") (:end . 146)\n (:start . 140) (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 150) (:start . 147)\n (:id . 70))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 155) (:start . 151)\n (:id . 71))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 162)\n (:start . 156) (:id . 72))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 167) (:start . 163)\n (:id . 73))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 173)\n (:start . 168) (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 177) (:start . 174)\n (:id . 75))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 188)\n (:start . 178) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s3.243) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101024@unknown@formal@none@1@S@SCOPE may also serve as a complementary approach to the HLK method.@(((:tag . "NN") (:stem . "scope") (:form . "SCOPE") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "VB") (:stem . "serve") (:form . "serve") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 23) (:start . 21)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 25) (:start . 24)\n (:id . 47))\n ((:tag . "JJ") (:stem . "complementary") (:form . "complementary")\n (:end . 39) (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 48)\n (:start . 40) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n (:id . 51))\n ((:tag . "NNP") (:stem . "HLK") (:form . "HLK") (:end . 59) (:start . 56)\n (:id . 52))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 66)\n (:start . 60) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n (:id . 54)))@@@1@13@((:hcues ((:id . :x3.244.1) (:span 6 9)))\n (:hscopes ((:id . :x3.244.1) (:span 6 66)))\n (:identifiers (:sid . :s3.244) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101025@unknown@formal@none@1@S@For example, the parameters of many methods can be set to search for specific classes of motifs (such as bipartite versus non-bipartite motifs).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 27)\n (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 47))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 35) (:start . 31)\n (:id . 48))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 43)\n (:start . 36) (:id . 49))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 47) (:start . 44)\n (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 50) (:start . 48)\n (:id . 51))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 54) (:start . 51)\n (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 57) (:start . 55)\n (:id . 53))\n ((:tag . "VB") (:stem . "search") (:form . "search") (:end . 64)\n (:start . 58) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 68) (:start . 65)\n (:id . 55))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 77)\n (:start . 69) (:id . 56))\n ((:tag . "NNS") (:stem . "class") (:form . "classes") (:end . 85)\n (:start . 78) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n (:id . 58))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 95)\n (:start . 89) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n (:id . 60))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 101) (:start . 97)\n (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 104) (:start . 102)\n (:id . 62))\n ((:tag . "JJ") (:stem . "bipartite") (:form . "bipartite") (:end . 114)\n (:start . 105) (:id . 63))\n ((:tag . "IN") (:stem . "versus") (:form . "versus") (:end . 121)\n (:start . 115) (:id . 64))\n ((:tag . "JJ") (:stem . "non-bipartite") (:form . "non-bipartite")\n (:end . 135) (:start . 122) (:id . 65))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 142)\n (:start . 136) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s3.245) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101026@unknown@formal@none@1@S@Thus, analogous to the ensemble method described in this paper, one may build a hierarchical ensemble that first searches each motif class by the HLK method using a number of algorithms or random restarts, and then uses the SCOPE method to choose the best result from among the motif classes.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "analogous") (:form . "analogous") (:end . 15)\n (:start . 6) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 18) (:start . 16)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 46))\n ((:tag . "JJ") (:stem . "ensemble") (:form . "ensemble") (:end . 31)\n (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 38)\n (:start . 32) (:id . 48))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 48)\n (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n (:id . 50))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 56) (:start . 52)\n (:id . 51))\n ((:tag . "NN") (:stem . "paper") (:form . "paper") (:end . 62) (:start . 57)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n (:id . 53))\n ((:tag . "PRP") (:stem . "one") (:form . "one") (:end . 67) (:start . 64)\n (:id . 54))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 71) (:start . 68)\n (:id . 55))\n ((:tag . "VB") (:stem . "build") (:form . "build") (:end . 77) (:start . 72)\n (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 79) (:start . 78)\n (:id . 57))\n ((:tag . "JJ") (:stem . "hierarchical") (:form . "hierarchical") (:end . 92)\n (:start . 80) (:id . 58))\n ((:tag . "NN") (:stem . "ensemble") (:form . "ensemble") (:end . 101)\n (:start . 93) (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 106) (:start . 102)\n (:id . 60))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 112)\n (:start . 107) (:id . 61))\n ((:tag . "VBZ") (:stem . "search") (:form . "searches") (:end . 121)\n (:start . 113) (:id . 62))\n ((:tag . "DT") (:stem . "each") (:form . 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"NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 185)\n (:start . 175) (:id . 74))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 188) (:start . 186)\n (:id . 75))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 195)\n (:start . 189) (:id . 76))\n ((:tag . "NNS") (:stem . "restart") (:form . "restarts") (:end . 204)\n (:start . 196) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 205) (:start . 204)\n (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 209) (:start . 206)\n (:id . 79))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 214) (:start . 210)\n (:id . 80))\n ((:tag . "VBZ") (:stem . "use") (:form . "uses") (:end . 219) (:start . 215)\n (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 223) (:start . 220)\n (:id . 82))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 229)\n (:start . 224) (:id . 83))\n ((:tag . "NN") (:stem . "method") (:form . 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(:end . 271) (:start . 270)\n (:id . 82)))@@@1@41@((:hcues ((:id . :x3.248.1) (:span 175 178)))\n (:hscopes ((:id . :x3.248.1) (:span 162 270)))\n (:identifiers (:sid . :s3.248) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101030@unknown@formal@none@1@S@Certainly to maintain statistical validity, some correction must be made for multiple hypothesis testing.@(((:tag . "RB") (:stem . "certainly") (:form . "Certainly") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 12) (:start . 10)\n (:id . 43))\n ((:tag . "VB") (:stem . "maintain") (:form . "maintain") (:end . 21)\n (:start . 13) (:id . 44))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 33)\n (:start . 22) (:id . 45))\n ((:tag . "NN") (:stem . "validity") (:form . "validity") (:end . 42)\n (:start . 34) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . 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(:end . 105) (:start . 104)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.250) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101031@unknown@formal@none@1@S@Furthermore, the effects of multiple testing may bias the results in favor of one of the component algorithms.@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 24)\n (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 36)\n (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "testing") (:form . 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(:end . 254) (:start . 253)\n (:id . 85)))@@@1@44@((:identifiers (:sid . :s3.252) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101033@unknown@formal@none@1@S@Although our test set of 78 regulons gave us enough power to find significance between SCOPE and its components or other algorithms, it did not provide enough power to disentangle the effects of small improvements (such as the Bonferroni correction, the objective function that takes position bias into account, or scoring motifs based off one or both strands), especially in the rigorous cross-validation framework necessary to decipher precisely which aspects contribute significantly to the performance.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 12) (:start . 9)\n (:id . 43))\n ((:tag . "NN") (:stem . "test") (:form . 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(:end . 506) (:start . 505)\n (:id . 123)))@@@1@82@((:ncues ((:id . :x3.253.1) (:span 140 143)))\n (:nscopes ((:id . :x3.253.1) (:span 140 505)))\n (:identifiers (:sid . :s3.253) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101034@unknown@formal@none@1@S@Nevertheless, as larger datasets become available, SCOPE's efficient search strategy makes it an ideal platform for exploring the effect of focused improvements to the motif finding approach described, such as the use of complex objective functions that may better approximate biological significance.@(((:tag . "RB") (:stem . "nevertheless") (:form . "Nevertheless") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 16) (:start . 14)\n (:id . 44))\n ((:tag . "JJR") (:stem . "large") (:form . 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(:form . ".") (:end . 265) (:start . 264)\n (:id . 87)))@@@1@46@((:hcues ((:id . :x3.262.1) (:span 41 50)))\n (:hscopes ((:id . :x3.262.1) (:span 41 94)))\n (:identifiers (:sid . :s3.262) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101043@unknown@formal@none@1@S@Arguably, systematic parameter optimization for each of these programs may well yield higher accuracy scores than those reported here.@(((:tag . "RB") (:stem . "arguably") (:form . "Arguably") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "JJ") (:stem . "systematic") (:form . "systematic") (:end . 20)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "parameter") (:form . "parameter") (:end . 30)\n (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "optimization") (:form . "optimization") (:end . 43)\n (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 47) (:start . 44)\n (:id . 47))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 52) (:start . 48)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n (:id . 49))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 61) (:start . 56)\n (:id . 50))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 70)\n (:start . 62) (:id . 51))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 74) (:start . 71)\n (:id . 52))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 79) (:start . 75)\n (:id . 53))\n ((:tag . "VB") (:stem . "yield") (:form . "yield") (:end . 85) (:start . 80)\n (:id . 54))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 92) (:start . 86)\n (:id . 55))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 101)\n (:start . 93) (:id . 56))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 108)\n (:start . 102) (:id . 57))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 113) (:start . 109)\n (:id . 58))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 119)\n (:start . 114) (:id . 59))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 128)\n (:start . 120) (:id . 60))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 133) (:start . 129)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n (:id . 62)))@@@1@21@((:hcues ((:id . :x3.263.1) (:span 71 74)))\n (:hscopes ((:id . :x3.263.1) (:span 71 133)))\n (:identifiers (:sid . :s3.263) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101044@unknown@formal@none@1@S@However, in order to avoid the pitfall of overfitting to the dataset, such parameter optimization must be performed using cross-validation or some other resampling technique 92223.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 17) (:start . 12)\n (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 20) (:start . 18)\n (:id . 46))\n ((:tag . "VB") (:stem . "avoid") (:form . "avoid") (:end . 26) (:start . 21)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n (:id . 48))\n ((:tag . "NN") (:stem . "pitfall") (:form . "pitfall") (:end . 38)\n (:start . 31) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n (:id . 50))\n ((:tag . "VBG") (:stem . "overfitte") (:form . "overfitting") (:end . 53)\n (:start . 42) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n (:id . 53))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 68)\n (:start . 61) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n (:id . 55))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 74) (:start . 70)\n (:id . 56))\n ((:tag . "NN") (:stem . "parameter") (:form . "parameter") (:end . 84)\n (:start . 75) (:id . 57))\n ((:tag . "NN") (:stem . "optimization") (:form . "optimization") (:end . 97)\n (:start . 85) (:id . 58))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 102) (:start . 98)\n (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 105) (:start . 103)\n (:id . 60))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 115)\n (:start . 106) (:id . 61))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 121) (:start . 116)\n (:id . 62))\n ((:tag . "NN") (:stem . "cross-validation") (:form . "cross-validation")\n (:end . 138) (:start . 122) (:id . 63))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 141) (:start . 139)\n (:id . 64))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 146) (:start . 142)\n (:id . 65))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 152)\n (:start . 147) (:id . 66))\n ((:tag . "VBG") (:stem . "resample") (:form . "resampling") (:end . 163)\n (:start . 153) (:id . 67))\n ((:tag . "NN") (:stem . "technique") (:form . "technique") (:end . 173)\n (:start . 164) (:id . 68))\n ((:tag . "CD") (:stem . "92223") (:form . "92223") (:end . 179)\n (:start . 174) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s3.264) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101045@unknown@formal@none@1@S@We note that all the motif finders tested, including SCOPE, performed poorly on the Drosophila dataset.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "note") (:form . "note") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 46))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 26) (:start . 21)\n (:id . 47))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 34)\n (:start . 27) (:id . 48))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 41) (:start . 35)\n (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n (:id . 50))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 52)\n (:start . 43) (:id . 51))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 58) (:start . 53)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n (:id . 53))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 69)\n (:start . 60) (:id . 54))\n ((:tag . "RB") (:stem . "poorly") (:form . "poorly") (:end . 76)\n (:start . 70) (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 79) (:start . 77)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n (:id . 57))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 94)\n (:start . 84) (:id . 58))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 102)\n (:start . 95) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.265) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101046@unknown@formal@none@1@S@Although SCOPE had the highest accuracy on this dataset, that accuracy was significantly less than on the bacterial and yeast data.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 14) (:start . 9)\n (:id . 43))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 18) (:start . 15)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 30)\n (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 39)\n (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 42) (:start . 40)\n (:id . 48))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 47) (:start . 43)\n (:id . 49))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 55)\n (:start . 48) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n (:id . 51))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 61) (:start . 57)\n (:id . 52))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 70)\n (:start . 62) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 74) (:start . 71)\n (:id . 54))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 88) (:start . 75) (:id . 55))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 93) (:start . 89)\n (:id . 56))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 98) (:start . 94)\n (:id . 57))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 101) (:start . 99)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n (:id . 59))\n ((:tag . "JJ") (:stem . "bacterial") (:form . "bacterial") (:end . 115)\n (:start . 106) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 119) (:start . 116)\n (:id . 61))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 125)\n (:start . 120) (:id . 62))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 130)\n (:start . 126) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.266) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101047@unknown@formal@none@1@S@Especially poor performance on Drosophila was also reported in the Tompa et al. performance comparison, indicating that this difficulty is not limited to the current dataset 5.@(((:tag . "RB") (:stem . "especially") (:form . "Especially") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "poor") (:form . "poor") (:end . 15) (:start . 11)\n (:id . 43))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 27)\n (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 30) (:start . 28)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 41)\n (:start . 31) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 45) (:start . 42)\n (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 50) (:start . 46)\n (:id . 48))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 59)\n (:start . 51) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n (:id . 51))\n ((:tag . "NNP") (:stem . "Tompa") (:form . "Tompa") (:end . 72) (:start . 67)\n (:id . 52))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 75) (:start . 73)\n (:id . 53))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 79) (:start . 76)\n (:id . 54))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 91)\n (:start . 80) (:id . 55))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 102)\n (:start . 92) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n (:id . 57))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 114)\n (:start . 104) (:id . 58))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 119) (:start . 115)\n (:id . 59))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 124) (:start . 120)\n (:id . 60))\n ((:tag . "NN") (:stem . "difficulty") (:form . "difficulty") (:end . 135)\n (:start . 125) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 138) (:start . 136)\n (:id . 62))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 142) (:start . 139)\n (:id . 63))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 150)\n (:start . 143) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 153) (:start . 151)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 157) (:start . 154)\n (:id . 66))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 165)\n (:start . 158) (:id . 67))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 173)\n (:start . 166) (:id . 68))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 175) (:start . 174)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x3.267.2) (:span 104 119)))\n (:ncues ((:id . :x3.267.1) (:span 139 142)))\n (:hscopes ((:id . :x3.267.2) (:span 104 173)))\n (:nscopes ((:id . :x3.267.1) (:span 120 173)))\n (:identifiers (:sid . :s3.267) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101048@unknown@formal@none@1@S@One possible cause of poor performance in this study is that the ""regulons"" are derived from enhancer regions defined in an earlier computational paper 24.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "cause") (:form . "cause") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "JJ") (:stem . "poor") (:form . "poor") (:end . 26) (:start . 22)\n (:id . 46))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 38)\n (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n (:id . 48))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 46) (:start . 42)\n (:id . 49))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 52) (:start . 47)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 55) (:start . 53)\n (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 60) (:start . 56)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n (:id . 53))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 66) (:start . 65)\n (:id . 54))\n ((:tag . "NNS") (:stem . "”regulons") (:form . "”regulons") (:end . 75)\n (:start . 66) (:id . 55))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 76) (:start . 75)\n (:id . 56))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 77) (:start . 76)\n (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 81) (:start . 78)\n (:id . 58))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 89)\n (:start . 82) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 94) (:start . 90)\n (:id . 60))\n ((:tag . "NN") (:stem . "enhancer") (:form . "enhancer") (:end . 103)\n (:start . 95) (:id . 61))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 111)\n (:start . 104) (:id . 62))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 119)\n (:start . 112) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 122) (:start . 120)\n (:id . 64))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 125) (:start . 123)\n (:id . 65))\n ((:tag . "JJR") (:stem . "early") (:form . "earlier") (:end . 133)\n (:start . 126) (:id . 66))\n ((:tag . "JJ") (:stem . "computational") (:form . "computational")\n (:end . 147) (:start . 134) (:id . 67))\n ((:tag . "NN") (:stem . "paper") (:form . "paper") (:end . 153)\n (:start . 148) (:id . 68))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 156) (:start . 154)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x3.268.1) (:span 4 12)))\n (:hscopes ((:id . :x3.268.1) (:span 4 153)))\n (:identifiers (:sid . :s3.268) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101050@unknown@formal@none@1@S@Thus, the background sequences used by SCOPE and the other programs may not be representative of the ""true"" background model of enhancers, leading to inaccurate statistics.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n (:id . 44))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 20)\n (:start . 10) (:id . 45))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 30)\n (:start . 21) (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 35) (:start . 31)\n (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 38) (:start . 36)\n (:id . 48))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 44) (:start . 39)\n (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n (:id . 51))\n ((:tag . "JJ") (:stem . "other") (:form . 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"''") (:form . "”") (:end . 109) (:start . 108)\n (:id . 63))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 120)\n (:start . 110) (:id . 64))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 126)\n (:start . 121) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n (:id . 66))\n ((:tag . "NNS") (:stem . "enhancer") (:form . "enhancers") (:end . 139)\n (:start . 130) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n (:id . 68))\n ((:tag . "VBG") (:stem . "lead") (:form . "leading") (:end . 148)\n (:start . 141) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 151) (:start . 149)\n (:id . 70))\n ((:tag . "JJ") (:stem . "inaccurate") (:form . "inaccurate") (:end . 162)\n (:start . 152) (:id . 71))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 173)\n (:start . 163) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n (:id . 73)))@@@1@32@((:hcues ((:id . :x3.270.2) (:span 68 71)))\n (:ncues ((:id . :x3.270.1) (:span 72 75)))\n (:hscopes ((:id . :x3.270.2) (:span 68 173)))\n (:nscopes ((:id . :x3.270.1) (:span 72 173)))\n (:identifiers (:sid . :s3.270) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101051@unknown@formal@none@1@S@The persistently poor performance of motif finders on Drosophila regulons thus highlights the importance of using well-defined background sequences to calibrate the statistics of the objective functions being optimized.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "persistently") (:form . "persistently") (:end . 16)\n (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "poor") (:form . "poor") (:end . 21) (:start . 17)\n (:id . 44))\n ((:tag . "NN") (:stem . "performance") (:form . 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(:end . 106) (:start . 105)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.272) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101053@unknown@formal@none@1@S@It is possible that using such algorithms to define a collection of background enhancer sequences may improve the performance of SCOPE, as well as that of the other motif finders, on Drosophila.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 14)\n (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 25) (:start . 20)\n (:id . 46))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 30) (:start . 26)\n (:id . 47))\n ((:tag . 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"DT") (:stem . "the") (:form . "the") (:end . 158) (:start . 155)\n (:id . 69))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 164)\n (:start . 159) (:id . 70))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 170)\n (:start . 165) (:id . 71))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 178)\n (:start . 171) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 179) (:start . 178)\n (:id . 73))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 182) (:start . 180)\n (:id . 74))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 193)\n (:start . 183) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n (:id . 76)))@@@1@35@((:hcues ((:id . :x3.273.1) (:span 98 101)) ((:id . :x3.273.2) (:span 6 14)))\n (:hscopes ((:id . :x3.273.1) (:span 98 193))\n ((:id . :x3.273.2) (:span 6 193)))\n (:identifiers (:sid . :s3.273) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101054@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s3.274) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Title|)))@oe@9-2-2011 5101055@unknown@formal@none@1@S@Ensemble methods hold the potential for providing improvements in motif finding accuracy without resorting to the use of additional data (such as phylogenetic information or characterization of the domain structure of the transcription factor), which are not always available.@(((:tag . 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"(") (:end . 138) (:start . 137)\n (:id . 62))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 142) (:start . 138)\n (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 145) (:start . 143)\n (:id . 64))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 158)\n (:start . 146) (:id . 65))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 170)\n (:start . 159) (:id . 66))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 173) (:start . 171)\n (:id . 67))\n ((:tag . "NN") (:stem . "characterization") (:form . "characterization")\n (:end . 190) (:start . 174) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 193) (:start . 191)\n (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 197) (:start . 194)\n (:id . 70))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 204)\n (:start . 198) (:id . 71))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 214)\n (:start . 205) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 217) (:start . 215)\n (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 221) (:start . 218)\n (:id . 74))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n (:end . 235) (:start . 222) (:id . 75))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 242)\n (:start . 236) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 243) (:start . 242)\n (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 244) (:start . 243)\n (:id . 78))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 250)\n (:start . 245) (:id . 79))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 254) (:start . 251)\n (:id . 80))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 258) (:start . 255)\n (:id . 81))\n ((:tag . "RB") (:stem . "always") (:form . "always") (:end . 265)\n (:start . 259) (:id . 82))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 275)\n (:start . 266) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 276) (:start . 275)\n (:id . 84)))@@@1@43@((:ncues ((:id . :x3.275.1) (:span 89 96)))\n (:nscopes ((:id . :x3.275.1) (:span 89 275)))\n (:identifiers (:sid . :s3.275) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101056@unknown@formal@none@1@S@Typically, ensemble learning methods are plagued with certain liabilities, such as increased runtimes, logistical complexity and a multiplicity of nuisance parameters, all of which grow with the number of programs run.@(((:tag . "RB") (:stem . "typically") (:form . "Typically") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "VB") (:stem . "ensemble") (:form . "ensemble") (:end . 19)\n (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "learning") (:form . "learning") (:end . 28)\n (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 36)\n (:start . 29) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 40) (:start . 37)\n (:id . 47))\n ((:tag . "VBN") (:stem . "plague") (:form . "plagued") (:end . 48)\n (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 53) (:start . 49)\n (:id . 49))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 61)\n (:start . 54) (:id . 50))\n ((:tag . "NNS") (:stem . "liability") (:form . "liabilities") (:end . 73)\n (:start . 62) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n (:id . 52))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 79) (:start . 75)\n (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 82) (:start . 80)\n (:id . 54))\n ((:tag . 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(:end . 201) (:start . 200)\n (:id . 81)))@@@1@40@((:identifiers (:sid . :s3.284) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101065@unknown@formal@none@1@S@The Phi score can be defined as follows: let U be a unique numbering of all the bases in the upstream sequences of a given gene set, and IU(m) ⊆ U be the set of bases that are covered by actual instances of m in U.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Phi") (:form . "Phi") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 17) (:start . 14)\n (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 20) (:start . 18)\n (:id . 46))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 28)\n (:start . 21) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 31) (:start . 29)\n (:id . 48))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 39)\n (:start . 32) (:id . 49))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 40) (:start . 39)\n (:id . 50))\n ((:tag . "VB") (:stem . "let") (:form . "let") (:end . 44) (:start . 41)\n (:id . 51))\n ((:tag . "NNP") (:stem . "U") (:form . "U") (:end . 46) (:start . 45)\n (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 49) (:start . 47)\n (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n (:id . 54))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 58)\n (:start . 52) (:id . 55))\n ((:tag . "NN") (:stem . "numbering") (:form . "numbering") (:end . 68)\n (:start . 59) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n (:id . 57))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 75) (:start . 72)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n (:id . 59))\n ((:tag . "NNS") (:stem . "base") (:form . "bases") (:end . 85) (:start . 80)\n (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n (:id . 62))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 101)\n (:start . 93) (:id . 63))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 111)\n (:start . 102) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 116) (:start . 115)\n (:id . 66))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 122)\n (:start . 117) (:id . 67))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 127) (:start . 123)\n (:id . 68))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 131) (:start . 128)\n (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 136) (:start . 133)\n (:id . 71))\n ((:tag . "NNP") (:stem . "IU(m)") (:form . "IU(m)") (:end . 142)\n (:start . 137) (:id . 72))\n ((:tag . "NNP") (:stem . "⊆") (:form . "⊆") (:end . 144) (:start . 143)\n (:id . 73))\n ((:tag . "NNP") (:stem . "U") (:form . "U") (:end . 146) (:start . 145)\n (:id . 74))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 149) (:start . 147)\n (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n (:id . 76))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 157) (:start . 154)\n (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 160) (:start . 158)\n (:id . 78))\n ((:tag . "NNS") (:stem . "base") (:form . "bases") (:end . 166)\n (:start . 161) (:id . 79))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 171) (:start . 167)\n (:id . 80))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 175) (:start . 172)\n (:id . 81))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 183)\n (:start . 176) (:id . 82))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 186) (:start . 184)\n (:id . 83))\n ((:tag . "JJ") (:stem . "actual") (:form . "actual") (:end . 193)\n (:start . 187) (:id . 84))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 203)\n (:start . 194) (:id . 85))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 206) (:start . 204)\n (:id . 86))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 208) (:start . 207)\n (:id . 87))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 211) (:start . 209)\n (:id . 88))\n ((:tag . "NNP") (:stem . "U") (:form . "U") (:end . 213) (:start . 212)\n (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n (:id . 90)))@@@1@49@((:identifiers (:sid . :s3.285) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101066@unknown@formal@none@1@S@Phi is then defined as the ratio of the number of bases occupied by the actual instances of both the motifs, to the total number of bases occupied by the actual instances of either of the two motifs:@(((:tag . "NNP") (:stem . "Phi") (:form . "Phi") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 6) (:start . 4)\n (:id . 43))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 19)\n (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 22) (:start . 20)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 47))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 32) (:start . 27)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 50))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 46)\n (:start . 40) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n (:id . 52))\n ((:tag . "NNS") (:stem . "base") (:form . "bases") (:end . 55) (:start . 50)\n (:id . 53))\n ((:tag . "VBN") (:stem . "occupy") (:form . "occupied") (:end . 64)\n (:start . 56) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 67) (:start . 65)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n (:id . 56))\n ((:tag . "JJ") (:stem . "actual") (:form . "actual") (:end . 78)\n (:start . 72) (:id . 57))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 88)\n (:start . 79) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n (:id . 59))\n ((:tag . "PDT") (:stem . "both") (:form . "both") (:end . 96) (:start . 92)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n (:id . 61))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 107)\n (:start . 101) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 111) (:start . 109)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n (:id . 65))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 121)\n (:start . 116) (:id . 66))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 128)\n (:start . 122) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n (:id . 68))\n ((:tag . "NNS") (:stem . "base") (:form . "bases") (:end . 137)\n (:start . 132) (:id . 69))\n ((:tag . "VBN") (:stem . "occupy") (:form . "occupied") (:end . 146)\n (:start . 138) (:id . 70))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 149) (:start . 147)\n (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n (:id . 72))\n ((:tag . "JJ") (:stem . "actual") (:form . "actual") (:end . 160)\n (:start . 154) (:id . 73))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 170)\n (:start . 161) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 173) (:start . 171)\n (:id . 75))\n ((:tag . "DT") (:stem . "either") (:form . "either") (:end . 180)\n (:start . 174) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 183) (:start . 181)\n (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 187) (:start . 184)\n (:id . 78))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 191) (:start . 188)\n (:id . 79))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 198)\n (:start . 192) (:id . 80))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 199) (:start . 198)\n (:id . 81)))@@@1@40@((:identifiers (:sid . :s3.286) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101067@unknown@formal@none@1@S@ΦU(m1, m2) = [IU(m1) ∩ IU(m2)]/[IU(m1) ∪ IU(m2)].@(((:tag . "NNP") (:stem . "ΦU(m1") (:form . "ΦU(m1") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "m2") (:form . "m2") (:end . 9) (:start . 7)\n (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 10) (:start . 9)\n (:id . 45))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 12) (:start . 11)\n (:id . 46))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 14) (:start . 13)\n (:id . 47))\n ((:tag . "FW") (:stem . "IU(m1)") (:form . "IU(m1)") (:end . 20)\n (:start . 14) (:id . 48))\n ((:tag . "NN") (:stem . "∩") (:form . "∩") (:end . 22) (:start . 21)\n (:id . 49))\n ((:tag . "FW") (:stem . "IU(m2)]/[IU(m1)") (:form . "IU(m2)]/[IU(m1)")\n (:end . 38) (:start . 23) (:id . 50))\n ((:tag . "NN") (:stem . "∪") (:form . "∪") (:end . 40) (:start . 39)\n (:id . 51))\n ((:tag . "FW") (:stem . "IU(m2)") (:form . "IU(m2)") (:end . 47)\n (:start . 41) (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 48) (:start . 47)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.287) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101068@unknown@formal@none@1@S@This metric therefore takes both false positives and false negatives into account at the level of the individual bases that are actually covered by the motif.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "metric") (:form . "metric") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 21)\n (:start . 12) (:id . 44))\n ((:tag . "VBZ") (:stem . "take") (:form . "takes") (:end . 27) (:start . 22)\n (:id . 45))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 32) (:start . 28)\n (:id . 46))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 38) (:start . 33)\n (:id . 47))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 48)\n (:start . 39) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n (:id . 49))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 58) (:start . 53)\n (:id . 50))\n ((:tag . "NNS") (:stem . "negative") (:form . "negatives") (:end . 68)\n (:start . 59) (:id . 51))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 73) (:start . 69)\n (:id . 52))\n ((:tag . "NN") (:stem . "account") (:form . "account") (:end . 81)\n (:start . 74) (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 84) (:start . 82)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n (:id . 55))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 94) (:start . 89)\n (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n (:id . 58))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 112)\n (:start . 102) (:id . 59))\n ((:tag . "NNS") (:stem . "base") (:form . "bases") (:end . 118)\n (:start . 113) (:id . 60))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 123) (:start . 119)\n (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 127) (:start . 124)\n (:id . 62))\n ((:tag . "RB") (:stem . "actually") (:form . "actually") (:end . 136)\n (:start . 128) (:id . 63))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 144)\n (:start . 137) (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 147) (:start . 145)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n (:id . 66))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 157)\n (:start . 152) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s3.288) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101070@unknown@formal@none@1@S@Changing the denominator of the Phi equation to be IU(mi) yields the sensitivity (if mi represents the true binding sites) or the positive predictive value (PPV, if mi represents the reported binding sites).@(((:tag . "VBG") (:stem . "change") (:form . "Changing") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 43))\n ((:tag . "NN") (:stem . "denominator") (:form . "denominator") (:end . 24)\n (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Phi") (:form . "Phi") (:end . 35) (:start . 32)\n (:id . 47))\n ((:tag . "NN") (:stem . "equation") (:form . "equation") (:end . 44)\n (:start . 36) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 50) (:start . 48)\n (:id . 50))\n ((:tag . "JJ") (:stem . "IU(mi)") (:form . "IU(mi)") (:end . 57)\n (:start . 51) (:id . 51))\n ((:tag . "VBZ") (:stem . "yield") (:form . "yields") (:end . 64)\n (:start . 58) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n (:id . 53))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 80)\n (:start . 69) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n (:id . 55))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 84) (:start . 82)\n (:id . 56))\n ((:tag . "NN") (:stem . "mi") (:form . "mi") (:end . 87) (:start . 85)\n (:id . 57))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 98)\n (:start . 88) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n (:id . 59))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 107) (:start . 103)\n (:id . 60))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 115)\n (:start . 108) (:id . 61))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 121)\n (:start . 116) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 122) (:start . 121)\n (:id . 63))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 125) (:start . 123)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n (:id . 65))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 138)\n (:start . 130) (:id . 66))\n ((:tag . "JJ") (:stem . "predictive") (:form . "predictive") (:end . 149)\n (:start . 139) (:id . 67))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 155)\n (:start . 150) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 157) (:start . 156)\n (:id . 69))\n ((:tag . "NNP") (:stem . "PPV") (:form . "PPV") (:end . 160) (:start . 157)\n (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n (:id . 71))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 164) (:start . 162)\n (:id . 72))\n ((:tag . "NN") (:stem . "mi") (:form . "mi") (:end . 167) (:start . 165)\n (:id . 73))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 178)\n (:start . 168) (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 182) (:start . 179)\n (:id . 75))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 191)\n (:start . 183) (:id . 76))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 199)\n (:start . 192) (:id . 77))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 205)\n (:start . 200) (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 206) (:start . 205)\n (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n (:id . 80)))@@@1@39@((:identifiers (:sid . :s3.290) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101071@unknown@formal@none@1@S@See Additional file 1, section S3, for a discussion on the use of Phi score for measuring accuracy.@(((:tag . "VB") (:stem . "see") (:form . "See") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 21) (:start . 20)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n (:id . 46))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 30)\n (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "s3") (:form . "S3") (:end . 33) (:start . 31)\n (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 38) (:start . 35)\n (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 40) (:start . 39)\n (:id . 51))\n ((:tag . "NN") (:stem . "discussion") (:form . "discussion") (:end . 51)\n (:start . 41) (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 54) (:start . 52)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n (:id . 54))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 62) (:start . 59)\n (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n (:id . 56))\n ((:tag . "NNP") (:stem . "Phi") (:form . "Phi") (:end . 69) (:start . 66)\n (:id . 57))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 75) (:start . 70)\n (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 79) (:start . 76)\n (:id . 59))\n ((:tag . "VBG") (:stem . "measure") (:form . "measuring") (:end . 89)\n (:start . 80) (:id . 60))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 98)\n (:start . 90) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.291) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101072@unknown@formal@none@1@S@Objective functions for Statistical Significance@(((:tag . "JJ") (:stem . "objective") (:form . "Objective") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 19)\n (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 23) (:start . 20)\n (:id . 44))\n ((:tag . "JJ") (:stem . "statistical") (:form . "Statistical") (:end . 35)\n (:start . 24) (:id . 45))\n ((:tag . "NN") (:stem . "significance") (:form . "Significance") (:end . 48)\n (:start . 36) (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.292) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101073@unknown@formal@none@1@S@In line with other motif finders, we have used statistical significance as a surrogate for biological significance.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 24) (:start . 19)\n (:id . 46))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 32)\n (:start . 25) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 36) (:start . 34)\n (:id . 49))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 41) (:start . 37)\n (:id . 50))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 46) (:start . 42)\n (:id . 51))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 58)\n (:start . 47) (:id . 52))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 71)\n (:start . 59) (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 74) (:start . 72)\n (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 76) (:start . 75)\n (:id . 55))\n ((:tag . "NN") (:stem . "surrogate") (:form . "surrogate") (:end . 86)\n (:start . 77) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 90) (:start . 87)\n (:id . 57))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 101)\n (:start . 91) (:id . 58))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 114)\n (:start . 102) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.293) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101074@unknown@formal@none@1@S@Since the latter cannot be defined without data that obviates the need for computational motif finding, objective functions that approximate biological significance are critical.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "JJ") (:stem . "latter") (:form . "latter") (:end . 16)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "cannot") (:form . "cannot") (:end . 23)\n (:start . 17) (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 34)\n (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 42)\n (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 47) (:start . 43)\n (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 52) (:start . 48)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "obviate") (:form . "obviates") (:end . 61)\n (:start . 53) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n (:id . 52))\n ((:tag . "NN") (:stem . "need") (:form . "need") (:end . 70) (:start . 66)\n (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 74) (:start . 71)\n (:id . 54))\n ((:tag . "JJ") (:stem . "computational") (:form . "computational")\n (:end . 88) (:start . 75) (:id . 55))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 94) (:start . 89)\n (:id . 56))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 102)\n (:start . 95) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n (:id . 58))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 113)\n (:start . 104) (:id . 59))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 123)\n (:start . 114) (:id . 60))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 128) (:start . 124)\n (:id . 61))\n ((:tag . "VBP") (:stem . "approximate") (:form . "approximate") (:end . 140)\n (:start . 129) (:id . 62))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 151)\n (:start . 141) (:id . 63))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 164)\n (:start . 152) (:id . 64))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 168) (:start . 165)\n (:id . 65))\n ((:tag . "JJ") (:stem . "critical") (:form . "critical") (:end . 177)\n (:start . 169) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n (:id . 67)))@@@1@26@((:ncues ((:id . :x3.294.1) (:span 35 42)) ((:id . :x3.294.2) (:span 17 23)))\n (:nscopes ((:id . :x3.294.1) (:span 35 102))\n ((:id . :x3.294.2) (:span 6 102)))\n (:identifiers (:sid . :s3.294) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101075@unknown@formal@none@1@S@In this section, we detail the objective functions we used and their effect on SCOPE's performance.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 15)\n (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 19) (:start . 17)\n (:id . 46))\n ((:tag . "VBP") (:stem . "detail") (:form . "detail") (:end . 26)\n (:start . 20) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n (:id . 48))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 40)\n (:start . 31) (:id . 49))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 50)\n (:start . 41) (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 53) (:start . 51)\n (:id . 51))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 58) (:start . 54)\n (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n (:id . 53))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 68)\n (:start . 63) (:id . 54))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 75)\n (:start . 69) (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 78) (:start . 76)\n (:id . 56))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 84) (:start . 79)\n (:id . 57))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 86) (:start . 84)\n (:id . 58))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 98)\n (:start . 87) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.295) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101076@unknown@formal@none@1@S@For any motif m, each objective function provides a definition for p(m), the probability of observing a motif with the same sufficient statistics as m assuming a particular null model.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 15) (:start . 14)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n (:id . 46))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 21) (:start . 17)\n (:id . 47))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 31)\n (:start . 22) (:id . 48))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 40)\n (:start . 32) (:id . 49))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 49)\n (:start . 41) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n (:id . 51))\n ((:tag . "NN") (:stem . "definition") (:form . "definition") (:end . 62)\n (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 66) (:start . 63)\n (:id . 53))\n ((:tag . "NNP") (:stem . "p(m)") (:form . "p(m)") (:end . 71) (:start . 67)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n (:id . 56))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 88)\n (:start . 77) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n (:id . 58))\n ((:tag . "VBG") (:stem . "observe") (:form . "observing") (:end . 101)\n (:start . 92) (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 103) (:start . 102)\n (:id . 60))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 109)\n (:start . 104) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 114) (:start . 110)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n (:id . 63))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 123) (:start . 119)\n (:id . 64))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 134)\n (:start . 124) (:id . 65))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 145)\n (:start . 135) (:id . 66))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 148) (:start . 146)\n (:id . 67))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 150) (:start . 149)\n (:id . 68))\n ((:tag . "VBG") (:stem . "assume") (:form . "assuming") (:end . 159)\n (:start . 151) (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 161) (:start . 160)\n (:id . 70))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 172)\n (:start . 162) (:id . 71))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 177) (:start . 173)\n (:id . 72))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 183)\n (:start . 178) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.296) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101077@unknown@formal@none@1@S@This p-value is used in the computation of the Sig score (see Results).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "p-value") (:form . "p-value") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 23) (:start . 21)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "computation") (:form . "computation") (:end . 39)\n (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Sig") (:form . "Sig") (:end . 50) (:start . 47)\n (:id . 51))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 56) (:start . 51)\n (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n (:id . 53))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 61) (:start . 58)\n (:id . 54))\n ((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 69)\n (:start . 62) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.297) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101078@unknown@formal@none@1@S@Overrepresentation@(((:tag . "NNP") (:stem . "Overrepresentation") (:form . "Overrepresentation")\n (:end . 18) (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s3.298) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101080@unknown@formal@none@1@S@In the context of consensus motifs, overrepresentation is expressed in terms of a multinomial model, in which each position i in each gene j is a random variable Xij that can take on any motif allowed by the particular motif model.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 14)\n (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 27)\n (:start . 18) (:id . 46))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 34)\n (:start . 28) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n (:id . 48))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n (:end . 54) (:start . 36) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 57) (:start . 55)\n (:id . 50))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 67)\n (:start . 58) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 70) (:start . 68)\n (:id . 52))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 76) (:start . 71)\n (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 81) (:start . 80)\n (:id . 55))\n ((:tag . "JJ") (:stem . "multinomial") (:form . "multinomial") (:end . 93)\n (:start . 82) (:id . 56))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 99) (:start . 94)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 109)\n (:start . 104) (:id . 60))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 114) (:start . 110)\n (:id . 61))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 123)\n (:start . 115) (:id . 62))\n ((:tag . "NN") (:stem . "i") (:form . "i") (:end . 125) (:start . 124)\n (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 128) (:start . 126)\n (:id . 64))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 133) (:start . 129)\n (:id . 65))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 138) (:start . 134)\n (:id . 66))\n ((:tag . "NN") (:stem . "j") (:form . "j") (:end . 140) (:start . 139)\n (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 143) (:start . 141)\n (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 145) (:start . 144)\n (:id . 69))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 152)\n (:start . 146) (:id . 70))\n ((:tag . "JJ") (:stem . "variable") (:form . "variable") (:end . 161)\n (:start . 153) (:id . 71))\n ((:tag . "NNP") (:stem . "Xij") (:form . "Xij") (:end . 165) (:start . 162)\n (:id . 72))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 170) (:start . 166)\n (:id . 73))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 174) (:start . 171)\n (:id . 74))\n ((:tag . "VB") (:stem . "take") (:form . "take") (:end . 179) (:start . 175)\n (:id . 75))\n ((:tag . "RP") (:stem . "on") (:form . "on") (:end . 182) (:start . 180)\n (:id . 76))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 186) (:start . 183)\n (:id . 77))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 192)\n (:start . 187) (:id . 78))\n ((:tag . "VBN") (:stem . "allow") (:form . "allowed") (:end . 200)\n (:start . 193) (:id . 79))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 203) (:start . 201)\n (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 207) (:start . 204)\n (:id . 81))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 218)\n (:start . 208) (:id . 82))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 224)\n (:start . 219) (:id . 83))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 230)\n (:start . 225) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 231) (:start . 230)\n (:id . 85)))@@@1@44@((:identifiers (:sid . :s3.300) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101081@unknown@formal@none@1@S@The probability of seeing m at least C(m) times in the regulon can be approximated by the Poisson distribution: p(m) = ∑k≥C(m) [(λke-λ)/k! ] where λ is the expectation of C(m) with respect to the null motif distribution and the number of positions in the regulon.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n (:id . 44))\n ((:tag . "VBG") (:stem . "see") (:form . "seeing") (:end . 25) (:start . 19)\n (:id . 45))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 27) (:start . 26)\n (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 30) (:start . 28)\n (:id . 47))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 36) (:start . 31)\n (:id . 48))\n ((:tag . "CD") (:stem . "C(m)") (:form . "C(m)") (:end . 41) (:start . 37)\n (:id . 49))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 47) (:start . 42)\n (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n (:id . 52))\n ((:tag . "NN") (:stem . "regulon") (:form . "regulon") (:end . 62)\n (:start . 55) (:id . 53))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 66) (:start . 63)\n (:id . 54))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 69) (:start . 67)\n (:id . 55))\n ((:tag . "VBN") (:stem . "approximate") (:form . "approximated") (:end . 82)\n (:start . 70) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 85) (:start . 83)\n (:id . 57))\n ((:tag . "DT") (:stem . 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(:end . 138) (:start . 137)\n (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 140) (:start . 139)\n (:id . 69))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 146)\n (:start . 141) (:id . 70))\n ((:tag . "NNP") (:stem . "λ") (:form . "λ") (:end . 148) (:start . 147)\n (:id . 71))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 151) (:start . 149)\n (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n (:id . 73))\n ((:tag . "NN") (:stem . "expectation") (:form . "expectation") (:end . 167)\n (:start . 156) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 170) (:start . 168)\n (:id . 75))\n ((:tag . "NN") (:stem . "C(m)") (:form . "C(m)") (:end . 175) (:start . 171)\n (:id . 76))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 180) (:start . 176)\n (:id . 77))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 188)\n (:start . 181) (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 191) (:start . 189)\n (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 195) (:start . 192)\n (:id . 80))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 200) (:start . 196)\n (:id . 81))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 206)\n (:start . 201) (:id . 82))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 219)\n (:start . 207) (:id . 83))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 223) (:start . 220)\n (:id . 84))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 227) (:start . 224)\n (:id . 85))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 234)\n (:start . 228) (:id . 86))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 237) (:start . 235)\n (:id . 87))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 247)\n (:start . 238) (:id . 88))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 250) (:start . 248)\n (:id . 89))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 254) (:start . 251)\n (:id . 90))\n ((:tag . "NN") (:stem . "regulon") (:form . "regulon") (:end . 262)\n (:start . 255) (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 263) (:start . 262)\n (:id . 92)))@@@1@51@((:identifiers (:sid . :s3.301) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101082@unknown@formal@none@1@S@A detailed justification of this approach was given by Carlson et al. 11.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "detailed") (:form . "detailed") (:end . 10)\n (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "justification") (:form . "justification")\n (:end . 24) (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n (:id . 45))\n ((:tag . "DT") (:stem . 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(:end . 73) (:start . 72)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.302) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101083@unknown@formal@none@1@S@The expectation λ is most accurately modeled using Maximum Likelihood Estimators (MLEs) computed as the actual proportion of any given motif in the complete set of all upstream sequences in the genome 10.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "expectation") (:form . "expectation") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "λ") (:form . "λ") (:end . 17) (:start . 16)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 20) (:start . 18)\n (:id . 45))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 25) (:start . 21)\n (:id . 46))\n ((:tag . "RB") (:stem . "accurately") (:form . 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(:end . 204) (:start . 203)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s3.303) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101084@unknown@formal@none@1@S@These MLEs are implemented as lookups of exact substrings, which can be performed efficiently using a suffix array data structure 101112.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNPS") (:stem . "MLE") (:form . "MLEs") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "VBN") (:stem . "implement") (:form . "implemented") (:end . 26)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "NNS") (:stem . "lookup") (:form . "lookups") (:end . 37)\n (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . 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"NN") (:stem . "suffix") (:form . "suffix") (:end . 108)\n (:start . 102) (:id . 59))\n ((:tag . "NN") (:stem . "array") (:form . "array") (:end . 114)\n (:start . 109) (:id . 60))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 119)\n (:start . 115) (:id . 61))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 129)\n (:start . 120) (:id . 62))\n ((:tag . "CD") (:stem . "101112") (:form . "101112") (:end . 136)\n (:start . 130) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.304) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101085@unknown@formal@none@1@S@Coverage@(((:tag . "NNP") (:stem . "Coverage") (:form . "Coverage") (:end . 8)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s3.305) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101086@unknown@formal@none@1@S@A simple modification to the overrepresentation objective function is coverage, which is identical to overrepresentation with the modification that C(m) is the number of upstream regions in the regulon that have one or more instances of m and λ, the expectation of C(m), is determined from the proportion of upstream regions in the genome that contain the motif.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "simple") (:form . "simple") (:end . 8) (:start . 2)\n (:id . 43))\n ((:tag . "NN") (:stem . "modification") (:form . "modification") (:end . 21)\n (:start . 9) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 24) (:start . 22)\n (:id . 45))\n ((:tag . 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",") (:end . 270) (:start . 269)\n (:id . 87))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 273) (:start . 271)\n (:id . 88))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 284)\n (:start . 274) (:id . 89))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 289) (:start . 285)\n (:id . 90))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 293) (:start . 290)\n (:id . 91))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 304)\n (:start . 294) (:id . 92))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 307) (:start . 305)\n (:id . 93))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 316)\n (:start . 308) (:id . 94))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 324)\n (:start . 317) (:id . 95))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 327) (:start . 325)\n (:id . 96))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 331) (:start . 328)\n (:id . 97))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 338)\n (:start . 332) (:id . 98))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 343) (:start . 339)\n (:id . 99))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 351)\n (:start . 344) (:id . 100))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 355) (:start . 352)\n (:id . 101))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 361)\n (:start . 356) (:id . 102))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 362) (:start . 361)\n (:id . 103)))@@@1@62@((:identifiers (:sid . :s3.306) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101087@unknown@formal@none@1@S@While this objective function prevents a single upstream region from dominating a motif's score, it fails to account for multiple instances of a binding site in a single gene that may arise due to cooperative binding.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 20)\n (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 29)\n (:start . 21) (:id . 45))\n ((:tag . "VBZ") (:stem . "prevent") (:form . "prevents") (:end . 38)\n (:start . 30) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 40) (:start . 39)\n (:id . 47))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 47)\n (:start . 41) (:id . 48))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 56)\n (:start . 48) (:id . 49))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 63)\n (:start . 57) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 68) (:start . 64)\n (:id . 51))\n ((:tag . "VBG") (:stem . "dominate") (:form . "dominating") (:end . 79)\n (:start . 69) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 81) (:start . 80)\n (:id . 53))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 87) (:start . 82)\n (:id . 54))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 89) (:start . 87)\n (:id . 55))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 95) (:start . 90)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n (:id . 57))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 99) (:start . 97)\n (:id . 58))\n ((:tag . "VBZ") (:stem . "fail") (:form . "fails") (:end . 105)\n (:start . 100) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 108) (:start . 106)\n (:id . 60))\n ((:tag . "VB") (:stem . "account") (:form . "account") (:end . 116)\n (:start . 109) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 120) (:start . 117)\n (:id . 62))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 129)\n (:start . 121) (:id . 63))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 139)\n (:start . 130) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 144) (:start . 143)\n (:id . 66))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 152)\n (:start . 145) (:id . 67))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 157) (:start . 153)\n (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 160) (:start . 158)\n (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 162) (:start . 161)\n (:id . 70))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 169)\n (:start . 163) (:id . 71))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 174) (:start . 170)\n (:id . 72))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 179) (:start . 175)\n (:id . 73))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 183) (:start . 180)\n (:id . 74))\n ((:tag . "VB") (:stem . "arise") (:form . "arise") (:end . 189)\n (:start . 184) (:id . 75))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 193) (:start . 190)\n (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 196) (:start . 194)\n (:id . 77))\n ((:tag . "JJ") (:stem . "cooperative") (:form . "cooperative") (:end . 208)\n (:start . 197) (:id . 78))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 216)\n (:start . 209) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 217) (:start . 216)\n (:id . 80)))@@@1@39@((:hcues ((:id . :x3.307.1) (:span 180 183)))\n (:ncues ((:id . :x3.307.2) (:span 100 105)))\n (:hscopes ((:id . :x3.307.1) (:span 180 216)))\n (:nscopes ((:id . :x3.307.2) (:span 100 216)))\n (:identifiers (:sid . :s3.307) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101088@unknown@formal@none@1@S@Positional bias@(((:tag . "JJ") (:stem . "positional") (:form . "Positional") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "bia") (:form . "bias") (:end . 15) (:start . 11)\n (:id . 43)))@@@1@2@((:identifiers (:sid . :s3.308) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101090@unknown@formal@none@1@S@One well known example is TBP (TATA-binding protein), which localizes the RNA polymerase complex by binding the TATA-box motif roughly 25 bases upstream of the transcription start site 30.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 22)\n (:start . 15) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n (:id . 46))\n ((:tag . "NNP") (:stem . "TBP") (:form . "TBP") (:end . 29) (:start . 26)\n (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 31) (:start . 30)\n (:id . 48))\n ((:tag . "JJ") (:stem . "tata-binding") (:form . "TATA-binding") (:end . 43)\n (:start . 31) (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 51)\n (:start . 44) (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 59) (:start . 54)\n (:id . 53))\n ((:tag . "VBZ") (:stem . "localize") (:form . "localizes") (:end . 69)\n (:start . 60) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n (:id . 55))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 77) (:start . 74)\n (:id . 56))\n ((:tag . "NN") (:stem . "polymerase") (:form . "polymerase") (:end . 88)\n (:start . 78) (:id . 57))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 96)\n (:start . 89) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 99) (:start . 97)\n (:id . 59))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 107)\n (:start . 100) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n (:id . 61))\n ((:tag . "NN") (:stem . "tata-box") (:form . "TATA-box") (:end . 120)\n (:start . 112) (:id . 62))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 126)\n (:start . 121) (:id . 63))\n ((:tag . "RB") (:stem . "roughly") (:form . "roughly") (:end . 134)\n (:start . 127) (:id . 64))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 137) (:start . 135)\n (:id . 65))\n ((:tag . "NNS") (:stem . "base") (:form . "bases") (:end . 143)\n (:start . 138) (:id . 66))\n ((:tag . "RB") (:stem . "upstream") (:form . "upstream") (:end . 152)\n (:start . 144) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n (:id . 69))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n (:end . 173) (:start . 160) (:id . 70))\n ((:tag . "NN") (:stem . "start") (:form . "start") (:end . 179)\n (:start . 174) (:id . 71))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 184) (:start . 180)\n (:id . 72))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 187) (:start . 185)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.310) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101091@unknown@formal@none@1@S@While other examples of binding sites with positional restrictions are well known, few motif finders incorporate position in their scoring function.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 20)\n (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 45))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 31)\n (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 37) (:start . 32)\n (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 42) (:start . 38)\n (:id . 48))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 53)\n (:start . 43) (:id . 49))\n ((:tag . "NNS") (:stem . "restriction") (:form . "restrictions") (:end . 66)\n (:start . 54) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 70) (:start . 67)\n (:id . 51))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 75) (:start . 71)\n (:id . 52))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 81) (:start . 76)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n (:id . 54))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 86) (:start . 83)\n (:id . 55))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 92) (:start . 87)\n (:id . 56))\n ((:tag . "NNS") (:stem . "finder") (:form . "finders") (:end . 100)\n (:start . 93) (:id . 57))\n ((:tag . "JJ") (:stem . "incorporate") (:form . "incorporate") (:end . 112)\n (:start . 101) (:id . 58))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 121)\n (:start . 113) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 124) (:start . 122)\n (:id . 60))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 130)\n (:start . 125) (:id . 61))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 138)\n (:start . 131) (:id . 62))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 147)\n (:start . 139) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.311) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101092@unknown@formal@none@1@S@In the case where all upstream regions are the same length, the Kolmogorov-Smirnov (KS) statistic provides a natural test for positional bias.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 17) (:start . 12)\n (:id . 45))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 30)\n (:start . 22) (:id . 47))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 38)\n (:start . 31) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 42) (:start . 39)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n (:id . 50))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 51) (:start . 47)\n (:id . 51))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 58)\n (:start . 52) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Kolmogorov-Smirnov") (:form . "Kolmogorov-Smirnov")\n (:end . 82) (:start . 64) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n (:id . 56))\n ((:tag . "NNP") (:stem . "KS") (:form . "KS") (:end . 86) (:start . 84)\n (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 87) (:start . 86)\n (:id . 58))\n ((:tag . "JJ") (:stem . "statistic") (:form . "statistic") (:end . 97)\n (:start . 88) (:id . 59))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 106)\n (:start . 98) (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 108) (:start . 107)\n (:id . 61))\n ((:tag . "JJ") (:stem . "natural") (:form . "natural") (:end . 116)\n (:start . 109) (:id . 62))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 121) (:start . 117)\n (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 125) (:start . 122)\n (:id . 64))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 136)\n (:start . 126) (:id . 65))\n ((:tag . "NN") (:stem . "bias") (:form . "bias") (:end . 141) (:start . 137)\n (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s3.312) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101093@unknown@formal@none@1@S@The Kolmogorov-Smirnov (KS) statistic is a non-parametric statistic that measures the probability that two samples are drawn from the same distribution.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Kolmogorov-Smirnov") (:form . "Kolmogorov-Smirnov")\n (:end . 22) (:start . 4) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 24) (:start . 23)\n (:id . 44))\n ((:tag . "NNP") (:stem . "KS") (:form . "KS") (:end . 26) (:start . 24)\n (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 27) (:start . 26)\n (:id . 46))\n ((:tag . "JJ") (:stem . "statistic") (:form . "statistic") (:end . 37)\n (:start . 28) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 40) (:start . 38)\n (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 42) (:start . 41)\n (:id . 49))\n ((:tag . "JJ") (:stem . "non-parametric") (:form . "non-parametric")\n (:end . 57) (:start . 43) (:id . 50))\n ((:tag . "NN") (:stem . "statistic") (:form . "statistic") (:end . 67)\n (:start . 58) (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 72) (:start . 68)\n (:id . 52))\n ((:tag . "VBZ") (:stem . "measure") (:form . "measures") (:end . 81)\n (:start . 73) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n (:id . 54))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 97)\n (:start . 86) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 102) (:start . 98)\n (:id . 56))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 106) (:start . 103)\n (:id . 57))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 114)\n (:start . 107) (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 118) (:start . 115)\n (:id . 59))\n ((:tag . "VBN") (:stem . "draw") (:form . "drawn") (:end . 124)\n (:start . 119) (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 129) (:start . 125)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n (:id . 62))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 138) (:start . 134)\n (:id . 63))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 151)\n (:start . 139) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.313) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101094@unknown@formal@none@1@S@Let X be the sample that we wish to compare to some reference sample Y.@(((:tag . "VB") (:stem . "let") (:form . "Let") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "X") (:form . "X") (:end . 5) (:start . 4)\n (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 8) (:start . 6)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 45))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 19)\n (:start . 13) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n (:id . 47))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 27) (:start . 25)\n (:id . 48))\n ((:tag . "VBP") (:stem . "wish") (:form . "wish") (:end . 32) (:start . 28)\n (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n (:id . 50))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 43)\n (:start . 36) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 46) (:start . 44)\n (:id . 52))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 51) (:start . 47)\n (:id . 53))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 61)\n (:start . 52) (:id . 54))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 68)\n (:start . 62) (:id . 55))\n ((:tag . "NN") (:stem . "y") (:form . "Y") (:end . 70) (:start . 69)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.314) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101095@unknown@formal@none@1@S@The KS statistic is defined to be the maximum absolute difference between the unbiased cumulative distribution functions of X and Y.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "KS") (:form . "KS") (:end . 6) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "statistic") (:form . "statistic") (:end . 16)\n (:start . 7) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 27)\n (:start . 20) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 33) (:start . 31)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n (:id . 49))\n ((:tag . "JJ") (:stem . "maximum") (:form . "maximum") (:end . 45)\n (:start . 38) (:id . 50))\n ((:tag . "JJ") (:stem . "absolute") (:form . "absolute") (:end . 54)\n (:start . 46) (:id . 51))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 65)\n (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 73)\n (:start . 66) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n (:id . 54))\n ((:tag . "JJ") (:stem . "unbiased") (:form . "unbiased") (:end . 86)\n (:start . 78) (:id . 55))\n ((:tag . "JJ") (:stem . "cumulative") (:form . "cumulative") (:end . 97)\n (:start . 87) (:id . 56))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 110)\n (:start . 98) (:id . 57))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 120)\n (:start . 111) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n (:id . 59))\n ((:tag . "NNP") (:stem . "X") (:form . "X") (:end . 125) (:start . 124)\n (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n (:id . 61))\n ((:tag . "NNP") (:stem . "Y") (:form . "Y") (:end . 131) (:start . 130)\n (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.315) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101096@unknown@formal@none@1@S@The KS statistic has a well-defined distribution from which a p-value can be easily computed.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "KS") (:form . "KS") (:end . 6) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "statistic") (:form . "statistic") (:end . 16)\n (:start . 7) (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n (:id . 46))\n ((:tag . "JJ") (:stem . "well-defined") (:form . "well-defined") (:end . 35)\n (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 48)\n (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 53) (:start . 49)\n (:id . 49))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 59) (:start . 54)\n (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 61) (:start . 60)\n (:id . 51))\n ((:tag . "NN") (:stem . "p-value") (:form . "p-value") (:end . 69)\n (:start . 62) (:id . 52))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 73) (:start . 70)\n (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 76) (:start . 74)\n (:id . 54))\n ((:tag . "RB") (:stem . "easily") (:form . "easily") (:end . 83)\n (:start . 77) (:id . 55))\n ((:tag . "VBN") (:stem . "compute") (:form . "computed") (:end . 92)\n (:start . 84) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.316) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101097@unknown@formal@none@1@S@Kuiper's variation was used to increase sensitivity in the tails of the distribution 31.@(((:tag . "NNP") (:stem . "Kuiper") (:form . "Kuiper") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 8) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "variation") (:form . "variation") (:end . 18)\n (:start . 9) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 27) (:start . 23)\n (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n (:id . 47))\n ((:tag . "VB") (:stem . "increase") (:form . "increase") (:end . 39)\n (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 51)\n (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n (:id . 51))\n ((:tag . "NNS") (:stem . "tail") (:form . "tails") (:end . 64) (:start . 59)\n (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n (:id . 54))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 84)\n (:start . 72) (:id . 55))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 87) (:start . 85)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.317) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101098@unknown@formal@none@1@S@In the context of motifs, we defined the test sample X for a motif m to be the set of starting positions (with respect to transcription start sites) of m in the regulon.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 14)\n (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n (:id . 45))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 24)\n (:start . 18) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n (:id . 47))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 28) (:start . 26)\n (:id . 48))\n ((:tag . "VBD") (:stem . "define") (:form . "defined") (:end . 36)\n (:start . 29) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n (:id . 50))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 45) (:start . 41)\n (:id . 51))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 52)\n (:start . 46) (:id . 52))\n ((:tag . "NN") (:stem . "x") (:form . "X") (:end . 54) (:start . 53)\n (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 58) (:start . 55)\n (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 60) (:start . 59)\n (:id . 55))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 66) (:start . 61)\n (:id . 56))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 68) (:start . 67)\n (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 74) (:start . 72)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n (:id . 60))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 82) (:start . 79)\n (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n (:id . 62))\n ((:tag . "VBG") (:stem . "start") (:form . "starting") (:end . 94)\n (:start . 86) (:id . 63))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 104)\n (:start . 95) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 110) (:start . 106)\n (:id . 66))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 118)\n (:start . 111) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 121) (:start . 119)\n (:id . 68))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n (:end . 135) (:start . 122) (:id . 69))\n ((:tag . "NN") (:stem . "start") (:form . "start") (:end . 141)\n (:start . 136) (:id . 70))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 147)\n (:start . 142) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n (:id . 73))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 153) (:start . 152)\n (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 156) (:start . 154)\n (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 160) (:start . 157)\n (:id . 76))\n ((:tag . "NN") (:stem . "regulon") (:form . "regulon") (:end . 168)\n (:start . 161) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n (:id . 78)))@@@1@37@((:identifiers (:sid . :s3.318) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101100@unknown@formal@none@1@S@Thus, pKS(m) is a measure of how m is localized differently in the regulon than in the genome as a whole.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "pKS(m)") (:form . "pKS(m)") (:end . 12)\n (:start . 6) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 17) (:start . 16)\n (:id . 46))\n ((:tag . "NN") (:stem . "measure") (:form . "measure") (:end . 25)\n (:start . 18) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n (:id . 48))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 32) (:start . 29)\n (:id . 49))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 34) (:start . 33)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 37) (:start . 35)\n (:id . 51))\n ((:tag . "VBN") (:stem . "localize") (:form . "localized") (:end . 47)\n (:start . 38) (:id . 52))\n ((:tag . "RB") (:stem . "differently") (:form . "differently") (:end . 59)\n (:start . 48) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n (:id . 55))\n ((:tag . "NN") (:stem . "regulon") (:form . "regulon") (:end . 74)\n (:start . 67) (:id . 56))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 79) (:start . 75)\n (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n (:id . 59))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 93)\n (:start . 87) (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 96) (:start . 94)\n (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 98) (:start . 97)\n (:id . 62))\n ((:tag . "NN") (:stem . "whole") (:form . "whole") (:end . 104) (:start . 99)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.320) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101101@unknown@formal@none@1@S@It is also possible to define Y as the uniform distribution; however, we found that many motifs had non-uniform distributions throughout all upstream regions of the genome, possibly as an artifact of the non-uniform AT/CG distributions in upstream regions 32.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 10) (:start . 6)\n (:id . 44))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 19)\n (:start . 11) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 22) (:start . 20)\n (:id . 46))\n ((:tag . "VB") (:stem . "define") (:form . "define") (:end . 29)\n (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "y") (:form . "Y") (:end . 31) (:start . 30)\n (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 34) (:start . 32)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n (:id . 50))\n ((:tag . "JJ") (:stem . "uniform") (:form . "uniform") (:end . 46)\n (:start . 39) (:id . 51))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 59)\n (:start . 47) (:id . 52))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 60) (:start . 59)\n (:id . 53))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 68)\n (:start . 61) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n (:id . 55))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 72) (:start . 70)\n (:id . 56))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 78) (:start . 73)\n (:id . 57))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 83) (:start . 79)\n (:id . 58))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 88) (:start . 84)\n (:id . 59))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 95)\n (:start . 89) (:id . 60))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 99) (:start . 96)\n (:id . 61))\n ((:tag . "JJ") (:stem . "non-uniform") (:form . "non-uniform") (:end . 111)\n (:start . 100) (:id . 62))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n (:end . 125) (:start . 112) (:id . 63))\n ((:tag . "IN") (:stem . "throughout") (:form . "throughout") (:end . 136)\n (:start . 126) (:id . 64))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 140) (:start . 137)\n (:id . 65))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 149)\n (:start . 141) (:id . 66))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 157)\n (:start . 150) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 160) (:start . 158)\n (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 164) (:start . 161)\n (:id . 69))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 171)\n (:start . 165) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 172) (:start . 171)\n (:id . 71))\n ((:tag . "RB") (:stem . "possibly") (:form . "possibly") (:end . 181)\n (:start . 173) (:id . 72))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 184) (:start . 182)\n (:id . 73))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 187) (:start . 185)\n (:id . 74))\n ((:tag . "NN") (:stem . "artifact") (:form . "artifact") (:end . 196)\n (:start . 188) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 199) (:start . 197)\n (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 203) (:start . 200)\n (:id . 77))\n ((:tag . "JJ") (:stem . "non-uniform") (:form . "non-uniform") (:end . 215)\n (:start . 204) (:id . 78))\n ((:tag . "NN") (:stem . "at/cg") (:form . "AT/CG") (:end . 221)\n (:start . 216) (:id . 79))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n (:end . 235) (:start . 222) (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 238) (:start . 236)\n (:id . 81))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 247)\n (:start . 239) (:id . 82))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 255)\n (:start . 248) (:id . 83))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 258) (:start . 256)\n (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 259) (:start . 258)\n (:id . 85)))@@@1@44@((:hcues ((:id . :x3.321.1) (:span 173 181))\n ((:id . :x3.321.2) (:span 11 19)))\n (:hscopes ((:id . :x3.321.1) (:span 173 255))\n ((:id . :x3.321.2) (:span 11 59)))\n (:identifiers (:sid . :s3.321) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101102@unknown@formal@none@1@S@Combining overrepresentation and positional bias@(((:tag . "VBG") (:stem . "combine") (:form . "Combining") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n (:end . 28) (:start . 10) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n (:id . 44))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 43)\n (:start . 33) (:id . 45))\n ((:tag . "NNS") (:stem . "bia") (:form . "bias") (:end . 48) (:start . 44)\n (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.322) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101103@unknown@formal@none@1@S@Since overrepresentation and KS are independent, the probabilities can simply be multiplied together to yield the probability of randomly sampling a motif with a given degree of overrepresentation and positional bias.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n (:end . 24) (:start . 6) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 28) (:start . 25)\n (:id . 44))\n ((:tag . "NN") (:stem . "ks") (:form . "KS") (:end . 31) (:start . 29)\n (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n (:id . 46))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 47)\n (:start . 36) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n (:id . 49))\n ((:tag . "NNS") (:stem . "probability") (:form . "probabilities") (:end . 66)\n (:start . 53) (:id . 50))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 70) (:start . 67)\n (:id . 51))\n ((:tag . "RB") (:stem . "simply") (:form . "simply") (:end . 77)\n (:start . 71) (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 80) (:start . 78)\n (:id . 53))\n ((:tag . "VBN") (:stem . "multiply") (:form . "multiplied") (:end . 91)\n (:start . 81) (:id . 54))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 100)\n (:start . 92) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 103) (:start . 101)\n (:id . 56))\n ((:tag . "VB") (:stem . "yield") (:form . "yield") (:end . 109)\n (:start . 104) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n (:id . 58))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 125)\n (:start . 114) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 128) (:start . 126)\n (:id . 60))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 137)\n (:start . 129) (:id . 61))\n ((:tag . "VBG") (:stem . "sample") (:form . "sampling") (:end . 146)\n (:start . 138) (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 148) (:start . 147)\n (:id . 63))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 154)\n (:start . 149) (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 159) (:start . 155)\n (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 161) (:start . 160)\n (:id . 66))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 167)\n (:start . 162) (:id . 67))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 174)\n (:start . 168) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 177) (:start . 175)\n (:id . 69))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n (:end . 196) (:start . 178) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 200) (:start . 197)\n (:id . 71))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 211)\n (:start . 201) (:id . 72))\n ((:tag . "NN") (:stem . "bias") (:form . "bias") (:end . 216) (:start . 212)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 217) (:start . 216)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.323) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101104@unknown@formal@none@1@S@Motif orientation@(((:tag . "NN") (:stem . "motif") (:form . "Motif") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "orientation") (:form . "orientation") (:end . 17)\n (:start . 6) (:id . 43)))@@@1@2@((:identifiers (:sid . :s3.324) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101105@unknown@formal@none@1@S@Many transcription factors will bind motifs on either DNA strand.@(((:tag . "JJ") (:stem . "many") (:form . "Many") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n (:end . 18) (:start . 5) (:id . 43))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 26)\n (:start . 19) (:id . 44))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 31) (:start . 27)\n (:id . 45))\n ((:tag . "VB") (:stem . "bind") (:form . "bind") (:end . 36) (:start . 32)\n (:id . 46))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 43)\n (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 46) (:start . 44)\n (:id . 48))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 53)\n (:start . 47) (:id . 49))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 57) (:start . 54)\n (:id . 50))\n ((:tag . "NN") (:stem . "strand") (:form . "strand") (:end . 64)\n (:start . 58) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s3.325) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101106@unknown@formal@none@1@S@Others, such as the general transcription factor TBP (TATA-Binding Protein), require a specific orientation and will only function if bound to motifs on a specific DNA strand 30.@(((:tag . "NNS") (:stem . "other") (:form . "Others") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 46))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 27)\n (:start . 20) (:id . 47))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n (:end . 41) (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 48)\n (:start . 42) (:id . 49))\n ((:tag . "NNP") (:stem . "TBP") (:form . "TBP") (:end . 52) (:start . 49)\n (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n (:id . 51))\n ((:tag . "NNP") (:stem . "TATA-Binding") (:form . "TATA-Binding") (:end . 66)\n (:start . 54) (:id . 52))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 74)\n (:start . 67) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n (:id . 55))\n ((:tag . "VBP") (:stem . "require") (:form . "require") (:end . 84)\n (:start . 77) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 86) (:start . 85)\n (:id . 57))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 95)\n (:start . 87) (:id . 58))\n ((:tag . "NN") (:stem . "orientation") (:form . "orientation") (:end . 107)\n (:start . 96) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n (:id . 60))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 116) (:start . 112)\n (:id . 61))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 121) (:start . 117)\n (:id . 62))\n ((:tag . "VB") (:stem . "function") (:form . "function") (:end . 130)\n (:start . 122) (:id . 63))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 133) (:start . 131)\n (:id . 64))\n ((:tag . "VBN") (:stem . "bind") (:form . "bound") (:end . 139)\n (:start . 134) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n (:id . 66))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 149)\n (:start . 143) (:id . 67))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 152) (:start . 150)\n (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 154) (:start . 153)\n (:id . 69))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 163)\n (:start . 155) (:id . 70))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 167) (:start . 164)\n (:id . 71))\n ((:tag . "NN") (:stem . "strand") (:form . "strand") (:end . 174)\n (:start . 168) (:id . 72))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 177) (:start . 175)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.326) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101107@unknown@formal@none@1@S@In scoring a motif m, a choice must therefore be made as to whether or not the reverse complement mR of m will be considered to be the same motif as m.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 20) (:start . 19)\n (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n (:id . 48))\n ((:tag . "NN") (:stem . "choice") (:form . "choice") (:end . 30)\n (:start . 24) (:id . 49))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 35) (:start . 31)\n (:id . 50))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 45)\n (:start . 36) (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 48) (:start . 46)\n (:id . 52))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 53) (:start . 49)\n (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 56) (:start . 54)\n (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n (:id . 55))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 67)\n (:start . 60) (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 70) (:start . 68)\n (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 74) (:start . 71)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n (:id . 59))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 86)\n (:start . 79) (:id . 60))\n ((:tag . "NN") (:stem . "complement") (:form . "complement") (:end . 97)\n (:start . 87) (:id . 61))\n ((:tag . "NNP") (:stem . "mR") (:form . "mR") (:end . 100) (:start . 98)\n (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n (:id . 63))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 105) (:start . 104)\n (:id . 64))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 110) (:start . 106)\n (:id . 65))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 113) (:start . 111)\n (:id . 66))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 124)\n (:start . 114) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 127) (:start . 125)\n (:id . 68))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 130) (:start . 128)\n (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n (:id . 70))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 139) (:start . 135)\n (:id . 71))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 145)\n (:start . 140) (:id . 72))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 148) (:start . 146)\n (:id . 73))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 150) (:start . 149)\n (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n (:id . 75)))@@@1@34@((:hcues ((:id . :x3.327.1) (:span 114 124))\n ((:id . :x3.327.2) (:span 60 74)))\n (:hscopes ((:id . :x3.327.1) (:span 75 150))\n ((:id . :x3.327.2) (:span 60 150)))\n (:identifiers (:sid . :s3.327) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101108@unknown@formal@none@1@S@Most programs assume motif orientation does not matter and so define m = mR.@(((:tag . "JJS") (:stem . "most") (:form . "Most") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "VBP") (:stem . "assume") (:form . "assume") (:end . 20)\n (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 26) (:start . 21)\n (:id . 45))\n ((:tag . "NN") (:stem . "orientation") (:form . "orientation") (:end . 38)\n (:start . 27) (:id . 46))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 43) (:start . 39)\n (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 47) (:start . 44)\n (:id . 48))\n ((:tag . "NN") (:stem . "matter") (:form . "matter") (:end . 54)\n (:start . 48) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n (:id . 50))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 61) (:start . 59)\n (:id . 51))\n ((:tag . "VB") (:stem . "define") (:form . "define") (:end . 68)\n (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 70) (:start . 69)\n (:id . 53))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 72) (:start . 71)\n (:id . 54))\n ((:tag . "NNP") (:stem . "mR") (:form . "mR") (:end . 75) (:start . 73)\n (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n (:id . 56)))@@@1@15@((:ncues ((:id . :x3.328.1) (:span 44 47)))\n (:nscopes ((:id . :x3.328.1) (:span 44 54)))\n (:identifiers (:sid . :s3.328) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101110@unknown@formal@none@1@S@We thus chose to attach a flag to each motif, indicating whether or not the motif should be orientation-neutral.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "choose") (:form . "chose") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "VB") (:stem . "attach") (:form . "attach") (:end . 23)\n (:start . 17) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 25) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "flag") (:form . "flag") (:end . 30) (:start . 26)\n (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 33) (:start . 31)\n (:id . 49))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 38) (:start . 34)\n (:id . 50))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 44) (:start . 39)\n (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n (:id . 52))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 56)\n (:start . 46) (:id . 53))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 64)\n (:start . 57) (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 67) (:start . 65)\n (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 71) (:start . 68)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n (:id . 57))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 81) (:start . 76)\n (:id . 58))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 88)\n (:start . 82) (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 91) (:start . 89)\n (:id . 60))\n ((:tag . "JJ") (:stem . "orientation-neutral")\n (:form . "orientation-neutral") (:end . 111) (:start . 92) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n (:id . 62)))@@@1@21@((:hcues ((:id . :x3.330.1) (:span 82 88)) ((:id . :x3.330.2) (:span 57 71)))\n (:hscopes ((:id . :x3.330.1) (:span 72 111))\n ((:id . :x3.330.2) (:span 57 111)))\n (:identifiers (:sid . :s3.330) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101111@unknown@formal@none@1@S@BEAM and SPACER thus enumerate and evaluate all motifs with both values of this flag.@(((:tag . "NN") (:stem . "beam") (:form . "BEAM") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "spacer") (:form . "SPACER") (:end . 15) (:start . 9)\n (:id . 44))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "VB") (:stem . "enumerate") (:form . "enumerate") (:end . 30)\n (:start . 21) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "VB") (:stem . "evaluate") (:form . "evaluate") (:end . 43)\n (:start . 35) (:id . 48))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 47) (:start . 44)\n (:id . 49))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 54)\n (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 59) (:start . 55)\n (:id . 51))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 64) (:start . 60)\n (:id . 52))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 71)\n (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n (:id . 54))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 79) (:start . 75)\n (:id . 55))\n ((:tag . "NN") (:stem . "flag") (:form . "flag") (:end . 84) (:start . 80)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.331) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101112@unknown@formal@none@1@S@SCOPE reports that orientation does matter (i.e. m ≠ mR) for 17% of the regulons in our biological test set.@(((:tag . "NN") (:stem . "scope") (:form . "SCOPE") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "report") (:form . "reports") (:end . 13)\n (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "orientation") (:form . "orientation") (:end . 30)\n (:start . 19) (:id . 45))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 35) (:start . 31)\n (:id . 46))\n ((:tag . "NN") (:stem . "matter") (:form . "matter") (:end . 42)\n (:start . 36) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 44) (:start . 43)\n (:id . 48))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 48) (:start . 44)\n (:id . 49))\n ((:tag . "FW") (:stem . "m") (:form . "m") (:end . 50) (:start . 49)\n (:id . 50))\n ((:tag . "FW") (:stem . "≠") (:form . "≠") (:end . 52) (:start . 51)\n (:id . 51))\n ((:tag . "NNP") (:stem . "mR") (:form . "mR") (:end . 55) (:start . 53)\n (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 56) (:start . 55)\n (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 60) (:start . 57)\n (:id . 54))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 63) (:start . 61)\n (:id . 55))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 64) (:start . 63)\n (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n (:id . 58))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 80)\n (:start . 72) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 83) (:start . 81)\n (:id . 60))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 87) (:start . 84)\n (:id . 61))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 98)\n (:start . 88) (:id . 62))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 103) (:start . 99)\n (:id . 63))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 107) (:start . 104)\n (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.332) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101113@unknown@formal@none@1@S@Reuse of structural domain–domain interactions in protein networks@(((:tag . "NNP") (:stem . "Reuse") (:form . "Reuse") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 8) (:start . 6)\n (:id . 43))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 19)\n (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "domain–domain") (:form . "domain–domain")\n (:end . 33) (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 46)\n (:start . 34) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 57)\n (:start . 50) (:id . 48))\n ((:tag . "NNS") (:stem . "network") (:form . "networks") (:end . 66)\n (:start . 58) (:id . 49)))@@@1@8@((:identifiers (:sid . :s4.1) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011 5101114@unknown@formal@none@1@S@Abstract@(((:tag . "NN") (:stem . "abstract") (:form . "Abstract") (:end . 8)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.2) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101115@unknown@formal@none@1@S@Background@(((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 10)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.3) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101116@unknown@formal@none@1@S@Protein interactions are thought to be largely mediated by interactions between structural domains.@(((:tag . "NN") (:stem . "protein") (:form . "Protein") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 20)\n (:start . 8) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 24) (:start . 21)\n (:id . 44))\n ((:tag . "VBN") (:stem . "think") (:form . "thought") (:end . 32)\n (:start . 25) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 38) (:start . 36)\n (:id . 47))\n ((:tag . "RB") (:stem . "largely") (:form . "largely") (:end . 46)\n (:start . 39) (:id . 48))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 55)\n (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 58) (:start . 56)\n (:id . 50))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 71)\n (:start . 59) (:id . 51))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 79)\n (:start . 72) (:id . 52))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 90)\n (:start . 80) (:id . 53))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 98)\n (:start . 91) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 55)))@@@1@14@((:hcues ((:id . :x4.4.1) (:span 25 32)))\n (:hscopes ((:id . :x4.4.1) (:span 0 98)))\n (:identifiers (:sid . :s4.4) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101117@unknown@formal@none@1@S@Databases such as iPfam relate interactions in protein structures to known domain families.@(((:tag . "NNS") (:stem . "database") (:form . "Databases") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 14) (:start . 10)\n (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 17) (:start . 15)\n (:id . 44))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 23) (:start . 18)\n (:id . 45))\n ((:tag . "NN") (:stem . "relate") (:form . "relate") (:end . 30)\n (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 43)\n (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 54)\n (:start . 47) (:id . 49))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 65)\n (:start . 55) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n (:id . 51))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 74) (:start . 69)\n (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 81)\n (:start . 75) (:id . 53))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 90)\n (:start . 82) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s4.5) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101118@unknown@formal@none@1@S@Here, we investigate how the domain interactions from the iPfam database are distributed in protein interactions taken from the HPRD, MPact, BioGRID, DIP and IntAct databases.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n (:id . 44))\n ((:tag . "VBP") (:stem . "investigate") (:form . "investigate") (:end . 20)\n (:start . 9) (:id . 45))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 24) (:start . 21)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n (:id . 47))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 35)\n (:start . 29) (:id . 48))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 48)\n (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 53) (:start . 49)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n (:id . 51))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 63) (:start . 58)\n (:id . 52))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 72)\n (:start . 64) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 76) (:start . 73)\n (:id . 54))\n ((:tag . "VBN") (:stem . "distribute") (:form . "distributed") (:end . 88)\n (:start . 77) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 99)\n (:start . 92) (:id . 57))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 112)\n (:start . 100) (:id . 58))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 118)\n (:start . 113) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 123) (:start . 119)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n (:id . 61))\n ((:tag . "NNP") (:stem . "HPRD") (:form . "HPRD") (:end . 132) (:start . 128)\n (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n (:id . 63))\n ((:tag . "NNP") (:stem . "MPact") (:form . "MPact") (:end . 139)\n (:start . 134) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n (:id . 65))\n ((:tag . "NNP") (:stem . "BioGRID") (:form . "BioGRID") (:end . 148)\n (:start . 141) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n (:id . 67))\n ((:tag . "NNP") (:stem . "DIP") (:form . "DIP") (:end . 153) (:start . 150)\n (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 157) (:start . 154)\n (:id . 69))\n ((:tag . "NNP") (:stem . "IntAct") (:form . "IntAct") (:end . 164)\n (:start . 158) (:id . 70))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 174)\n (:start . 165) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n (:id . 72)))@@@1@31@((:identifiers (:sid . :s4.6) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101120@unknown@formal@none@1@S@We find that known structural domain interactions can only explain a subset of 4–19% of the available protein interactions, nevertheless this fraction is still significantly bigger than expected by chance.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 29)\n (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 36)\n (:start . 30) (:id . 47))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 49)\n (:start . 37) (:id . 48))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 53) (:start . 50)\n (:id . 49))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 58) (:start . 54)\n (:id . 50))\n ((:tag . "VB") (:stem . "explain") (:form . "explain") (:end . 66)\n (:start . 59) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 68) (:start . 67)\n (:id . 52))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 75)\n (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n (:id . 54))\n ((:tag . "CD") (:stem . "4–19") (:form . "4–19") (:end . 83) (:start . 79)\n (:id . 55))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 84) (:start . 83)\n (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n (:id . 58))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 101)\n (:start . 92) (:id . 59))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 109)\n (:start . 102) (:id . 60))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 122)\n (:start . 110) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n (:id . 62))\n ((:tag . "RB") (:stem . "nevertheless") (:form . "nevertheless") (:end . 136)\n (:start . 124) (:id . 63))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 141) (:start . 137)\n (:id . 64))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 150)\n (:start . 142) (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 153) (:start . 151)\n (:id . 66))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 159)\n (:start . 154) (:id . 67))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 173) (:start . 160) (:id . 68))\n ((:tag . "JJR") (:stem . "big") (:form . "bigger") (:end . 180)\n (:start . 174) (:id . 69))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 185) (:start . 181)\n (:id . 70))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 194)\n (:start . 186) (:id . 71))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 197) (:start . 195)\n (:id . 72))\n ((:tag . "NN") (:stem . "chance") (:form . "chance") (:end . 204)\n (:start . 198) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s4.8) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101121@unknown@formal@none@1@S@There is a correlation between the frequency of a domain interaction and the connectivity of the proteins it occurs in.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 22)\n (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 30)\n (:start . 23) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 44)\n (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 56)\n (:start . 50) (:id . 51))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 68)\n (:start . 57) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n (:id . 54))\n ((:tag . "NN") (:stem . "connectivity") (:form . "connectivity") (:end . 89)\n (:start . 77) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n (:id . 57))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 105)\n (:start . 97) (:id . 58))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 108) (:start . 106)\n (:id . 59))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 115)\n (:start . 109) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 118) (:start . 116)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.9) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101122@unknown@formal@none@1@S@Furthermore, a large proportion of protein interactions can be attributed to a small number of domain interactions.@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 14) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 31)\n (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 42)\n (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 55)\n (:start . 43) (:id . 49))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 59) (:start . 56)\n (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 62) (:start . 60)\n (:id . 51))\n ((:tag . "VBN") (:stem . "attribute") (:form . "attributed") (:end . 73)\n (:start . 63) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 76) (:start . 74)\n (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 78) (:start . 77)\n (:id . 54))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 84) (:start . 79)\n (:id . 55))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 91)\n (:start . 85) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n (:id . 57))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 101)\n (:start . 95) (:id . 58))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 114)\n (:start . 102) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.10) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101123@unknown@formal@none@1@S@We conclude that many, but not all, domain interactions constitute reusable modules of molecular recognition.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "conclude") (:form . "conclude") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 21) (:start . 17)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n (:id . 46))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 26) (:start . 23)\n (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 30) (:start . 27)\n (:id . 48))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 34) (:start . 31)\n (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 42)\n (:start . 36) (:id . 51))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 55)\n (:start . 43) (:id . 52))\n ((:tag . "VBP") (:stem . "constitute") (:form . "constitute") (:end . 66)\n (:start . 56) (:id . 53))\n ((:tag . "JJ") (:stem . "reusable") (:form . "reusable") (:end . 75)\n (:start . 67) (:id . 54))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 83)\n (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n (:id . 56))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 96)\n (:start . 87) (:id . 57))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 108)\n (:start . 97) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.11) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101124@unknown@formal@none@1@S@A substantial proportion of domain interactions are conserved between E. coli, S. cerevisiae and H. sapiens.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "substantial") (:form . "substantial") (:end . 13)\n (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 24)\n (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 34)\n (:start . 28) (:id . 46))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 47)\n (:start . 35) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 51) (:start . 48)\n (:id . 48))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 61)\n (:start . 52) (:id . 49))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 69)\n (:start . 62) (:id . 50))\n ((:tag . "NNP") (:stem . "E.") (:form . "E.") (:end . 72) (:start . 70)\n (:id . 51))\n ((:tag . "NNP") (:stem . "coli") (:form . "coli") (:end . 77) (:start . 73)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n (:id . 53))\n ((:tag . "NNP") (:stem . "S.") (:form . "S.") (:end . 81) (:start . 79)\n (:id . 54))\n ((:tag . "NNP") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 92)\n (:start . 82) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n (:id . 56))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 99) (:start . 97)\n (:id . 57))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 107)\n (:start . 100) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.12) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101125@unknown@formal@none@1@S@These domains are related to essential cellular functions, suggesting that many domain interactions were already present in the last universal common ancestor.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 13)\n (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 25)\n (:start . 18) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 38)\n (:start . 29) (:id . 47))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 47)\n (:start . 39) (:id . 48))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 57)\n (:start . 48) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n (:id . 50))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 69)\n (:start . 59) (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 74) (:start . 70)\n (:id . 52))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 79) (:start . 75)\n (:id . 53))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 86)\n (:start . 80) (:id . 54))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 99)\n (:start . 87) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 104) (:start . 100)\n (:id . 56))\n ((:tag . "RB") (:stem . "already") (:form . "already") (:end . 112)\n (:start . 105) (:id . 57))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 120)\n (:start . 113) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 123) (:start . 121)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n (:id . 60))\n ((:tag . "JJ") (:stem . "last") (:form . "last") (:end . 132) (:start . 128)\n (:id . 61))\n ((:tag . "JJ") (:stem . "universal") (:form . "universal") (:end . 142)\n (:start . 133) (:id . 62))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 149)\n (:start . 143) (:id . 63))\n ((:tag . "NN") (:stem . "ancestor") (:form . "ancestor") (:end . 158)\n (:start . 150) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n (:id . 65)))@@@1@24@((:hcues ((:id . :x4.13.1) (:span 59 69)))\n (:hscopes ((:id . :x4.13.1) (:span 59 158)))\n (:identifiers (:sid . :s4.13) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101126@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.14) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101127@unknown@formal@none@1@S@Our results support the concept of domain interactions as reusable, conserved building blocks of protein interactions, but also highlight the limitations currently imposed by the small number of available protein structures.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "support") (:form . "support") (:end . 19)\n (:start . 12) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 31)\n (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . 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"by") (:end . 174) (:start . 172)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 178) (:start . 175)\n (:id . 68))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 184)\n (:start . 179) (:id . 69))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 191)\n (:start . 185) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 194) (:start . 192)\n (:id . 71))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 204)\n (:start . 195) (:id . 72))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 212)\n (:start . 205) (:id . 73))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 223)\n (:start . 213) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 224) (:start . 223)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s4.15) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101128@unknown@formal@none@1@S@Background@(((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 10)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.16) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011 5101130@unknown@formal@none@1@S@Such families of related sequence regions, collected in the Pfam database 1, usually constitute structurally and functionally conserved modules.@(((:tag . "JJ") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 44))\n ((:tag . "JJ") (:stem . "related") (:form . "related") (:end . 24)\n (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 33)\n (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 41)\n (:start . 34) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n (:id . 48))\n ((:tag . "VBN") (:stem . "collect") (:form . "collected") (:end . 52)\n (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n (:id . 51))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 64) (:start . 60)\n (:id . 52))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 73)\n (:start . 65) (:id . 53))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 75) (:start . 74)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n (:id . 55))\n ((:tag . "RB") (:stem . "usually") (:form . "usually") (:end . 84)\n (:start . 77) (:id . 56))\n ((:tag . "VBP") (:stem . "constitute") (:form . "constitute") (:end . 95)\n (:start . 85) (:id . 57))\n ((:tag . "RB") (:stem . "structurally") (:form . "structurally") (:end . 108)\n (:start . 96) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n (:id . 59))\n ((:tag . "RB") (:stem . "functionally") (:form . "functionally") (:end . 125)\n (:start . 113) (:id . 60))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 135)\n (:start . 126) (:id . 61))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 143)\n (:start . 136) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s4.18) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101131@unknown@formal@none@1@S@It is assumed that binding interfaces, too, are conserved evolutionary modules that are reused between proteins of different functions and retained during evolution 23.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "VBN") (:stem . "assume") (:form . "assumed") (:end . 13)\n (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n (:id . 45))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 26)\n (:start . 19) (:id . 46))\n ((:tag . "NNS") (:stem . "interface") (:form . "interfaces") (:end . 37)\n (:start . 27) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n (:id . 48))\n ((:tag . "RB") (:stem . "too") (:form . "too") (:end . 42) (:start . 39)\n (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 47) (:start . 44)\n (:id . 51))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 57)\n (:start . 48) (:id . 52))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 70)\n (:start . 58) (:id . 53))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 78)\n (:start . 71) (:id . 54))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 83) (:start . 79)\n (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 87) (:start . 84)\n (:id . 56))\n ((:tag . "VBN") (:stem . "reuse") (:form . "reused") (:end . 94)\n (:start . 88) (:id . 57))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 102)\n (:start . 95) (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 111)\n (:start . 103) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n (:id . 60))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 124)\n (:start . 115) (:id . 61))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 134)\n (:start . 125) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 138) (:start . 135)\n (:id . 63))\n ((:tag . "VBN") (:stem . "retain") (:form . "retained") (:end . 147)\n (:start . 139) (:id . 64))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 154)\n (:start . 148) (:id . 65))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 164)\n (:start . 155) (:id . 66))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 167) (:start . 165)\n (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n (:id . 68)))@@@1@27@((:hcues ((:id . :x4.19.1) (:span 6 13)))\n (:hscopes ((:id . :x4.19.1) (:span 6 164)))\n (:identifiers (:sid . :s4.19) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101132@unknown@formal@none@1@S@Therefore, domain–domain interactions are often regarded as the currency of protein–protein interactions.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "NN") (:stem . "domain–domain") (:form . "domain–domain")\n (:end . 24) (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 37)\n (:start . 25) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 41) (:start . 38)\n (:id . 46))\n ((:tag . "RB") (:stem . "often") (:form . 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(:end . 105) (:start . 104)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s4.20) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101133@unknown@formal@none@1@S@Based on this assumption, Ng et al. described an approach to predict domain–domain interactions using literature curation, evolutionary history and the distribution of domains in protein interactions 4.@(((:tag . "VBN") (:stem . "base") (:form . "Based") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 8) (:start . 6)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "assumption") (:form . "assumption") (:end . 24)\n (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Ng") (:form . "Ng") (:end . 28) (:start . 26)\n (:id . 47))\n ((:tag . 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"in") (:end . 178) (:start . 176)\n (:id . 68))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 186)\n (:start . 179) (:id . 69))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 199)\n (:start . 187) (:id . 70))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 201) (:start . 200)\n (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n (:id . 72)))@@@1@31@((:identifiers (:sid . :s4.21) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101134@unknown@formal@none@1@S@Wuchty et al. compared the relationship between this set of predicted interacting domain pairs to the domain coocurrence network 5.@(((:tag . "NNP") (:stem . "Wuchty") (:form . "Wuchty") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 9) (:start . 7)\n (:id . 43))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") 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(:end . 131) (:start . 130)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.22) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101135@unknown@formal@none@1@S@More recently, other groups have come up with sophisticated statistical methods to estimate putatively interacting domain pairs, based on the assumption of domain reusability 678910.@(((:tag . "RBR") (:stem . "more") (:form . "More") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 27)\n (:start . 21) (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 32) (:start . 28)\n (:id . 47))\n ((:tag . "VBN") (:stem . 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"678910") (:end . 181)\n (:start . 175) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n (:id . 69)))@@@1@28@((:hcues ((:id . :x4.23.1) (:span 142 152)) ((:id . :x4.23.2) (:span 92 102)))\n (:hscopes ((:id . :x4.23.1) (:span 142 174))\n ((:id . :x4.23.2) (:span 92 127)))\n (:identifiers (:sid . :s4.23) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101136@unknown@formal@none@1@S@However, none of these approaches offers structural evidence that the predicted domain pairs are able to form an interaction.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "none") (:form . "none") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "DT") (:stem . 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"are") (:end . 96) (:start . 93)\n (:id . 56))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 101) (:start . 97)\n (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 104) (:start . 102)\n (:id . 58))\n ((:tag . "VB") (:stem . "form") (:form . "form") (:end . 109) (:start . 105)\n (:id . 59))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 112) (:start . 110)\n (:id . 60))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 124)\n (:start . 113) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n (:id . 62)))@@@1@21@((:ncues ((:id . :x4.24.1) (:span 9 13)))\n (:nscopes ((:id . :x4.24.1) (:span 9 124)))\n (:identifiers (:sid . :s4.24) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101137@unknown@formal@none@1@S@For complexes with known structure, it has been shown that domains can mediate interactions 1112.@(((:tag . 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"of") (:end . 31) (:start . 29)\n (:id . 46))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 41)\n (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n (:id . 49))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 52) (:start . 49)\n (:id . 50))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 61)\n (:start . 53) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n (:id . 52))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 72)\n (:start . 65) (:id . 53))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 83)\n (:start . 73) (:id . 54))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 86) (:start . 84)\n (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 89) (:start . 87)\n (:id . 56))\n ((:tag . "RB") (:stem . 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(:end . 128) (:start . 127)\n (:id . 63)))@@@1@22@((:hcues ((:id . :x4.30.1) (:span 34 41)))\n (:hscopes ((:id . :x4.30.1) (:span 34 127)))\n (:identifiers (:sid . :s4.30) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101143@unknown@formal@none@1@S@High-throughput experiments 161718 and extensive literature curation efforts 19 have yielded large databases of protein interactions 2021222324.@(((:tag . "JJ") (:stem . "high-throughput") (:form . "High-throughput")\n (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 27)\n (:start . 16) (:id . 43))\n ((:tag . "CD") (:stem . "161718") (:form . "161718") (:end . 34)\n (:start . 28) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n (:id . 45))\n ((:tag . "JJ") (:stem . "extensive") (:form . "extensive") (:end . 48)\n (:start . 39) (:id . 46))\n ((:tag . "NN") (:stem . 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(:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.34) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101147@unknown@formal@none@1@S@In this study, we investigate how pairs of protein families taken from iPfam are distributed in experimental protein interactions from five major model species.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n (:id . 46))\n ((:tag . "VBP") (:stem . "investigate") (:form . "investigate") (:end . 29)\n (:start . 18) (:id . 47))\n ((:tag . "WRB") (:stem . 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(:end . 160) (:start . 159)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.35) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101148@unknown@formal@none@1@S@This allows us to address a number of questions:: what proportion of each organism's protein interaction network, its interactome, can be attributed to a known domain–domain interaction?@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "allow") (:form . "allows") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 17) (:start . 15)\n (:id . 45))\n ((:tag . "VB") (:stem . "address") (:form . "address") (:end . 25)\n (:start . 18) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 27) (:start . 26)\n (:id . 47))\n ((:tag . "NN") (:stem . 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"experimental") (:end . 54)\n (:start . 42) (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 62)\n (:start . 55) (:id . 49))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 75)\n (:start . 63) (:id . 50)))@@@1@9@((:identifiers (:sid . :s4.39) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101152@unknown@formal@none@1@S@We analysed the distribution of Pfam families known to interact from a PDB structure (iPfam domain pairs) in experimentally derived protein interactions (experimental interactions).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "analyse") (:form . "analysed") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "distribution") (:form . 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"(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n (:id . 56))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 91) (:start . 86)\n (:id . 57))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 98)\n (:start . 92) (:id . 58))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 104) (:start . 99)\n (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n (:id . 61))\n ((:tag . "RB") (:stem . "experimentally") (:form . "experimentally")\n (:end . 123) (:start . 109) (:id . 62))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 131)\n (:start . 124) (:id . 63))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 139)\n (:start . 132) (:id . 64))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 152)\n (:start . 140) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n (:id . 66))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 166)\n (:start . 154) (:id . 67))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 179)\n (:start . 167) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s4.40) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101153@unknown@formal@none@1@S@The experimental interactions were filtered to only include interactions with exactly two partners (see Methods).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 16)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 29)\n (:start . 17) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 34) (:start . 30)\n (:id . 45))\n ((:tag . "VBN") (:stem . "filter") (:form . "filtered") (:end . 43)\n (:start . 35) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 46) (:start . 44)\n (:id . 47))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 51) (:start . 47)\n (:id . 48))\n ((:tag . "VB") (:stem . "include") (:form . "include") (:end . 59)\n (:start . 52) (:id . 49))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 72)\n (:start . 60) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 77) (:start . 73)\n (:id . 51))\n ((:tag . "RB") (:stem . "exactly") (:form . "exactly") (:end . 85)\n (:start . 78) (:id . 52))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 89) (:start . 86)\n (:id . 53))\n ((:tag . "NNS") (:stem . "partner") (:form . "partners") (:end . 98)\n (:start . 90) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n (:id . 55))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 103) (:start . 100)\n (:id . 56))\n ((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 111)\n (:start . 104) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.41) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101154@unknown@formal@none@1@S@The fraction of experimental interactions that contain at least one iPfam domain pair is referred to as the iPfam coverage.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 28)\n (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 41)\n (:start . 29) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 46) (:start . 42)\n (:id . 47))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 54)\n (:start . 47) (:id . 48))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 57) (:start . 55)\n (:id . 49))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 63) (:start . 58)\n (:id . 50))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 67) (:start . 64)\n (:id . 51))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 73) (:start . 68)\n (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 80)\n (:start . 74) (:id . 53))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 85) (:start . 81)\n (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 88) (:start . 86)\n (:id . 55))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 97)\n (:start . 89) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 103) (:start . 101)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n (:id . 59))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 113)\n (:start . 108) (:id . 60))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 122)\n (:start . 114) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.42) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101155@unknown@formal@none@1@S@Accordingly, the fraction of experimental interactions that contains any pair of Pfam domains (excluding the iPfam domain pairs) is called the Pfam coverage.@(((:tag . "RB") (:stem . "accordingly") (:form . "Accordingly") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 25)\n (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 41)\n (:start . 29) (:id . 47))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 54)\n (:start . 42) (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 59) (:start . 55)\n (:id . 49))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 68)\n (:start . 60) (:id . 50))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 72) (:start . 69)\n (:id . 51))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 77) (:start . 73)\n (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 85) (:start . 81)\n (:id . 54))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 93)\n (:start . 86) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n (:id . 56))\n ((:tag . "VBG") (:stem . "exclude") (:form . "excluding") (:end . 104)\n (:start . 95) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n (:id . 58))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 114)\n (:start . 109) (:id . 59))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 121)\n (:start . 115) (:id . 60))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 127)\n (:start . 122) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 128) (:start . 127)\n (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 131) (:start . 129)\n (:id . 63))\n ((:tag . "VBN") (:stem . "call") (:form . "called") (:end . 138)\n (:start . 132) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 142) (:start . 139)\n (:id . 65))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 147) (:start . 143)\n (:id . 66))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 156)\n (:start . 148) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s4.43) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101156@unknown@formal@none@1@S@Figure 1 shows the Pfam and iPfam coverage for the analysed species as a column chart.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 8) (:start . 7)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 27) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 33) (:start . 28)\n (:id . 48))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 42)\n (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 46) (:start . 43)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n (:id . 51))\n ((:tag . "VBN") (:stem . "analyse") (:form . "analysed") (:end . 59)\n (:start . 51) (:id . 52))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 67)\n (:start . 60) (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 70) (:start . 68)\n (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 72) (:start . 71)\n (:id . 55))\n ((:tag . "NN") (:stem . "column") (:form . "column") (:end . 79)\n (:start . 73) (:id . 56))\n ((:tag . "NN") (:stem . "chart") (:form . "chart") (:end . 85) (:start . 80)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s4.44) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101157@unknown@formal@none@1@S@The number of resolved protein interactions varies greatly between species, as does the size of the underlying proteome (see Table 1).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "VBN") (:stem . "resolve") (:form . "resolved") (:end . 22)\n (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 30)\n (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 43)\n (:start . 31) (:id . 47))\n ((:tag . "VBZ") (:stem . "vary") (:form . "varies") (:end . 50) (:start . 44)\n (:id . 48))\n ((:tag . "RB") (:stem . "greatly") (:form . "greatly") (:end . 58)\n (:start . 51) (:id . 49))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 66)\n (:start . 59) (:id . 50))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 74)\n (:start . 67) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 78) (:start . 76)\n (:id . 53))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 83) (:start . 79)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n (:id . 55))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 92) (:start . 88)\n (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n (:id . 58))\n ((:tag . "VBG") (:stem . "underlie") (:form . "underlying") (:end . 110)\n (:start . 100) (:id . 59))\n ((:tag . "NN") (:stem . "proteome") (:form . "proteome") (:end . 119)\n (:start . 111) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n (:id . 61))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 124) (:start . 121)\n (:id . 62))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 130)\n (:start . 125) (:id . 63))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 132) (:start . 131)\n (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s4.45) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101158@unknown@formal@none@1@S@The Pfam coverage, coloured red in Figure 1, lies between 49.46% and 66.73%.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 17)\n (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n (:id . 45))\n ((:tag . "VBD") (:stem . "colour") (:form . "coloured") (:end . 27)\n (:start . 19) (:id . 46))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 31) (:start . 28)\n (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 41)\n (:start . 35) (:id . 49))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 43) (:start . 42)\n (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n (:id . 51))\n ((:tag . "VBZ") (:stem . "lie") (:form . "lies") (:end . 49) (:start . 45)\n (:id . 52))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 57)\n (:start . 50) (:id . 53))\n ((:tag . "CD") (:stem . "49.46") (:form . "49.46") (:end . 63) (:start . 58)\n (:id . 54))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 64) (:start . 63)\n (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n (:id . 56))\n ((:tag . "CD") (:stem . "66.73") (:form . "66.73") (:end . 74) (:start . 69)\n (:id . 57))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 75) (:start . 74)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.46) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101160@unknown@formal@none@1@S@The iPfam coverage, shown in blue, is much smaller, ranging from 2.92% in D. melanogaster to 19.02% in H. sapiens.@(((:tag . "DT") (:stem . "the") (:form . 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",") (:end . 51) (:start . 50)\n (:id . 53))\n ((:tag . "VBG") (:stem . "range") (:form . "ranging") (:end . 59)\n (:start . 52) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 64) (:start . 60)\n (:id . 55))\n ((:tag . "CD") (:stem . "2.92") (:form . "2.92") (:end . 69) (:start . 65)\n (:id . 56))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 70) (:start . 69)\n (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n (:id . 58))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 76) (:start . 74)\n (:id . 59))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 89)\n (:start . 77) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 92) (:start . 90)\n (:id . 61))\n ((:tag . "CD") (:stem . "19.02") (:form . "19.02") (:end . 98) (:start . 93)\n (:id . 62))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 99) (:start . 98)\n (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 102) (:start . 100)\n (:id . 64))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 105) (:start . 103)\n (:id . 65))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 113)\n (:start . 106) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.48) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101161@unknown@formal@none@1@S@In S. cerevisiae the species with the most comprehensively studied interactome, the iPfam coverage is 4.47%.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 16)\n (:start . 6) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . 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"coverage") (:end . 98)\n (:start . 90) (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 101) (:start . 99)\n (:id . 57))\n ((:tag . "CD") (:stem . "4.47") (:form . "4.47") (:end . 106) (:start . 102)\n (:id . 58))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 107) (:start . 106)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.49) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101162@unknown@formal@none@1@S@Comparison of coverage of iPfam domain pairs on protein interactions@(((:tag . "NN") (:stem . "comparison") (:form . "Comparison") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 43))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 22)\n (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n (:id . 45))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 31) (:start . 26)\n (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 38)\n (:start . 32) (:id . 47))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 44) (:start . 39)\n (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 55)\n (:start . 48) (:id . 50))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 68)\n (:start . 56) (:id . 51)))@@@1@10@((:identifiers (:sid . :s4.50) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5101163@unknown@formal@none@1@S@Comparison of coverage of iPfam domain pairs on protein interactions.@(((:tag . "NN") (:stem . "comparison") (:form . "Comparison") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 43))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 22)\n (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n (:id . 45))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 31) (:start . 26)\n (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 38)\n (:start . 32) (:id . 47))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 44) (:start . 39)\n (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 55)\n (:start . 48) (:id . 50))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 68)\n (:start . 56) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s4.51) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101164@unknown@formal@none@1@S@For each species, the height of the column reflects the number of known protein–protein interactions in the data set.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 16)\n (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "NN") (:stem . "height") (:form . "height") (:end . 28)\n (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n (:id . 48))\n ((:tag . 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"the") (:end . 107) (:start . 104)\n (:id . 59))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 112)\n (:start . 108) (:id . 60))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 116) (:start . 113)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.52) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101165@unknown@formal@none@1@S@The columns are split according to the proportion of interactions that contain an iPfam domain pair (blue), that contain any other Pfam domains on both proteins (red), and those that contain no Pfam domain pair (yellow).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "column") (:form . "columns") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . 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"other") (:form . "other") (:end . 130)\n (:start . 125) (:id . 65))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 135) (:start . 131)\n (:id . 66))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 143)\n (:start . 136) (:id . 67))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 146) (:start . 144)\n (:id . 68))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 151) (:start . 147)\n (:id . 69))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 160)\n (:start . 152) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 162) (:start . 161)\n (:id . 71))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 165) (:start . 162)\n (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 166) (:start . 165)\n (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 171) (:start . 168)\n (:id . 75))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 177)\n (:start . 172) (:id . 76))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 182) (:start . 178)\n (:id . 77))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 190)\n (:start . 183) (:id . 78))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 193) (:start . 191)\n (:id . 79))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 198) (:start . 194)\n (:id . 80))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 205)\n (:start . 199) (:id . 81))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 210) (:start . 206)\n (:id . 82))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 212) (:start . 211)\n (:id . 83))\n ((:tag . "NN") (:stem . "yellow") (:form . "yellow") (:end . 218)\n (:start . 212) (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 219) (:start . 218)\n (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n (:id . 86)))@@@1@45@((:ncues ((:id . :x4.53.1) (:span 191 193)))\n (:nscopes ((:id . :x4.53.1) (:span 191 210)))\n (:identifiers (:sid . :s4.53) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101166@unknown@formal@none@1@S@iPfam domain pair coverage on protein interactions@(((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 12) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 17) (:start . 13)\n (:id . 44))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 26)\n (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 37)\n (:start . 30) (:id . 47))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 50)\n (:start . 38) (:id . 48)))@@@1@7@((:identifiers (:sid . :s4.54) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011 5101167@unknown@formal@none@1@S@For each species, we list the size of the proteome as defined in Integr8 and the fraction of this proteome that is represented in the protein interaction sets, followed by the total number of binary protein interactions and the fraction of those that contain an iPfam domain pair.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "species") (:form . "species") (:end . 16)\n (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 20) (:start . 18)\n (:id . 46))\n ((:tag . "VBP") (:stem . "list") (:form . "list") (:end . 25) (:start . 21)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n (:id . 48))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 34) (:start . 30)\n (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n (:id . 51))\n ((:tag . "NN") (:stem . "proteome") (:form . "proteome") (:end . 50)\n (:start . 42) (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 53) (:start . 51)\n (:id . 53))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 61)\n (:start . 54) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n (:id . 55))\n ((:tag . "NN") (:stem . "integr8") (:form . "Integr8") (:end . 72)\n (:start . 65) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n (:id . 58))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 89)\n (:start . 81) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n (:id . 60))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 97) (:start . 93)\n (:id . 61))\n ((:tag . "NN") (:stem . "proteome") (:form . "proteome") (:end . 106)\n (:start . 98) (:id . 62))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 111) (:start . 107)\n (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 114) (:start . 112)\n (:id . 64))\n ((:tag . "VBN") (:stem . "represent") (:form . "represented") (:end . 126)\n (:start . 115) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 129) (:start . 127)\n (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n (:id . 67))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 141)\n (:start . 134) (:id . 68))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 153)\n (:start . 142) (:id . 69))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 158) (:start . 154)\n (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 159) (:start . 158)\n (:id . 71))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 168)\n (:start . 160) (:id . 72))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 171) (:start . 169)\n (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 175) (:start . 172)\n (:id . 74))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 181)\n (:start . 176) (:id . 75))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 188)\n (:start . 182) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 191) (:start . 189)\n (:id . 77))\n ((:tag . "JJ") (:stem . "binary") (:form . "binary") (:end . 198)\n (:start . 192) (:id . 78))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 206)\n (:start . 199) (:id . 79))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 219)\n (:start . 207) (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 223) (:start . 220)\n (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 227) (:start . 224)\n (:id . 82))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 236)\n (:start . 228) (:id . 83))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 239) (:start . 237)\n (:id . 84))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 245)\n (:start . 240) (:id . 85))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 250) (:start . 246)\n (:id . 86))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 258)\n (:start . 251) (:id . 87))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 261) (:start . 259)\n (:id . 88))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 267)\n (:start . 262) (:id . 89))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 274)\n (:start . 268) (:id . 90))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 279) (:start . 275)\n (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 280) (:start . 279)\n (:id . 92)))@@@1@51@((:identifiers (:sid . :s4.55) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101168@unknown@formal@none@1@S@The last two columns show the results of the network shuffling experiments.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "last") (:form . "last") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "NNS") (:stem . "column") (:form . "columns") (:end . 20)\n (:start . 13) (:id . 45))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 25) (:start . 21)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n (:id . 47))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 37)\n (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n (:id . 50))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 52)\n (:start . 45) (:id . 51))\n ((:tag . "NN") (:stem . "shuffling") (:form . "shuffling") (:end . 62)\n (:start . 53) (:id . 52))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 74)\n (:start . 63) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s4.56) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101170@unknown@formal@none@1@S@However, the fact that only a small fraction of protein interactions contain known domain pairs could be a result of the scarcity of available structures of protein complexes.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 17) (:start . 13)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n (:id . 46))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 27) (:start . 23)\n (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n (:id . 48))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 35) (:start . 30)\n (:id . 49))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 44)\n (:start . 36) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 55)\n (:start . 48) (:id . 52))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 68)\n (:start . 56) (:id . 53))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 76)\n (:start . 69) (:id . 54))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 82) (:start . 77)\n (:id . 55))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 89)\n (:start . 83) (:id . 56))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 95) (:start . 90)\n (:id . 57))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 101) (:start . 96)\n (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 104) (:start . 102)\n (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 106) (:start . 105)\n (:id . 60))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 113)\n (:start . 107) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n (:id . 63))\n ((:tag . "NN") (:stem . "scarcity") (:form . "scarcity") (:end . 129)\n (:start . 121) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n (:id . 65))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 142)\n (:start . 133) (:id . 66))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 153)\n (:start . 143) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 156) (:start . 154)\n (:id . 68))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 164)\n (:start . 157) (:id . 69))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 174)\n (:start . 165) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n (:id . 71)))@@@1@30@((:hcues ((:id . :x4.58.1) (:span 96 101)))\n (:hscopes ((:id . :x4.58.1) (:span 96 174)))\n (:identifiers (:sid . :s4.58) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101171@unknown@formal@none@1@S@Therefore, we asked whether the observed iPfam coverage is larger than would be expected by chance.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "VBD") (:stem . "ask") (:form . "asked") (:end . 19) (:start . 14)\n (:id . 45))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 27)\n (:start . 20) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n (:id . 47))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 40)\n (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 46) (:start . 41)\n (:id . 49))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 55)\n (:start . 47) (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 58) (:start . 56)\n (:id . 51))\n ((:tag . "JJR") (:stem . "large") (:form . "larger") (:end . 65)\n (:start . 59) (:id . 52))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 70) (:start . 66)\n (:id . 53))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 76) (:start . 71)\n (:id . 54))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 79) (:start . 77)\n (:id . 55))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 88)\n (:start . 80) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 91) (:start . 89)\n (:id . 57))\n ((:tag . "NN") (:stem . "chance") (:form . "chance") (:end . 98)\n (:start . 92) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 59)))@@@1@18@((:hcues ((:id . :x4.59.1) (:span 80 88)) ((:id . :x4.59.2) (:span 71 76))\n ((:id . :x4.59.3) (:span 20 27)))\n (:hscopes ((:id . :x4.59.1) (:span 80 98)) ((:id . :x4.59.2) (:span 71 98))\n ((:id . :x4.59.3) (:span 20 98)))\n (:identifiers (:sid . :s4.59) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101172@unknown@formal@none@1@S@To test this, we created 1000 random networks per species using the algorithm described in Methods.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 16) (:start . 14)\n (:id . 46))\n ((:tag . "VBD") (:stem . "create") (:form . "created") (:end . 24)\n (:start . 17) (:id . 47))\n ((:tag . "CD") (:stem . "1000") (:form . "1000") (:end . 29) (:start . 25)\n (:id . 48))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 36)\n (:start . 30) (:id . 49))\n ((:tag . "NNS") (:stem . "network") (:form . "networks") (:end . 45)\n (:start . 37) (:id . 50))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 49) (:start . 46)\n (:id . 51))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 57)\n (:start . 50) (:id . 52))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 63) (:start . 58)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n (:id . 54))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 77)\n (:start . 68) (:id . 55))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 87)\n (:start . 78) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n (:id . 57))\n ((:tag . "NNP") (:stem . "Method") (:form . "Methods") (:end . 98)\n (:start . 91) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.60) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101173@unknown@formal@none@1@S@We then calculated the iPfam coverage on the protein interactions in each randomised network.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "calculate") (:form . "calculated") (:end . 18)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 28) (:start . 23)\n (:id . 46))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 37)\n (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 40) (:start . 38)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 52)\n (:start . 45) (:id . 50))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 65)\n (:start . 53) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n (:id . 52))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 73) (:start . 69)\n (:id . 53))\n ((:tag . "VBN") (:stem . "randomise") (:form . "randomised") (:end . 84)\n (:start . 74) (:id . 54))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 92)\n (:start . 85) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.61) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101174@unknown@formal@none@1@S@Mean and standard deviations of the randomisation experiments are shown in Table 1.@(((:tag . "JJ") (:stem . "mean") (:form . "Mean") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 17)\n (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "deviation") (:form . "deviations") (:end . 28)\n (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n (:id . 47))\n ((:tag . "NN") (:stem . "randomisation") (:form . "randomisation")\n (:end . 49) (:start . 36) (:id . 48))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 61)\n (:start . 50) (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 65) (:start . 62)\n (:id . 50))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 71) (:start . 66)\n (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n (:id . 52))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 80) (:start . 75)\n (:id . 53))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 82) (:start . 81)\n (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s4.62) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101175@unknown@formal@none@1@S@No P value (see Methods) was greater than 1.84 · 10-06.@(((:tag . "DT") (:stem . "no") (:form . "No") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 4) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 10) (:start . 5)\n (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 12) (:start . 11)\n (:id . 45))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 15) (:start . 12)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Method") (:form . "Methods") (:end . 23)\n (:start . 16) (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 24) (:start . 23)\n (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 28) (:start . 25)\n (:id . 49))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 36)\n (:start . 29) (:id . 50))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 41) (:start . 37)\n (:id . 51))\n ((:tag . "CD") (:stem . "1.84") (:form . "1.84") (:end . 46) (:start . 42)\n (:id . 52))\n ((:tag . "NN") (:stem . "·") (:form . "·") (:end . 48) (:start . 47)\n (:id . 53))\n ((:tag . "CD") (:stem . "10-06") (:form . "10-06") (:end . 54) (:start . 49)\n (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 55) (:start . 54)\n (:id . 55)))@@@1@14@((:ncues ((:id . :x4.63.1) (:span 0 2)))\n (:nscopes ((:id . :x4.63.1) (:span 0 46)))\n (:identifiers (:sid . :s4.63) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101176@unknown@formal@none@1@S@This proves that the observed iPfam coverage is significantly higher than expected and iPfam domain pairs are enriched in real experimental protein interactions.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "prove") (:form . "proves") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 29)\n (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 35) (:start . 30)\n (:id . 47))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 44)\n (:start . 36) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 61) (:start . 48) (:id . 50))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 68) (:start . 62)\n (:id . 51))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 73) (:start . 69)\n (:id . 52))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 82)\n (:start . 74) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n (:id . 54))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 92) (:start . 87)\n (:id . 55))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 99)\n (:start . 93) (:id . 56))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 105)\n (:start . 100) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 109) (:start . 106)\n (:id . 58))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 118)\n (:start . 110) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n (:id . 60))\n ((:tag . "JJ") (:stem . "real") (:form . "real") (:end . 126) (:start . 122)\n (:id . 61))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 139)\n (:start . 127) (:id . 62))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 147)\n (:start . 140) (:id . 63))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 160)\n (:start . 148) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.64) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101177@unknown@formal@none@1@S@Few iPfam domain pairs are responsible for a majority of the coverage@(((:tag . "JJ") (:stem . "few") (:form . "Few") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 16)\n (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 22) (:start . 17)\n (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "JJ") (:stem . "responsible") (:form . "responsible") (:end . 38)\n (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 42) (:start . 39)\n (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n (:id . 49))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 53)\n (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n (:id . 52))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 69)\n (:start . 61) (:id . 53)))@@@1@12@((:identifiers (:sid . :s4.65) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101178@unknown@formal@none@1@S@To understand why iPfam domain pairs occur more often in experimental interactions than expected by chance, we analysed the two largest data sets, S. cerevisiae and H. sapiens in more detail.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "understand") (:form . "understand") (:end . 13)\n (:start . 3) (:id . 43))\n ((:tag . "WRB") (:stem . "why") (:form . "why") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 23) (:start . 18)\n (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 30)\n (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 36) (:start . 31)\n (:id . 47))\n ((:tag . "VBP") (:stem . "occur") (:form . "occur") (:end . 42) (:start . 37)\n (:id . 48))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 47) (:start . 43)\n (:id . 49))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 53) (:start . 48)\n (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n (:id . 51))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 69)\n (:start . 57) (:id . 52))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 82)\n (:start . 70) (:id . 53))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 87) (:start . 83)\n (:id . 54))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 96)\n (:start . 88) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 99) (:start . 97)\n (:id . 56))\n ((:tag . "NN") (:stem . "chance") (:form . "chance") (:end . 106)\n (:start . 100) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n (:id . 58))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 110) (:start . 108)\n (:id . 59))\n ((:tag . "VBD") (:stem . "analyse") (:form . "analysed") (:end . 119)\n (:start . 111) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n (:id . 61))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 127) (:start . 124)\n (:id . 62))\n ((:tag . "JJS") (:stem . "large") (:form . "largest") (:end . 135)\n (:start . 128) (:id . 63))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 140)\n (:start . 136) (:id . 64))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 145) (:start . 141)\n (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n (:id . 66))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 149) (:start . 147)\n (:id . 67))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 160)\n (:start . 150) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 164) (:start . 161)\n (:id . 69))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 167) (:start . 165)\n (:id . 70))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 175)\n (:start . 168) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 178) (:start . 176)\n (:id . 72))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 183) (:start . 179)\n (:id . 73))\n ((:tag . "NN") (:stem . "detail") (:form . "detail") (:end . 190)\n (:start . 184) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s4.66) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101180@unknown@formal@none@1@S@In Figure 2, we compare the distribution of iPfam domain pairs on the number of experimental interactions for E. coli, S. cerevisiae and H. sapiens.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 11) (:start . 10)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n (:id . 46))\n ((:tag . "VBP") (:stem . "compare") (:form . "compare") (:end . 23)\n (:start . 16) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n (:id . 48))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 40)\n (:start . 28) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n (:id . 50))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 49) (:start . 44)\n (:id . 51))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 56)\n (:start . 50) (:id . 52))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 62) (:start . 57)\n (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 65) (:start . 63)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n (:id . 55))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 76)\n (:start . 70) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n (:id . 57))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 92)\n (:start . 80) (:id . 58))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 105)\n (:start . 93) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 109) (:start . 106)\n (:id . 60))\n ((:tag . "NNP") (:stem . "E.") (:form . "E.") (:end . 112) (:start . 110)\n (:id . 61))\n ((:tag . "NNP") (:stem . "coli") (:form . "coli") (:end . 117) (:start . 113)\n (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n (:id . 63))\n ((:tag . "NNP") (:stem . "S.") (:form . "S.") (:end . 121) (:start . 119)\n (:id . 64))\n ((:tag . "NNP") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 132)\n (:start . 122) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 136) (:start . 133)\n (:id . 66))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 139) (:start . 137)\n (:id . 67))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 147)\n (:start . 140) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s4.68) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101181@unknown@formal@none@1@S@This plot reflects how many iPfam domain pairs cover how many experimental interactions.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "plot") (:form . "plot") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "reflect") (:form . "reflects") (:end . 18)\n (:start . 10) (:id . 44))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 27) (:start . 23)\n (:id . 46))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 33) (:start . 28)\n (:id . 47))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 40)\n (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 46) (:start . 41)\n (:id . 49))\n ((:tag . "VBP") (:stem . "cover") (:form . "cover") (:end . 52) (:start . 47)\n (:id . 50))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 56) (:start . 53)\n (:id . 51))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 61) (:start . 57)\n (:id . 52))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 74)\n (:start . 62) (:id . 53))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 87)\n (:start . 75) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s4.69) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101182@unknown@formal@none@1@S@Domain pairs that cluster to the left of the plot can be called specific domain pairs, as they only occur in very few covered experimental interactions.@(((:tag . "NN") (:stem . "domain") (:form . "Domain") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 12) (:start . 7)\n (:id . 43))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 17) (:start . 13)\n (:id . 44))\n ((:tag . "VBP") (:stem . "cluster") (:form . "cluster") (:end . 25)\n (:start . 18) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n (:id . 47))\n ((:tag . "NN") (:stem . "left") (:form . "left") (:end . 37) (:start . 33)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n (:id . 50))\n ((:tag . "NN") (:stem . "plot") (:form . "plot") (:end . 49) (:start . 45)\n (:id . 51))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 53) (:start . 50)\n (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 56) (:start . 54)\n (:id . 53))\n ((:tag . "VBN") (:stem . "call") (:form . "called") (:end . 63) (:start . 57)\n (:id . 54))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 72)\n (:start . 64) (:id . 55))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 79)\n (:start . 73) (:id . 56))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 85) (:start . 80)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 89) (:start . 87)\n (:id . 59))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 94) (:start . 90)\n (:id . 60))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 99) (:start . 95)\n (:id . 61))\n ((:tag . "VBP") (:stem . "occur") (:form . "occur") (:end . 105)\n (:start . 100) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n (:id . 63))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 113) (:start . 109)\n (:id . 64))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 117) (:start . 114)\n (:id . 65))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 125)\n (:start . 118) (:id . 66))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 138)\n (:start . 126) (:id . 67))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 151)\n (:start . 139) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s4.70) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101183@unknown@formal@none@1@S@Conversely, domain pairs that cluster to the right of the plot occur in a large number of different covered experimental interactions and can be called promiscuous domain pairs.@(((:tag . "RB") (:stem . "conversely") (:form . "Conversely") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 18)\n (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 24) (:start . 19)\n (:id . 45))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 29) (:start . 25)\n (:id . 46))\n ((:tag . "VBP") (:stem . "cluster") (:form . "cluster") (:end . 37)\n (:start . 30) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n (:id . 49))\n ((:tag . "NN") (:stem . "right") (:form . "right") (:end . 50) (:start . 45)\n (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n (:id . 52))\n ((:tag . "NN") (:stem . "plot") (:form . "plot") (:end . 62) (:start . 58)\n (:id . 53))\n ((:tag . "VBP") (:stem . "occur") (:form . "occur") (:end . 68) (:start . 63)\n (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 71) (:start . 69)\n (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n (:id . 56))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 79) (:start . 74)\n (:id . 57))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 86)\n (:start . 80) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n (:id . 59))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 99)\n (:start . 90) (:id . 60))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 107)\n (:start . 100) (:id . 61))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 120)\n (:start . 108) (:id . 62))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 133)\n (:start . 121) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n (:id . 64))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 141) (:start . 138)\n (:id . 65))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 144) (:start . 142)\n (:id . 66))\n ((:tag . "VBN") (:stem . "call") (:form . "called") (:end . 151)\n (:start . 145) (:id . 67))\n ((:tag . "JJ") (:stem . "promiscuous") (:form . "promiscuous") (:end . 163)\n (:start . 152) (:id . 68))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 170)\n (:start . 164) (:id . 69))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 176)\n (:start . 171) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s4.71) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101184@unknown@formal@none@1@S@Frequencies of iPfam domain pairs in E. coli, S. cerevisiae and H. sapiens protein interactions@(((:tag . "NNS") (:stem . "frequency") (:form . "Frequencies") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 43))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 20) (:start . 15)\n (:id . 44))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 27)\n (:start . 21) (:id . 45))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 33) (:start . 28)\n (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n (:id . 47))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 39) (:start . 37)\n (:id . 48))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 44) (:start . 40)\n (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n (:id . 50))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 48) (:start . 46)\n (:id . 51))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 59)\n (:start . 49) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n (:id . 53))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 66) (:start . 64)\n (:id . 54))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 74)\n (:start . 67) (:id . 55))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 82)\n (:start . 75) (:id . 56))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 95)\n (:start . 83) (:id . 57)))@@@1@16@((:identifiers (:sid . :s4.72) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5101185@unknown@formal@none@1@S@Frequencies of iPfam domain pairs in E. coli, S. cerevisiae and H. sapiens protein interactions.@(((:tag . "NNS") (:stem . "frequency") (:form . "Frequencies") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 43))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 20) (:start . 15)\n (:id . 44))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 27)\n (:start . 21) (:id . 45))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 33) (:start . 28)\n (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n (:id . 47))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 39) (:start . 37)\n (:id . 48))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 44) (:start . 40)\n (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n (:id . 50))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 48) (:start . 46)\n (:id . 51))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 59)\n (:start . 49) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n (:id . 53))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 66) (:start . 64)\n (:id . 54))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 74)\n (:start . 67) (:id . 55))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 82)\n (:start . 75) (:id . 56))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 95)\n (:start . 83) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s4.73) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101186@unknown@formal@none@1@S@Each point in this graph represents a set of protein interactions.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 18) (:start . 14)\n (:id . 45))\n ((:tag . "NN") (:stem . "graph") (:form . "graph") (:end . 24) (:start . 19)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 35)\n (:start . 25) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n (:id . 48))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 41) (:start . 38)\n (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 52)\n (:start . 45) (:id . 51))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 65)\n (:start . 53) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s4.74) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101187@unknown@formal@none@1@S@The abscissa reflects the number of interactions in each set that contain the same iPfam domain pair.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "abscissa") (:form . "abscissa") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "reflect") (:form . "reflects") (:end . 21)\n (:start . 13) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 32)\n (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n (:id . 47))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 48)\n (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n (:id . 49))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 56) (:start . 52)\n (:id . 50))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 60) (:start . 57)\n (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 65) (:start . 61)\n (:id . 52))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 73)\n (:start . 66) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n (:id . 54))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 82) (:start . 78)\n (:id . 55))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 88) (:start . 83)\n (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 95)\n (:start . 89) (:id . 57))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 100) (:start . 96)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.75) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101188@unknown@formal@none@1@S@The ordinate shows the number of distinct such sets, each defined by a different iPfam domain pair.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "ordinate") (:form . "ordinate") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 29)\n (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n (:id . 47))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 41)\n (:start . 33) (:id . 48))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 46) (:start . 42)\n (:id . 49))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 51) (:start . 47)\n (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n (:id . 51))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 57) (:start . 53)\n (:id . 52))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 65)\n (:start . 58) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 68) (:start . 66)\n (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 70) (:start . 69)\n (:id . 55))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 80)\n (:start . 71) (:id . 56))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 86) (:start . 81)\n (:id . 57))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 93)\n (:start . 87) (:id . 58))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 98) (:start . 94)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.76) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101190@unknown@formal@none@1@S@Dotted lines denote fitted monomial functions, showing that the distributions follow a power law.@(((:tag . "JJ") (:stem . "dotted") (:form . "Dotted") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 12) (:start . 7)\n (:id . 43))\n ((:tag . 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"a") (:end . 86) (:start . 85)\n (:id . 54))\n ((:tag . "NN") (:stem . "power") (:form . "power") (:end . 92) (:start . 87)\n (:id . 55))\n ((:tag . "NN") (:stem . "law") (:form . "law") (:end . 96) (:start . 93)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s4.78) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101191@unknown@formal@none@1@S@All three distributions in Figure 2 resemble a power law distribution, according to the good fit of log-linear functions (log(f(x)) = k log x + log a) shown as dotted lines.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n (:end . 23) (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 26) (:start . 24)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 33)\n (:start . 27) (:id . 46))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 35) (:start . 34)\n (:id . 47))\n ((:tag . "VBP") (:stem . "resemble") (:form . "resemble") (:end . 44)\n (:start . 36) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 46) (:start . 45)\n (:id . 49))\n ((:tag . "NN") (:stem . "power") (:form . "power") (:end . 52) (:start . 47)\n (:id . 50))\n ((:tag . "NN") (:stem . "law") (:form . "law") (:end . 56) (:start . 53)\n (:id . 51))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 69)\n (:start . 57) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n (:id . 53))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 80)\n (:start . 71) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 83) (:start . 81)\n (:id . 55))\n ((:tag . 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(:end . 173) (:start . 172)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s4.79) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101192@unknown@formal@none@1@S@The slopes k of the H. sapiens and S. cerevisiae distributions are very similar (-1.53 and -1.60, respectively), while E. coli has a markedly smaller slope (-2.78).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "slope") (:form . "slopes") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "k") (:form . "k") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 46))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 22) (:start . 20)\n (:id . 47))\n ((:tag . "NNS") (:stem . "sapien") (:form . 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"CD") (:stem . "-1.60") (:form . "-1.60") (:end . 96) (:start . 91)\n (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n (:id . 60))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 110)\n (:start . 98) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n (:id . 63))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 118)\n (:start . 113) (:id . 64))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 121) (:start . 119)\n (:id . 65))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 126) (:start . 122)\n (:id . 66))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 130) (:start . 127)\n (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 132) (:start . 131)\n (:id . 68))\n ((:tag . "RB") (:stem . "markedly") (:form . "markedly") (:end . 141)\n (:start . 133) (:id . 69))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 149)\n (:start . 142) (:id . 70))\n ((:tag . "NN") (:stem . "slope") (:form . "slope") (:end . 155)\n (:start . 150) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 157) (:start . 156)\n (:id . 72))\n ((:tag . "CD") (:stem . "-2.78") (:form . "-2.78") (:end . 162)\n (:start . 157) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 163) (:start . 162)\n (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s4.80) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101193@unknown@formal@none@1@S@This suggests that the ratio of specific to promiscuous iPfam domain pairs is very similar in S. cerevisiae and H. sapiens, whereas E. coli features fewer multiply reoccurring iPfam domain pairs.@(((:tag . 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",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n (:id . 63))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 131)\n (:start . 124) (:id . 64))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 134) (:start . 132)\n (:id . 65))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 139) (:start . 135)\n (:id . 66))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 148)\n (:start . 140) (:id . 67))\n ((:tag . "JJR") (:stem . "few") (:form . "fewer") (:end . 154) (:start . 149)\n (:id . 68))\n ((:tag . "JJ") (:stem . "multiply") (:form . "multiply") (:end . 163)\n (:start . 155) (:id . 69))\n ((:tag . "VBG") (:stem . "reoccurre") (:form . "reoccurring") (:end . 175)\n (:start . 164) (:id . 70))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 181)\n (:start . 176) (:id . 71))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 188)\n (:start . 182) (:id . 72))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 194)\n (:start . 189) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n (:id . 74)))@@@1@33@((:hcues ((:id . :x4.81.1) (:span 5 13)))\n (:hscopes ((:id . :x4.81.1) (:span 5 194)))\n (:identifiers (:sid . :s4.81) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101194@unknown@formal@none@1@S@The power law distribution of iPfam frequencies implies that the majority of covered protein interactions can be attributed to a minority of iPfam domain pairs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "power") (:form . "power") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "law") (:form . "law") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 26)\n (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . 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"interactions") (:end . 105)\n (:start . 93) (:id . 56))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 109) (:start . 106)\n (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 112) (:start . 110)\n (:id . 58))\n ((:tag . "VBN") (:stem . "attribute") (:form . "attributed") (:end . 123)\n (:start . 113) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 126) (:start . 124)\n (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 128) (:start . 127)\n (:id . 61))\n ((:tag . "NN") (:stem . "minority") (:form . "minority") (:end . 137)\n (:start . 129) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 140) (:start . 138)\n (:id . 63))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 146)\n (:start . 141) (:id . 64))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 153)\n (:start . 147) (:id . 65))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 159)\n (:start . 154) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n (:id . 67)))@@@1@26@((:hcues ((:id . :x4.82.1) (:span 106 109)) ((:id . :x4.82.2) (:span 48 55)))\n (:hscopes ((:id . :x4.82.1) (:span 106 159))\n ((:id . :x4.82.2) (:span 48 159)))\n (:identifiers (:sid . :s4.82) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101195@unknown@formal@none@1@S@51.7% of the iPfam domain pairs in S. cerevisiae and 45.3% in H. sapiens are seen in just one experimental interaction.@(((:tag . "CD") (:stem . "51.7") (:form . "51.7") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 5) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 8) (:start . 6)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 45))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 18) (:start . 13)\n (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 25)\n (:start . 19) (:id . 47))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 31) (:start . 26)\n (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n (:id . 49))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 37) (:start . 35)\n (:id . 50))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 48)\n (:start . 38) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n (:id . 52))\n ((:tag . "CD") (:stem . "45.3") (:form . "45.3") (:end . 57) (:start . 53)\n (:id . 53))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 58) (:start . 57)\n (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n (:id . 55))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 64) (:start . 62)\n (:id . 56))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 72)\n (:start . 65) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 76) (:start . 73)\n (:id . 58))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 81) (:start . 77)\n (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n (:id . 60))\n ((:tag . "RB") (:stem . "just") (:form . "just") (:end . 89) (:start . 85)\n (:id . 61))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 93) (:start . 90)\n (:id . 62))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 106)\n (:start . 94) (:id . 63))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 118)\n (:start . 107) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.83) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101196@unknown@formal@none@1@S@Conversely, 92.4% of H. sapiens and 85.4% of S. cerevisiae covered experimental interactions contain an iPfam domain pair that occurs more than once.@(((:tag . "RB") (:stem . "conversely") (:form . "Conversely") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 43))\n ((:tag . "CD") (:stem . "92.4") (:form . "92.4") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 46))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 23) (:start . 21)\n (:id . 47))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 31)\n (:start . 24) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n (:id . 49))\n ((:tag . "CD") (:stem . "85.4") (:form . "85.4") (:end . 40) (:start . 36)\n (:id . 50))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 41) (:start . 40)\n (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n (:id . 52))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 47) (:start . 45)\n (:id . 53))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 58)\n (:start . 48) (:id . 54))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 66)\n (:start . 59) (:id . 55))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 79)\n (:start . 67) (:id . 56))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 92)\n (:start . 80) (:id . 57))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 100)\n (:start . 93) (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 103) (:start . 101)\n (:id . 59))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 109)\n (:start . 104) (:id . 60))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 116)\n (:start . 110) (:id . 61))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 121) (:start . 117)\n (:id . 62))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 126) (:start . 122)\n (:id . 63))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 133)\n (:start . 127) (:id . 64))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 138) (:start . 134)\n (:id . 65))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 143) (:start . 139)\n (:id . 66))\n ((:tag . "RB") (:stem . "once") (:form . "once") (:end . 148) (:start . 144)\n (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s4.84) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101197@unknown@formal@none@1@S@Even more, half of the covered experimental interactions in H. sapiens contain an iPfam domain pair that occurs in more than 16 different experimental interactions (5 for S. cerevisiae).@(((:tag . "RB") (:stem . "even") (:form . "Even") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "half") (:form . "half") (:end . 15) (:start . 11)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 47))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 30)\n (:start . 23) (:id . 48))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 43)\n (:start . 31) (:id . 49))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 56)\n (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n (:id . 51))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 62) (:start . 60)\n (:id . 52))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 70)\n (:start . 63) (:id . 53))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 78)\n (:start . 71) (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 81) (:start . 79)\n (:id . 55))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 87) (:start . 82)\n (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 94)\n (:start . 88) (:id . 57))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 99) (:start . 95)\n (:id . 58))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 104) (:start . 100)\n (:id . 59))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 111)\n (:start . 105) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n (:id . 61))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 119) (:start . 115)\n (:id . 62))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 124) (:start . 120)\n (:id . 63))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 127) (:start . 125)\n (:id . 64))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 137)\n (:start . 128) (:id . 65))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 150)\n (:start . 138) (:id . 66))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 163)\n (:start . 151) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 165) (:start . 164)\n (:id . 68))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 166) (:start . 165)\n (:id . 69))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 170) (:start . 167)\n (:id . 70))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 173) (:start . 171)\n (:id . 71))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 184)\n (:start . 174) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 185) (:start . 184)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s4.85) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101198@unknown@formal@none@1@S@Degree distribution and iPfam domain pair frequency are correlated@(((:tag . "NN") (:stem . "degree") (:form . "Degree") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 19)\n (:start . 7) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n (:id . 44))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 29) (:start . 24)\n (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 36)\n (:start . 30) (:id . 46))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 41) (:start . 37)\n (:id . 47))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 51)\n (:start . 42) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 55) (:start . 52)\n (:id . 49))\n ((:tag . "VBN") (:stem . "correlate") (:form . "correlated") (:end . 66)\n (:start . 56) (:id . 50)))@@@1@9@((:identifiers (:sid . :s4.86) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101200@unknown@formal@none@1@S@For each node (i.e. protein) in the filtered H. sapiens and S. cerevisiae protein interaction network, we calculated its degree, defined as the number of adjacent edges (i.e. interactions).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "node") (:form . "node") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 15) (:start . 14)\n (:id . 45))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 19) (:start . 15)\n (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 27)\n (:start . 20) (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 28) (:start . 27)\n (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n (:id . 50))\n ((:tag . "VBN") (:stem . "filter") (:form . "filtered") (:end . 44)\n (:start . 36) (:id . 51))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 47) (:start . 45)\n (:id . 52))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 55)\n (:start . 48) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n (:id . 54))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 62) (:start . 60)\n (:id . 55))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 73)\n (:start . 63) (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 81)\n (:start . 74) (:id . 57))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 93)\n (:start . 82) (:id . 58))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 101)\n (:start . 94) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n (:id . 60))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 105) (:start . 103)\n (:id . 61))\n ((:tag . "VBD") (:stem . "calculate") (:form . "calculated") (:end . 116)\n (:start . 106) (:id . 62))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 120) (:start . 117)\n (:id . 63))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 127)\n (:start . 121) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n (:id . 65))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 136)\n (:start . 129) (:id . 66))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 139) (:start . 137)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n (:id . 68))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 150)\n (:start . 144) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 153) (:start . 151)\n (:id . 70))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 162)\n (:start . 154) (:id . 71))\n ((:tag . "NNS") (:stem . "edge") (:form . "edges") (:end . 168)\n (:start . 163) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 170) (:start . 169)\n (:id . 73))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 174) (:start . 170)\n (:id . 74))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 187)\n (:start . 175) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s4.88) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101201@unknown@formal@none@1@S@At the same time, we counted the number of iPfam domain pairs on the adjacent edges.@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 16) (:start . 12)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 20) (:start . 18)\n (:id . 47))\n ((:tag . "VBD") (:stem . "count") (:form . "counted") (:end . 28)\n (:start . 21) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n (:id . 49))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 39)\n (:start . 33) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n (:id . 51))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 48) (:start . 43)\n (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 55)\n (:start . 49) (:id . 53))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 61) (:start . 56)\n (:id . 54))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 64) (:start . 62)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n (:id . 56))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 77)\n (:start . 69) (:id . 57))\n ((:tag . "NNS") (:stem . "edge") (:form . "edges") (:end . 83) (:start . 78)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.89) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101202@unknown@formal@none@1@S@In Figure 3, we plot the mean number of iPfam domain pairs relative to the degree of the node.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 11) (:start . 10)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n (:id . 46))\n ((:tag . "VBP") (:stem . "plot") (:form . "plot") (:end . 20) (:start . 16)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n (:id . 48))\n ((:tag . "JJ") (:stem . "mean") (:form . "mean") (:end . 29) (:start . 25)\n (:id . 49))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 36)\n (:start . 30) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n (:id . 51))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 45) (:start . 40)\n (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 52)\n (:start . 46) (:id . 53))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 58) (:start . 53)\n (:id . 54))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 67)\n (:start . 59) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 70) (:start . 68)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n (:id . 57))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 81)\n (:start . 75) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n (:id . 60))\n ((:tag . "NN") (:stem . "node") (:form . "node") (:end . 93) (:start . 89)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.90) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101203@unknown@formal@none@1@S@Average frequency of iPfam domain pairs relative to degree of node@(((:tag . "JJ") (:stem . "average") (:form . "Average") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 17)\n (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 44))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 26) (:start . 21)\n (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 33)\n (:start . 27) (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 39) (:start . 34)\n (:id . 47))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 48)\n (:start . 40) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n (:id . 49))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 58)\n (:start . 52) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n (:id . 51))\n ((:tag . "NN") (:stem . "node") (:form . "node") (:end . 66) (:start . 62)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s4.91) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5101204@unknown@formal@none@1@S@Average frequency of iPfam domain pairs relative to degree of node.@(((:tag . "JJ") (:stem . "average") (:form . "Average") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 17)\n (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 44))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 26) (:start . 21)\n (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 33)\n (:start . 27) (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 39) (:start . 34)\n (:id . 47))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 48)\n (:start . 40) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n (:id . 49))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 58)\n (:start . 52) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n (:id . 51))\n ((:tag . "NN") (:stem . "node") (:form . "node") (:end . 66) (:start . 62)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s4.92) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101205@unknown@formal@none@1@S@Each point represents a protein in the interaction networks of H. sapiens (blue) and S. cerevisiae (green).@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 21)\n (:start . 11) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 31)\n (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n (:id . 48))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 50)\n (:start . 39) (:id . 49))\n ((:tag . "NNS") (:stem . "network") (:form . "networks") (:end . 59)\n (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n (:id . 51))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 65) (:start . 63)\n (:id . 52))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 73)\n (:start . 66) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n (:id . 54))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 79) (:start . 75)\n (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n (:id . 57))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 87) (:start . 85)\n (:id . 58))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 98)\n (:start . 88) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n (:id . 60))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 105)\n (:start . 100) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s4.93) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101206@unknown@formal@none@1@S@For each protein, we calculate the degree, defined as the number of interactions the protein is involved in.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 16)\n (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 20) (:start . 18)\n (:id . 46))\n ((:tag . "VBP") (:stem . "calculate") (:form . "calculate") (:end . 30)\n (:start . 21) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 48))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 41)\n (:start . 35) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n (:id . 50))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 50)\n (:start . 43) (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 53) (:start . 51)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n (:id . 53))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 64)\n (:start . 58) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n (:id . 55))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 80)\n (:start . 68) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n (:id . 57))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 92)\n (:start . 85) (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 95) (:start . 93)\n (:id . 59))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 104)\n (:start . 96) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.94) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101207@unknown@formal@none@1@S@On the y-axis, we show the average number of iPfam domain pairs in edges adjacent to proteins of degree x.@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "y-axis") (:form . "y-axis") (:end . 13) (:start . 7)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n (:id . 46))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 22) (:start . 18)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 48))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 34)\n (:start . 27) (:id . 49))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 41)\n (:start . 35) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n (:id . 51))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 50) (:start . 45)\n (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 57)\n (:start . 51) (:id . 53))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 63) (:start . 58)\n (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n (:id . 55))\n ((:tag . "NNS") (:stem . "edge") (:form . "edges") (:end . 72) (:start . 67)\n (:id . 56))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 81)\n (:start . 73) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 84) (:start . 82)\n (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 93)\n (:start . 85) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n (:id . 60))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 103)\n (:start . 97) (:id . 61))\n ((:tag . "NN") (:stem . "x") (:form . "x") (:end . 105) (:start . 104)\n (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s4.95) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101208@unknown@formal@none@1@S@We calculated a Spearman correlation of 0.68 and 0.71, for H. sapiens and S. cerevisiae.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "calculate") (:form . "calculated") (:end . 13)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 15) (:start . 14)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Spearman") (:form . "Spearman") (:end . 24)\n (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 36)\n (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n (:id . 47))\n ((:tag . "CD") (:stem . "0.68") (:form . "0.68") (:end . 44) (:start . 40)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n (:id . 49))\n ((:tag . "CD") (:stem . "0.71") (:form . "0.71") (:end . 53) (:start . 49)\n (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 58) (:start . 55)\n (:id . 52))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 61) (:start . 59)\n (:id . 53))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 69)\n (:start . 62) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n (:id . 55))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 76) (:start . 74)\n (:id . 56))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 87)\n (:start . 77) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s4.96) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101210@unknown@formal@none@1@S@We find that for proteins from a degree of 1 to 50, there is strong correlation in both H. sapiens and S. cerevisiae (Spearman correlation coefficients of 0.68 and 0.71, respectively) between degree and number of iPfam domain pairs on adjacent edges.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 25)\n (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 30) (:start . 26)\n (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n (:id . 48))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 39)\n (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n (:id . 50))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 44) (:start . 43)\n (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n (:id . 52))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 50) (:start . 48)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n (:id . 54))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 57) (:start . 52)\n (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 60) (:start . 58)\n (:id . 56))\n ((:tag . "JJ") (:stem . "strong") (:form . "strong") (:end . 67)\n (:start . 61) (:id . 57))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 79)\n (:start . 68) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n (:id . 59))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 87) (:start . 83)\n (:id . 60))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 90) (:start . 88)\n (:id . 61))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 98)\n (:start . 91) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n (:id . 63))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 105) (:start . 103)\n (:id . 64))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 116)\n (:start . 106) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 118) (:start . 117)\n (:id . 66))\n ((:tag . "NNP") (:stem . "Spearman") (:form . "Spearman") (:end . 126)\n (:start . 118) (:id . 67))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 138)\n (:start . 127) (:id . 68))\n ((:tag . "NNS") (:stem . "coefficient") (:form . "coefficients") (:end . 151)\n (:start . 139) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 154) (:start . 152)\n (:id . 70))\n ((:tag . "CD") (:stem . "0.68") (:form . "0.68") (:end . 159) (:start . 155)\n (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 163) (:start . 160)\n (:id . 72))\n ((:tag . "CD") (:stem . "0.71") (:form . "0.71") (:end . 168) (:start . 164)\n (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 169) (:start . 168)\n (:id . 74))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 182)\n (:start . 170) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 183) (:start . 182)\n (:id . 76))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 191)\n (:start . 184) (:id . 77))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 198)\n (:start . 192) (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 202) (:start . 199)\n (:id . 79))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 209)\n (:start . 203) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 212) (:start . 210)\n (:id . 81))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 218)\n (:start . 213) (:id . 82))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 225)\n (:start . 219) (:id . 83))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 231)\n (:start . 226) (:id . 84))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 234) (:start . 232)\n (:id . 85))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 243)\n (:start . 235) (:id . 86))\n ((:tag . "NNS") (:stem . "edge") (:form . "edges") (:end . 249)\n (:start . 244) (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 250) (:start . 249)\n (:id . 88)))@@@1@47@((:identifiers (:sid . :s4.98) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101211@unknown@formal@none@1@S@For the 1.2% of proteins in H. sapiens and 6.4% in S. cerevisiae which have a degree higher than 50, the correlation gradually diminishes.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "CD") (:stem . "1.2") (:form . "1.2") (:end . 11) (:start . 8)\n (:id . 44))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 12) (:start . 11)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 24)\n (:start . 16) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n (:id . 48))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 30) (:start . 28)\n (:id . 49))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 38)\n (:start . 31) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n (:id . 51))\n ((:tag . "CD") (:stem . "6.4") (:form . "6.4") (:end . 46) (:start . 43)\n (:id . 52))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 47) (:start . 46)\n (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n (:id . 54))\n ((:tag . "NNP") (:stem . "S.") (:form . "S.") (:end . 53) (:start . 51)\n (:id . 55))\n ((:tag . "NNS") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 64)\n (:start . 54) (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 70) (:start . 65)\n (:id . 57))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 75) (:start . 71)\n (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 77) (:start . 76)\n (:id . 59))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 84)\n (:start . 78) (:id . 60))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 91) (:start . 85)\n (:id . 61))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 96) (:start . 92)\n (:id . 62))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 99) (:start . 97)\n (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n (:id . 65))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 116)\n (:start . 105) (:id . 66))\n ((:tag . "RB") (:stem . "gradually") (:form . "gradually") (:end . 126)\n (:start . 117) (:id . 67))\n ((:tag . "VBZ") (:stem . "diminish") (:form . "diminishes") (:end . 137)\n (:start . 127) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s4.99) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101212@unknown@formal@none@1@S@Promiscuous domain pairs@(((:tag . "JJ") (:stem . "promiscuous") (:form . "Promiscuous") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 18)\n (:start . 12) (:id . 43))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 24) (:start . 19)\n (:id . 44)))@@@1@3@((:identifiers (:sid . :s4.100) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101213@unknown@formal@none@1@S@Additional file 1 contains a list of all iPfam domain pairs and their frequencies in the experimental protein interactions, while Additional file 4 lists the frequencies of the single domains.@(((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 15) (:start . 11)\n (:id . 43))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 17) (:start . 16)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 26)\n (:start . 18) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n (:id . 46))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n (:id . 48))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 40) (:start . 37)\n (:id . 49))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 46) (:start . 41)\n (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 53)\n (:start . 47) (:id . 51))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 59) (:start . 54)\n (:id . 52))\n ((:tag . "CC") (:stem . 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"Additional") (:end . 140)\n (:start . 130) (:id . 63))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 145) (:start . 141)\n (:id . 64))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 147) (:start . 146)\n (:id . 65))\n ((:tag . "NNS") (:stem . "list") (:form . "lists") (:end . 153)\n (:start . 148) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 157) (:start . 154)\n (:id . 67))\n ((:tag . "NNS") (:stem . "frequency") (:form . "frequencies") (:end . 169)\n (:start . 158) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 172) (:start . 170)\n (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 176) (:start . 173)\n (:id . 70))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 183)\n (:start . 177) (:id . 71))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 191)\n (:start . 184) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s4.101) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101214@unknown@formal@none@1@S@Interactions between protein kinase domains (Pkinase, Pfam acc. PF00069 and Pkinase_Tyr, Pfam acc. PF07714) are the most frequent iPfam domain pairs, as well as interactions involving recognition domains such as SH2 or SH3.@(((:tag . "NNS") (:stem . "interaction") (:form . "Interactions") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 20)\n (:start . 13) (:id . 43))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 28)\n (:start . 21) (:id . 44))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 35)\n (:start . 29) (:id . 45))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 43)\n (:start . 36) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . 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"pf07714") (:form . "PF07714") (:end . 106)\n (:start . 99) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 111) (:start . 108)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n (:id . 61))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 120) (:start . 116)\n (:id . 62))\n ((:tag . "JJ") (:stem . "frequent") (:form . "frequent") (:end . 129)\n (:start . 121) (:id . 63))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 135)\n (:start . 130) (:id . 64))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 142)\n (:start . 136) (:id . 65))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 148)\n (:start . 143) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n (:id . 67))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 152) (:start . 150)\n (:id . 68))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 157) (:start . 153)\n (:id . 69))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 160) (:start . 158)\n (:id . 70))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 173)\n (:start . 161) (:id . 71))\n ((:tag . "VBG") (:stem . "involve") (:form . "involving") (:end . 183)\n (:start . 174) (:id . 72))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 195)\n (:start . 184) (:id . 73))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 203)\n (:start . 196) (:id . 74))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 208) (:start . 204)\n (:id . 75))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 211) (:start . 209)\n (:id . 76))\n ((:tag . "NNP") (:stem . "SH2") (:form . "SH2") (:end . 215) (:start . 212)\n (:id . 77))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 218) (:start . 216)\n (:id . 78))\n ((:tag . "NNP") (:stem . "SH3") (:form . "SH3") (:end . 222) (:start . 219)\n (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 223) (:start . 222)\n (:id . 80)))@@@1@39@((:identifiers (:sid . :s4.102) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101215@unknown@formal@none@1@S@In S. cerevisiae, the Proteasome family (Pfam acc. PF00227, a family of peptidases) and WD40 (Pfam acc. PF00400, a repeat involved in multimer assembly) are also amongst the five most frequent iPfam domain pairs.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 16)\n (:start . 6) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . 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"of") (:end . 71) (:start . 69)\n (:id . 56))\n ((:tag . "NNS") (:stem . "peptidase") (:form . "peptidases") (:end . 82)\n (:start . 72) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n (:id . 59))\n ((:tag . "NNP") (:stem . "WD40") (:form . "WD40") (:end . 92) (:start . 88)\n (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 94) (:start . 93)\n (:id . 61))\n ((:tag . "NN") (:stem . "pfam") (:form . "Pfam") (:end . 98) (:start . 94)\n (:id . 62))\n ((:tag . "NN") (:stem . "acc.") (:form . "acc.") (:end . 103) (:start . 99)\n (:id . 63))\n ((:tag . "NN") (:stem . "pf00400") (:form . "PF00400") (:end . 111)\n (:start . 104) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 114) (:start . 113)\n (:id . 66))\n ((:tag . "NN") (:stem . "repeat") (:form . "repeat") (:end . 121)\n (:start . 115) (:id . 67))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 130)\n (:start . 122) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 133) (:start . 131)\n (:id . 69))\n ((:tag . "NN") (:stem . "multimer") (:form . "multimer") (:end . 142)\n (:start . 134) (:id . 70))\n ((:tag . "NN") (:stem . "assembly") (:form . "assembly") (:end . 151)\n (:start . 143) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n (:id . 72))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 156) (:start . 153)\n (:id . 73))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 161) (:start . 157)\n (:id . 74))\n ((:tag . "IN") (:stem . "amongst") (:form . "amongst") (:end . 169)\n (:start . 162) (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 173) (:start . 170)\n (:id . 76))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 178) (:start . 174)\n (:id . 77))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 183) (:start . 179)\n (:id . 78))\n ((:tag . "JJ") (:stem . "frequent") (:form . "frequent") (:end . 192)\n (:start . 184) (:id . 79))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 198)\n (:start . 193) (:id . 80))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 205)\n (:start . 199) (:id . 81))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 211)\n (:start . 206) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n (:id . 83)))@@@1@42@((:identifiers (:sid . :s4.103) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101216@unknown@formal@none@1@S@As expected, more frequent domains are also more likely to be found as pairs in interacting proteins.@(((:tag . "IN") (:stem . "as") (:form . 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"be") (:form . "be") (:end . 61) (:start . 59)\n (:id . 53))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 67) (:start . 62)\n (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 70) (:start . 68)\n (:id . 55))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 76) (:start . 71)\n (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n (:id . 57))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 91)\n (:start . 80) (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 100)\n (:start . 92) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n (:id . 60)))@@@1@19@((:hcues ((:id . :x4.104.1) (:span 49 55)))\n (:hscopes ((:id . :x4.104.1) (:span 13 100)))\n (:identifiers (:sid . :s4.104) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101217@unknown@formal@none@1@S@It should be noted however that in the PDB structures, some of the observed domain pairs (Pkinase_Tyr ↔ SH3_1, Pkinase_C ↔ Pkinase and others) are only seen to interact within one protein (intrachain interactions) as opposed to interactions between two distinct proteins (interchain interaction).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 12) (:start . 10)\n (:id . 44))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . 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"observed") (:end . 75)\n (:start . 67) (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 82)\n (:start . 76) (:id . 57))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 88) (:start . 83)\n (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n (:id . 59))\n ((:tag . "NNP") (:stem . "Pkinase_Tyr") (:form . "Pkinase_Tyr") (:end . 101)\n (:start . 90) (:id . 60))\n ((:tag . "NNP") (:stem . "↔") (:form . "↔") (:end . 103) (:start . 102)\n (:id . 61))\n ((:tag . "NNP") (:stem . "SH3_1") (:form . "SH3_1") (:end . 109)\n (:start . 104) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n (:id . 63))\n ((:tag . "NNP") (:stem . "Pkinase_C") (:form . "Pkinase_C") (:end . 120)\n (:start . 111) (:id . 64))\n ((:tag . "NNP") (:stem . "↔") (:form . "↔") (:end . 122) (:start . 121)\n (:id . 65))\n ((:tag . "NNP") (:stem . "Pkinase") (:form . 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"NN") (:stem . "protein") (:form . "protein") (:end . 187)\n (:start . 180) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 189) (:start . 188)\n (:id . 78))\n ((:tag . "JJ") (:stem . "intrachain") (:form . "intrachain") (:end . 199)\n (:start . 189) (:id . 79))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 212)\n (:start . 200) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 213) (:start . 212)\n (:id . 81))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 216) (:start . 214)\n (:id . 82))\n ((:tag . "VBN") (:stem . "oppose") (:form . "opposed") (:end . 224)\n (:start . 217) (:id . 83))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 227) (:start . 225)\n (:id . 84))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 240)\n (:start . 228) (:id . 85))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 248)\n (:start . 241) (:id . 86))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 252) (:start . 249)\n (:id . 87))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 261)\n (:start . 253) (:id . 88))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 270)\n (:start . 262) (:id . 89))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 272) (:start . 271)\n (:id . 90))\n ((:tag . "NN") (:stem . "interchain") (:form . "interchain") (:end . 282)\n (:start . 272) (:id . 91))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 294)\n (:start . 283) (:id . 92))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 295) (:start . 294)\n (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 296) (:start . 295)\n (:id . 94)))@@@1@53@((:identifiers (:sid . :s4.105) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101218@unknown@formal@none@1@S@The table in Additional file 5 lists the number of PDB structures for each iPfam domain pair, distinguishing between intrachain and interchain interactions.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "table") (:form . "table") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 12) (:start . 10)\n (:id . 44))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 23)\n (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 28) (:start . 24)\n (:id . 46))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 30) (:start . 29)\n (:id . 47))\n ((:tag . "NNS") (:stem . "list") (:form . "lists") (:end . 36) (:start . 31)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n (:id . 49))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 47)\n (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n (:id . 51))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 54) (:start . 51)\n (:id . 52))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 65)\n (:start . 55) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 69) (:start . 66)\n (:id . 54))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 74) (:start . 70)\n (:id . 55))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 80) (:start . 75)\n (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 87)\n (:start . 81) (:id . 57))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 92) (:start . 88)\n (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n (:id . 59))\n ((:tag . "VBG") (:stem . "distinguish") (:form . "distinguishing")\n (:end . 108) (:start . 94) (:id . 60))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 116)\n (:start . 109) (:id . 61))\n ((:tag . "JJ") (:stem . "intrachain") (:form . "intrachain") (:end . 127)\n (:start . 117) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 131) (:start . 128)\n (:id . 63))\n ((:tag . "JJ") (:stem . "interchain") (:form . "interchain") (:end . 142)\n (:start . 132) (:id . 64))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 155)\n (:start . 143) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s4.106) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101220@unknown@formal@none@1@S@A possible explanation for the occurrence of purely intrachain iPfam domain pairs in the covered experimental interactions is that they frequently cooccur together on the same protein with other iPfam domain pairs.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 10)\n (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "explanation") (:form . "explanation") (:end . 22)\n (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 26) (:start . 23)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "NN") (:stem . "occurrence") (:form . "occurrence") (:end . 41)\n (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n (:id . 48))\n ((:tag . "RB") (:stem . "purely") (:form . "purely") (:end . 51)\n (:start . 45) (:id . 49))\n ((:tag . "JJ") (:stem . "intrachain") (:form . "intrachain") (:end . 62)\n (:start . 52) (:id . 50))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 68) (:start . 63)\n (:id . 51))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 75)\n (:start . 69) (:id . 52))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 81) (:start . 76)\n (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n (:id . 55))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 96)\n (:start . 89) (:id . 56))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 109)\n (:start . 97) (:id . 57))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 122)\n (:start . 110) (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 125) (:start . 123)\n (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 130) (:start . 126)\n (:id . 60))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 135) (:start . 131)\n (:id . 61))\n ((:tag . "RB") (:stem . "frequently") (:form . "frequently") (:end . 146)\n (:start . 136) (:id . 62))\n ((:tag . "VBP") (:stem . "cooccur") (:form . "cooccur") (:end . 154)\n (:start . 147) (:id . 63))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 163)\n (:start . 155) (:id . 64))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 166) (:start . 164)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 170) (:start . 167)\n (:id . 66))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 175) (:start . 171)\n (:id . 67))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 183)\n (:start . 176) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 188) (:start . 184)\n (:id . 69))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 194)\n (:start . 189) (:id . 70))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 200)\n (:start . 195) (:id . 71))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 207)\n (:start . 201) (:id . 72))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 213)\n (:start . 208) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n (:id . 74)))@@@1@33@((:hcues ((:id . :x4.108.1) (:span 2 10)))\n (:hscopes ((:id . :x4.108.1) (:span 2 213)))\n (:identifiers (:sid . :s4.108) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101221@unknown@formal@none@1@S@A list of all combinations of iPfam domains (the domain architecture) on interacting proteins is given in Additional file 2.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 6) (:start . 2)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 9) (:start . 7)\n (:id . 44))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 13) (:start . 10)\n (:id . 45))\n ((:tag . "NNS") (:stem . "combination") (:form . "combinations") (:end . 26)\n (:start . 14) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 35) (:start . 30)\n (:id . 48))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 43)\n (:start . 36) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n (:id . 51))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 55)\n (:start . 49) (:id . 52))\n ((:tag . "NN") (:stem . "architecture") (:form . "architecture") (:end . 68)\n (:start . 56) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n (:id . 54))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 72) (:start . 70)\n (:id . 55))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 84)\n (:start . 73) (:id . 56))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 93)\n (:start . 85) (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 96) (:start . 94)\n (:id . 58))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 102) (:start . 97)\n (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 105) (:start . 103)\n (:id . 60))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 116)\n (:start . 106) (:id . 61))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 121) (:start . 117)\n (:id . 62))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 123) (:start . 122)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s4.109) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101222@unknown@formal@none@1@S@It reveals that certain iPfam domains such as SH2, SH3_1 or Pkinase_tyr frequently occur in the same architecture.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 23)\n (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 29) (:start . 24)\n (:id . 46))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 37)\n (:start . 30) (:id . 47))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 42) (:start . 38)\n (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 45) (:start . 43)\n (:id . 49))\n ((:tag . "NNP") (:stem . "SH2") (:form . "SH2") (:end . 49) (:start . 46)\n (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n (:id . 51))\n ((:tag . "NNP") (:stem . "SH3_1") (:form . "SH3_1") (:end . 56) (:start . 51)\n (:id . 52))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 59) (:start . 57)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Pkinase_tyr") (:form . "Pkinase_tyr") (:end . 71)\n (:start . 60) (:id . 54))\n ((:tag . "RB") (:stem . "frequently") (:form . "frequently") (:end . 82)\n (:start . 72) (:id . 55))\n ((:tag . "VBP") (:stem . "occur") (:form . "occur") (:end . 88) (:start . 83)\n (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n (:id . 58))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 100) (:start . 96)\n (:id . 59))\n ((:tag . "NN") (:stem . "architecture") (:form . "architecture") (:end . 113)\n (:start . 101) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s4.110) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101223@unknown@formal@none@1@S@Without further experiments, we cannot assign the correct interacting domains with certainty.@(((:tag . "IN") (:stem . "without") (:form . "Without") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 15)\n (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 27)\n (:start . 16) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 31) (:start . 29)\n (:id . 46))\n ((:tag . "VBP") (:stem . "cannot") (:form . "cannot") (:end . 38)\n (:start . 32) (:id . 47))\n ((:tag . "VB") (:stem . "assign") (:form . "assign") (:end . 45)\n (:start . 39) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "JJ") (:stem . "correct") (:form . "correct") (:end . 57)\n (:start . 50) (:id . 50))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 69)\n (:start . 58) (:id . 51))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 77)\n (:start . 70) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 82) (:start . 78)\n (:id . 53))\n ((:tag . "NN") (:stem . "certainty") (:form . "certainty") (:end . 92)\n (:start . 83) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n (:id . 55)))@@@1@14@((:hcues ((:id . :x4.111.1) (:span 32 45 78 92)))\n (:ncues ((:id . :x4.111.3) (:span 0 7)))\n (:hscopes ((:id . :x4.111.1) (:span 32 92)))\n (:nscopes ((:id . :x4.111.3) (:span 0 27)))\n (:identifiers (:sid . :s4.111) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101224@unknown@formal@none@1@S@This highlights a basic assumption of this study that could be a source of error.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "highlight") (:form . "highlights") (:end . 15)\n (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 17) (:start . 16)\n (:id . 44))\n ((:tag . "JJ") (:stem . "basic") (:form . "basic") (:end . 23) (:start . 18)\n (:id . 45))\n ((:tag . "NN") (:stem . "assumption") (:form . "assumption") (:end . 34)\n (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 42) (:start . 38)\n (:id . 48))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 48) (:start . 43)\n (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 53) (:start . 49)\n (:id . 50))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 59) (:start . 54)\n (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 62) (:start . 60)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n (:id . 53))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 71)\n (:start . 65) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n (:id . 55))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 80) (:start . 75)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n (:id . 57)))@@@1@16@((:hcues ((:id . :x4.112.1) (:span 54 59)))\n (:hscopes ((:id . :x4.112.1) (:span 54 80)))\n (:identifiers (:sid . :s4.112) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101225@unknown@formal@none@1@S@We assume that interacting proteins that contain an iPfam domain pair interact through these domains.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "assume") (:form . "assume") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 26)\n (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 35)\n (:start . 27) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 40) (:start . 36)\n (:id . 47))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 48)\n (:start . 41) (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 51) (:start . 49)\n (:id . 49))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 57) (:start . 52)\n (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 64)\n (:start . 58) (:id . 51))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 69) (:start . 65)\n (:id . 52))\n ((:tag . "VBP") (:stem . "interact") (:form . "interact") (:end . 78)\n (:start . 70) (:id . 53))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 86)\n (:start . 79) (:id . 54))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 92) (:start . 87)\n (:id . 55))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 100)\n (:start . 93) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n (:id . 57)))@@@1@16@((:hcues ((:id . :x4.113.1) (:span 3 9)))\n (:hscopes ((:id . :x4.113.1) (:span 3 100)))\n (:identifiers (:sid . :s4.113) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101226@unknown@formal@none@1@S@This, of course, is not necessarily the case.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 8) (:start . 6)\n (:id . 44))\n ((:tag . "NN") (:stem . "course") (:form . "course") (:end . 15) (:start . 9)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 19) (:start . 17)\n (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 23) (:start . 20)\n (:id . 48))\n ((:tag . "RB") (:stem . "necessarily") (:form . "necessarily") (:end . 35)\n (:start . 24) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 50))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 44) (:start . 40)\n (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 45) (:start . 44)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s4.114) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101227@unknown@formal@none@1@S@Although it has been shown that sequence similarity is linked to the mode of interaction 28, not every protein interaction that contains an iPfam domain pair is necessarily mediated by exactly this domain pair.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 11) (:start . 9)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 26) (:start . 21)\n (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 31) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 40)\n (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 51)\n (:start . 41) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 54) (:start . 52)\n (:id . 50))\n ((:tag . "VBN") (:stem . "link") (:form . "linked") (:end . 61) (:start . 55)\n (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n (:id . 53))\n ((:tag . "NN") (:stem . "mode") (:form . "mode") (:end . 73) (:start . 69)\n (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n (:id . 55))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 88)\n (:start . 77) (:id . 56))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 91) (:start . 89)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 96) (:start . 93)\n (:id . 59))\n ((:tag . "DT") (:stem . "every") (:form . "every") (:end . 102) (:start . 97)\n (:id . 60))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 110)\n (:start . 103) (:id . 61))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 122)\n (:start . 111) (:id . 62))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 127) (:start . 123)\n (:id . 63))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 136)\n (:start . 128) (:id . 64))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 139) (:start . 137)\n (:id . 65))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 145)\n (:start . 140) (:id . 66))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 152)\n (:start . 146) (:id . 67))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 157) (:start . 153)\n (:id . 68))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 160) (:start . 158)\n (:id . 69))\n ((:tag . "RB") (:stem . "necessarily") (:form . "necessarily") (:end . 172)\n (:start . 161) (:id . 70))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 181)\n (:start . 173) (:id . 71))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 184) (:start . 182)\n (:id . 72))\n ((:tag . "RB") (:stem . "exactly") (:form . "exactly") (:end . 192)\n (:start . 185) (:id . 73))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 197) (:start . 193)\n (:id . 74))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 204)\n (:start . 198) (:id . 75))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 209) (:start . 205)\n (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 210) (:start . 209)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s4.115) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101228@unknown@formal@none@1@S@To gain a rough estimate of the false positive rate due to this assumption, we counted how many protein pairs in the PDB contain an iPfam domain pair that does not mediate an interaction in one complex structure but does so in another.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "gain") (:form . "gain") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 9) (:start . 8)\n (:id . 44))\n ((:tag . "JJ") (:stem . "rough") (:form . "rough") (:end . 15) (:start . 10)\n (:id . 45))\n ((:tag . "NN") (:stem . "estimate") (:form . "estimate") (:end . 24)\n (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n (:id . 48))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 37) (:start . 32)\n (:id . 49))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 46)\n (:start . 38) (:id . 50))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 51) (:start . 47)\n (:id . 51))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 55) (:start . 52)\n (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n (:id . 53))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 63) (:start . 59)\n (:id . 54))\n ((:tag . "NN") (:stem . "assumption") (:form . "assumption") (:end . 74)\n (:start . 64) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n (:id . 56))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 78) (:start . 76)\n (:id . 57))\n ((:tag . "VBD") (:stem . "count") (:form . "counted") (:end . 86)\n (:start . 79) (:id . 58))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 90) (:start . 87)\n (:id . 59))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 95) (:start . 91)\n (:id . 60))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 103)\n (:start . 96) (:id . 61))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 109)\n (:start . 104) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 112) (:start . 110)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n (:id . 64))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 120) (:start . 117)\n (:id . 65))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 128)\n (:start . 121) (:id . 66))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 131) (:start . 129)\n (:id . 67))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 137)\n (:start . 132) (:id . 68))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 144)\n (:start . 138) (:id . 69))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 149) (:start . 145)\n (:id . 70))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 154) (:start . 150)\n (:id . 71))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 159) (:start . 155)\n (:id . 72))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 163) (:start . 160)\n (:id . 73))\n ((:tag . "VB") (:stem . "mediate") (:form . "mediate") (:end . 171)\n (:start . 164) (:id . 74))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 174) (:start . 172)\n (:id . 75))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 186)\n (:start . 175) (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 189) (:start . 187)\n (:id . 77))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 193) (:start . 190)\n (:id . 78))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 201)\n (:start . 194) (:id . 79))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 211)\n (:start . 202) (:id . 80))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 215) (:start . 212)\n (:id . 81))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 220) (:start . 216)\n (:id . 82))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 223) (:start . 221)\n (:id . 83))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 226) (:start . 224)\n (:id . 84))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 234)\n (:start . 227) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 235) (:start . 234)\n (:id . 86)))@@@1@45@((:ncues ((:id . :x4.116.1) (:span 160 163)))\n (:nscopes ((:id . :x4.116.1) (:span 160 211)))\n (:identifiers (:sid . :s4.116) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101230@unknown@formal@none@1@S@This means that for more than 32% of the protein interactions in the PDB, the iPfam domain pair assignment is correct.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "mean") (:form . "means") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 24) (:start . 20)\n (:id . 46))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 29) (:start . 25)\n (:id . 47))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 32) (:start . 30)\n (:id . 48))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 33) (:start . 32)\n (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 48)\n (:start . 41) (:id . 52))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 61)\n (:start . 49) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n (:id . 55))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 72) (:start . 69)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n (:id . 58))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 83) (:start . 78)\n (:id . 59))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 90)\n (:start . 84) (:id . 60))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 95) (:start . 91)\n (:id . 61))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 106)\n (:start . 96) (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 109) (:start . 107)\n (:id . 63))\n ((:tag . "JJ") (:stem . "correct") (:form . "correct") (:end . 117)\n (:start . 110) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.118) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101231@unknown@formal@none@1@S@For the remaining 68%, the iPfam domain pair assignments are wrong in one case but correct in another.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 17)\n (:start . 8) (:id . 44))\n ((:tag . "CD") (:stem . "68") (:form . "68") (:end . 20) (:start . 18)\n (:id . 45))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 21) (:start . 20)\n (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 48))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 32) (:start . 27)\n (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 39)\n (:start . 33) (:id . 50))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 44) (:start . 40)\n (:id . 51))\n ((:tag . "NNS") (:stem . "assignment") (:form . "assignments") (:end . 56)\n (:start . 45) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 60) (:start . 57)\n (:id . 53))\n ((:tag . "JJ") (:stem . "wrong") (:form . "wrong") (:end . 66) (:start . 61)\n (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 69) (:start . 67)\n (:id . 55))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 73) (:start . 70)\n (:id . 56))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 78) (:start . 74)\n (:id . 57))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 82) (:start . 79)\n (:id . 58))\n ((:tag . "VBP") (:stem . "correct") (:form . "correct") (:end . 90)\n (:start . 83) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 93) (:start . 91)\n (:id . 60))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 101)\n (:start . 94) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.119) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101232@unknown@formal@none@1@S@The real false positive rate is likely to be smaller, because some iPfam domain pairs might still independently mediate an interaction with a different, possibly unknown, partner protein.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "real") (:form . "real") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 28) (:start . 24)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 31) (:start . 29)\n (:id . 47))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 38)\n (:start . 32) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 44) (:start . 42)\n (:id . 50))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 52)\n (:start . 45) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n (:id . 52))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 61)\n (:start . 54) (:id . 53))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 66) (:start . 62)\n (:id . 54))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 72) (:start . 67)\n (:id . 55))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 79)\n (:start . 73) (:id . 56))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 85) (:start . 80)\n (:id . 57))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 91) (:start . 86)\n (:id . 58))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 97) (:start . 92)\n (:id . 59))\n ((:tag . "RB") (:stem . "independently") (:form . "independently")\n (:end . 111) (:start . 98) (:id . 60))\n ((:tag . "VB") (:stem . "mediate") (:form . "mediate") (:end . 119)\n (:start . 112) (:id . 61))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 122) (:start . 120)\n (:id . 62))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 134)\n (:start . 123) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 139) (:start . 135)\n (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 141) (:start . 140)\n (:id . 65))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 151)\n (:start . 142) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n (:id . 67))\n ((:tag . "RB") (:stem . "possibly") (:form . "possibly") (:end . 161)\n (:start . 153) (:id . 68))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 169)\n (:start . 162) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 170) (:start . 169)\n (:id . 70))\n ((:tag . "NN") (:stem . "partner") (:form . "partner") (:end . 178)\n (:start . 171) (:id . 71))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 186)\n (:start . 179) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n (:id . 73)))@@@1@32@((:hcues ((:id . :x4.120.1) (:span 153 161)) ((:id . :x4.120.2) (:span 86 91))\n ((:id . :x4.120.3) (:span 32 38)))\n (:hscopes ((:id . :x4.120.1) (:span 153 169))\n ((:id . :x4.120.2) (:span 86 186)) ((:id . :x4.120.3) (:span 0 52)))\n (:identifiers (:sid . :s4.120) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101233@unknown@formal@none@1@S@iPfam domain pairs are enriched in S. cerevisiae complexes@(((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 12) (:start . 6)\n (:id . 43))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 31)\n (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n (:id . 47))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 37) (:start . 35)\n (:id . 48))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 48)\n (:start . 38) (:id . 49))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 58)\n (:start . 49) (:id . 50)))@@@1@9@((:identifiers (:sid . :s4.121) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101234@unknown@formal@none@1@S@We tested whether iPfam domain pairs are enriched in known protein complexes from S. cerevisiae.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "test") (:form . "tested") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 17)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 23) (:start . 18)\n (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 30)\n (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 36) (:start . 31)\n (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 40) (:start . 37)\n (:id . 48))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 49)\n (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n (:id . 50))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 58) (:start . 53)\n (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 66)\n (:start . 59) (:id . 52))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 76)\n (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 81) (:start . 77)\n (:id . 54))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 84) (:start . 82)\n (:id . 55))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 95)\n (:start . 85) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n (:id . 57)))@@@1@16@((:hcues ((:id . :x4.122.1) (:span 10 17)))\n (:hscopes ((:id . :x4.122.1) (:span 10 95)))\n (:identifiers (:sid . :s4.122) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101235@unknown@formal@none@1@S@This is interesting firstly because domain–domain interactions are thought to be more common in obligate interactions.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "JJ") (:stem . "interesting") (:form . "interesting") (:end . 19)\n (:start . 8) (:id . 44))\n ((:tag . "RB") (:stem . "firstly") (:form . "firstly") (:end . 27)\n (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 35)\n (:start . 28) (:id . 46))\n ((:tag . "NN") (:stem . "domain–domain") (:form . "domain–domain")\n (:end . 49) (:start . 36) (:id . 47))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 62)\n (:start . 50) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 66) (:start . 63)\n (:id . 49))\n ((:tag . "VBN") (:stem . "think") (:form . "thought") (:end . 74)\n (:start . 67) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 77) (:start . 75)\n (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 80) (:start . 78)\n (:id . 52))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 85) (:start . 81)\n (:id . 53))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 92)\n (:start . 86) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 95) (:start . 93)\n (:id . 55))\n ((:tag . "JJ") (:stem . "obligate") (:form . "obligate") (:end . 104)\n (:start . 96) (:id . 56))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 117)\n (:start . 105) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n (:id . 58)))@@@1@17@((:hcues ((:id . :x4.123.1) (:span 67 74)))\n (:hscopes ((:id . :x4.123.1) (:span 36 117)))\n (:identifiers (:sid . :s4.123) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101236@unknown@formal@none@1@S@Secondly, the described modularity of known S. cerevisiae complexes lends support to the assumption that the underlying iPfam domain pairs are modular.@(((:tag . "RB") (:stem . "secondly") (:form . "Secondly") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 23)\n (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "modularity") (:form . "modularity") (:end . 34)\n (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n (:id . 47))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 43) (:start . 38)\n (:id . 48))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 46) (:start . 44)\n (:id . 49))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 57)\n (:start . 47) (:id . 50))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 67)\n (:start . 58) (:id . 51))\n ((:tag . "VBZ") (:stem . "lend") (:form . "lends") (:end . 73) (:start . 68)\n (:id . 52))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 81)\n (:start . 74) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 84) (:start . 82)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n (:id . 55))\n ((:tag . "NN") (:stem . "assumption") (:form . "assumption") (:end . 99)\n (:start . 89) (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 104) (:start . 100)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n (:id . 58))\n ((:tag . "VBG") (:stem . "underlie") (:form . "underlying") (:end . 119)\n (:start . 109) (:id . 59))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 125)\n (:start . 120) (:id . 60))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 132)\n (:start . 126) (:id . 61))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 138)\n (:start . 133) (:id . 62))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 142) (:start . 139)\n (:id . 63))\n ((:tag . "JJ") (:stem . "modular") (:form . "modular") (:end . 150)\n (:start . 143) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n (:id . 65)))@@@1@24@((:hcues ((:id . :x4.124.1) (:span 89 99)))\n (:hscopes ((:id . :x4.124.1) (:span 89 150)))\n (:identifiers (:sid . :s4.124) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101237@unknown@formal@none@1@S@In fact, we find a two-fold enrichment for iPfam domain pairs in the complexes described by Gavin et al. 29.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n (:id . 45))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 16) (:start . 12)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 18) (:start . 17)\n (:id . 47))\n ((:tag . "JJ") (:stem . "two-fold") (:form . "two-fold") (:end . 27)\n (:start . 19) (:id . 48))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 38)\n (:start . 28) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 42) (:start . 39)\n (:id . 50))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 48) (:start . 43)\n (:id . 51))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 55)\n (:start . 49) (:id . 52))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 61) (:start . 56)\n (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n (:id . 55))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 78)\n (:start . 69) (:id . 56))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 88)\n (:start . 79) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 91) (:start . 89)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Gavin") (:form . "Gavin") (:end . 97) (:start . 92)\n (:id . 59))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 100) (:start . 98)\n (:id . 60))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 104) (:start . 101)\n (:id . 61))\n ((:tag . "CD") (:stem . "29") (:form . "29") (:end . 107) (:start . 105)\n (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s4.125) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101238@unknown@formal@none@1@S@From the 294 binary protein interactions in this data set, 24 contained an iPfam domain pair, which corresponds to a coverage of 8.16% (P value 2.7 · 10-47).@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "CD") (:stem . "294") (:form . "294") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "JJ") (:stem . "binary") (:form . "binary") (:end . 19)\n (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 27)\n (:start . 20) (:id . 46))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 40)\n (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n (:id . 48))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 48) (:start . 44)\n (:id . 49))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 53) (:start . 49)\n (:id . 50))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 57) (:start . 54)\n (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n (:id . 52))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 61) (:start . 59)\n (:id . 53))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 71)\n (:start . 62) (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 74) (:start . 72)\n (:id . 55))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 80) (:start . 75)\n (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 87)\n (:start . 81) (:id . 57))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 92) (:start . 88)\n (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 99) (:start . 94)\n (:id . 60))\n ((:tag . "VBZ") (:stem . "correspond") (:form . "corresponds") (:end . 111)\n (:start . 100) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 114) (:start . 112)\n (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 116) (:start . 115)\n (:id . 63))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 125)\n (:start . 117) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 128) (:start . 126)\n (:id . 65))\n ((:tag . "CD") (:stem . "8.16") (:form . "8.16") (:end . 133) (:start . 129)\n (:id . 66))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 134) (:start . 133)\n (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 136) (:start . 135)\n (:id . 68))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 137) (:start . 136)\n (:id . 69))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 143)\n (:start . 138) (:id . 70))\n ((:tag . "CD") (:stem . "2.7") (:form . "2.7") (:end . 147) (:start . 144)\n (:id . 71))\n ((:tag . "HYPH") (:stem . "·") (:form . "·") (:end . 149) (:start . 148)\n (:id . 72))\n ((:tag . "CD") (:stem . "10-47") (:form . "10-47") (:end . 155)\n (:start . 150) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s4.126) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101240@unknown@formal@none@1@S@From 491 complexes described by Gavin et al., 157 contained at least one pair of proteins with an iPfam domain pair (31.9%).@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "491") (:form . "491") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 18)\n (:start . 9) (:id . 44))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 28)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 31) (:start . 29)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Gavin") (:form . "Gavin") (:end . 37) (:start . 32)\n (:id . 47))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 40) (:start . 38)\n (:id . 48))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 44) (:start . 41)\n (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n (:id . 50))\n ((:tag . "CD") (:stem . "157") (:form . "157") (:end . 49) (:start . 46)\n (:id . 51))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 59)\n (:start . 50) (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 62) (:start . 60)\n (:id . 53))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 68) (:start . 63)\n (:id . 54))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 72) (:start . 69)\n (:id . 55))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 77) (:start . 73)\n (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n (:id . 57))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 89)\n (:start . 81) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 94) (:start . 90)\n (:id . 59))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 97) (:start . 95)\n (:id . 60))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 103) (:start . 98)\n (:id . 61))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 110)\n (:start . 104) (:id . 62))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 115) (:start . 111)\n (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n (:id . 64))\n ((:tag . "CD") (:stem . "31.9") (:form . "31.9") (:end . 121) (:start . 117)\n (:id . 65))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 122) (:start . 121)\n (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 123) (:start . 122)\n (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s4.128) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101241@unknown@formal@none@1@S@In total we found 617 pairs of proteins that contained an iPfam domain pair.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "total") (:form . "total") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 17) (:start . 12)\n (:id . 45))\n ((:tag . "CD") (:stem . "617") (:form . "617") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 27) (:start . 22)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 48))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 39)\n (:start . 31) (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 44) (:start . 40)\n (:id . 50))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 54)\n (:start . 45) (:id . 51))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 57) (:start . 55)\n (:id . 52))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 63) (:start . 58)\n (:id . 53))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 70)\n (:start . 64) (:id . 54))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 75) (:start . 71)\n (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.129) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101242@unknown@formal@none@1@S@Interestingly, we find that the distribution of iPfam domain pairs on complexes is uneven.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n (:id . 44))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 22) (:start . 18)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 27) (:start . 23)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n (:id . 47))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 44)\n (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 53) (:start . 48)\n (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 60)\n (:start . 54) (:id . 51))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 66) (:start . 61)\n (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 69) (:start . 67)\n (:id . 53))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 79)\n (:start . 70) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 82) (:start . 80)\n (:id . 55))\n ((:tag . "JJ") (:stem . "uneven") (:form . "uneven") (:end . 89)\n (:start . 83) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s4.130) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101243@unknown@formal@none@1@S@When we drew 617 protein pairs randomly from all possible protein pairs in the complexes, we covered 192 complexes on average, with a standard deviation of 7.22.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "VBD") (:stem . "draw") (:form . "drew") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "CD") (:stem . "617") (:form . "617") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 24)\n (:start . 17) (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 30) (:start . 25)\n (:id . 47))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 39)\n (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 44) (:start . 40)\n (:id . 49))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 48) (:start . 45)\n (:id . 50))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 57)\n (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 65)\n (:start . 58) (:id . 52))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 71) (:start . 66)\n (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n (:id . 55))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 88)\n (:start . 79) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n (:id . 57))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 92) (:start . 90)\n (:id . 58))\n ((:tag . "VBD") (:stem . "cover") (:form . "covered") (:end . 100)\n (:start . 93) (:id . 59))\n ((:tag . "CD") (:stem . "192") (:form . "192") (:end . 104) (:start . 101)\n (:id . 60))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 114)\n (:start . 105) (:id . 61))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 117) (:start . 115)\n (:id . 62))\n ((:tag . "NN") (:stem . "average") (:form . "average") (:end . 125)\n (:start . 118) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 131) (:start . 127)\n (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 133) (:start . 132)\n (:id . 66))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 142)\n (:start . 134) (:id . 67))\n ((:tag . "NN") (:stem . "deviation") (:form . "deviation") (:end . 152)\n (:start . 143) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n (:id . 69))\n ((:tag . "CD") (:stem . "7.22") (:form . "7.22") (:end . 160) (:start . 156)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s4.131) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101244@unknown@formal@none@1@S@The probability of covering only 157 complexes is just 6.24 · 10-07.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n (:id . 44))\n ((:tag . "VBG") (:stem . "cover") (:form . "covering") (:end . 27)\n (:start . 19) (:id . 45))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 32) (:start . 28)\n (:id . 46))\n ((:tag . "CD") (:stem . "157") (:form . "157") (:end . 36) (:start . 33)\n (:id . 47))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 46)\n (:start . 37) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 49) (:start . 47)\n (:id . 49))\n ((:tag . "RB") (:stem . "just") (:form . "just") (:end . 54) (:start . 50)\n (:id . 50))\n ((:tag . "CD") (:stem . "6.24") (:form . "6.24") (:end . 59) (:start . 55)\n (:id . 51))\n ((:tag . "IN") (:stem . "·") (:form . "·") (:end . 61) (:start . 60)\n (:id . 52))\n ((:tag . "CD") (:stem . "10-07") (:form . "10-07") (:end . 67) (:start . 62)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s4.132) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101245@unknown@formal@none@1@S@Thus, some complexes contain a greater number of iPfam domain pairs, while other complexes do not contain any at all.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 10) (:start . 6)\n (:id . 44))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 20)\n (:start . 11) (:id . 45))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 28)\n (:start . 21) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n (:id . 47))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 38)\n (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 45)\n (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n (:id . 50))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 54) (:start . 49)\n (:id . 51))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 61)\n (:start . 55) (:id . 52))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 67) (:start . 62)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n (:id . 54))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 74) (:start . 69)\n (:id . 55))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 80) (:start . 75)\n (:id . 56))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 90)\n (:start . 81) (:id . 57))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 93) (:start . 91)\n (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 97) (:start . 94)\n (:id . 59))\n ((:tag . "VB") (:stem . "contain") (:form . "contain") (:end . 105)\n (:start . 98) (:id . 60))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 109) (:start . 106)\n (:id . 61))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 112) (:start . 110)\n (:id . 62))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 116) (:start . 113)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n (:id . 64)))@@@1@23@((:ncues ((:id . :x4.133.1) (:span 94 97)))\n (:nscopes ((:id . :x4.133.1) (:span 94 116)))\n (:identifiers (:sid . :s4.133) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101246@unknown@formal@none@1@S@This suggests that some sets of domain pairs are specific to certain complexes or pathways.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 23) (:start . 19)\n (:id . 45))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 28) (:start . 24)\n (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n (:id . 47))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 38)\n (:start . 32) (:id . 48))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 44) (:start . 39)\n (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 48) (:start . 45)\n (:id . 50))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 57)\n (:start . 49) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n (:id . 52))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 68)\n (:start . 61) (:id . 53))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 78)\n (:start . 69) (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 81) (:start . 79)\n (:id . 55))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 90)\n (:start . 82) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n (:id . 57)))@@@1@16@((:hcues ((:id . :x4.134.1) (:span 5 13)))\n (:hscopes ((:id . :x4.134.1) (:span 5 90)))\n (:identifiers (:sid . :s4.134) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101247@unknown@formal@none@1@S@Typical examples are the RNA polymerase II complex (IntAct id: EBI-815049) or the U1 snRNP complex which contain numerous iPfam domain pairs that are specific to these complexes.@(((:tag . "JJ") (:stem . "typical") (:form . "Typical") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 16)\n (:start . 8) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 20) (:start . 17)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n (:id . 45))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "NN") (:stem . "polymerase") (:form . "polymerase") (:end . 39)\n (:start . 29) (:id . 47))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 42) (:start . 40)\n (:id . 48))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 50)\n (:start . 43) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n (:id . 50))\n ((:tag . "NNP") (:stem . "IntAct") (:form . "IntAct") (:end . 58)\n (:start . 52) (:id . 51))\n ((:tag . "NN") (:stem . "id") (:form . "id") (:end . 61) (:start . 59)\n (:id . 52))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 62) (:start . 61)\n (:id . 53))\n ((:tag . "NNP") (:stem . "EBI-815049") (:form . "EBI-815049") (:end . 73)\n (:start . 63) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 74) (:start . 73)\n (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 77) (:start . 75)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n (:id . 57))\n ((:tag . "NN") (:stem . "u1") (:form . "U1") (:end . 84) (:start . 82)\n (:id . 58))\n ((:tag . "NN") (:stem . "snrnp") (:form . "snRNP") (:end . 90) (:start . 85)\n (:id . 59))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 98)\n (:start . 91) (:id . 60))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 104)\n (:start . 99) (:id . 61))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 112)\n (:start . 105) (:id . 62))\n ((:tag . "JJ") (:stem . "numerous") (:form . "numerous") (:end . 121)\n (:start . 113) (:id . 63))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 127)\n (:start . 122) (:id . 64))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 134)\n (:start . 128) (:id . 65))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 140)\n (:start . 135) (:id . 66))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 145) (:start . 141)\n (:id . 67))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 149) (:start . 146)\n (:id . 68))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 158)\n (:start . 150) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 161) (:start . 159)\n (:id . 70))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 167)\n (:start . 162) (:id . 71))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 177)\n (:start . 168) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s4.135) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101248@unknown@formal@none@1@S@iPfam domain pairs are conserved between species@(((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 12) (:start . 6)\n (:id . 43))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 32)\n (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 40)\n (:start . 33) (:id . 47))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 48)\n (:start . 41) (:id . 48)))@@@1@7@((:identifiers (:sid . :s4.136) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101250@unknown@formal@none@1@S@We call an iPfam domain pair conserved when the same pair is observed in experimental interactions of two different species.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "call") (:form . "call") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 10) (:start . 8)\n (:id . 44))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 16) (:start . 11)\n (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 23)\n (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 28) (:start . 24)\n (:id . 47))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 38)\n (:start . 29) (:id . 48))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 43) (:start . 39)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n (:id . 50))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 52) (:start . 48)\n (:id . 51))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 57) (:start . 53)\n (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 60) (:start . 58)\n (:id . 53))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 69)\n (:start . 61) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n (:id . 55))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 85)\n (:start . 73) (:id . 56))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 98)\n (:start . 86) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 101) (:start . 99)\n (:id . 58))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 105) (:start . 102)\n (:id . 59))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 115)\n (:start . 106) (:id . 60))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 123)\n (:start . 116) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.138) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101251@unknown@formal@none@1@S@The matrix in Table 2 shows the pair-wise conservation of iPfam domain pairs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 19) (:start . 14)\n (:id . 45))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 21) (:start . 20)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 27) (:start . 22)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n (:id . 48))\n ((:tag . "JJ") (:stem . "pair-wise") (:form . "pair-wise") (:end . 41)\n (:start . 32) (:id . 49))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 54)\n (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n (:id . 51))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 63) (:start . 58)\n (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 70)\n (:start . 64) (:id . 53))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 76) (:start . 71)\n (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s4.139) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101252@unknown@formal@none@1@S@For each species, a maximum of 40% to 90% of iPfam domain pairs can also be found in another species, although not all overlaps are as large.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 16)\n (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 19) (:start . 18)\n (:id . 46))\n ((:tag . "NN") (:stem . "maximum") (:form . "maximum") (:end . 27)\n (:start . 20) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 48))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 33) (:start . 31)\n (:id . 49))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 34) (:start . 33)\n (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n (:id . 51))\n ((:tag . "CD") (:stem . "90") (:form . "90") (:end . 40) (:start . 38)\n (:id . 52))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 41) (:start . 40)\n (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n (:id . 54))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 50) (:start . 45)\n (:id . 55))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 57)\n (:start . 51) (:id . 56))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 63) (:start . 58)\n (:id . 57))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 67) (:start . 64)\n (:id . 58))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 72) (:start . 68)\n (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 75) (:start . 73)\n (:id . 60))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 81) (:start . 76)\n (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n (:id . 62))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 92)\n (:start . 85) (:id . 63))\n ((:tag . "NN") (:stem . "species") (:form . "species") (:end . 100)\n (:start . 93) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n (:id . 65))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 110)\n (:start . 102) (:id . 66))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 114) (:start . 111)\n (:id . 67))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 118) (:start . 115)\n (:id . 68))\n ((:tag . "NNS") (:stem . "overlap") (:form . "overlaps") (:end . 127)\n (:start . 119) (:id . 69))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 131) (:start . 128)\n (:id . 70))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 134) (:start . 132)\n (:id . 71))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 140)\n (:start . 135) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s4.140) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101253@unknown@formal@none@1@S@Matrix of mutual shared iPfam domain pairs@(((:tag . "NNP") (:stem . "Matrix") (:form . "Matrix") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 9) (:start . 7)\n (:id . 43))\n ((:tag . "JJ") (:stem . "mutual") (:form . "mutual") (:end . 16)\n (:start . 10) (:id . 44))\n ((:tag . "JJ") (:stem . "shared") (:form . "shared") (:end . 23)\n (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 29) (:start . 24)\n (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 36)\n (:start . 30) (:id . 47))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 42) (:start . 37)\n (:id . 48)))@@@1@7@((:identifiers (:sid . :s4.141) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|TableLegend|)))@oe@9-2-2011 5101254@unknown@formal@none@1@S@The Table shows the number of co-occurences of iPfam domain pairs between two species.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Table") (:form . "Table") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 15) (:start . 10)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 26)\n (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 47))\n ((:tag . "NNS") (:stem . "co-occurence") (:form . "co-occurences")\n (:end . 43) (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n (:id . 49))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 52) (:start . 47)\n (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 59)\n (:start . 53) (:id . 51))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 65) (:start . 60)\n (:id . 52))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 73)\n (:start . 66) (:id . 53))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 77) (:start . 74)\n (:id . 54))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 85)\n (:start . 78) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.142) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101255@unknown@formal@none@1@S@The right-most column lists the total number of unique iPfam pairs found in each species' experimental interactions.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "right-most") (:form . "right-most") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "column") (:form . "column") (:end . 21)\n (:start . 15) (:id . 44))\n ((:tag . "VBZ") (:stem . "list") (:form . "lists") (:end . 27) (:start . 22)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n (:id . 46))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 37) (:start . 32)\n (:id . 47))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 44)\n (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 54)\n (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 60) (:start . 55)\n (:id . 51))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 66) (:start . 61)\n (:id . 52))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 72) (:start . 67)\n (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 75) (:start . 73)\n (:id . 54))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 80) (:start . 76)\n (:id . 55))\n ((:tag . "NN") (:stem . "species") (:form . "species") (:end . 88)\n (:start . 81) (:id . 56))\n ((:tag . "POS") (:stem . "'") (:form . "’") (:end . 89) (:start . 88)\n (:id . 57))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 102)\n (:start . 90) (:id . 58))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 115)\n (:start . 103) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.143) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101256@unknown@formal@none@1@S@Figure 4 shows a Venn diagram of the mutual overlaps between the two eukaryotes S. cerevisiae and H. sapiens and the prokaryote E. coli.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 8) (:start . 7)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Venn") (:form . "Venn") (:end . 21) (:start . 17)\n (:id . 46))\n ((:tag . "NN") (:stem . "diagram") (:form . "diagram") (:end . 29)\n (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n (:id . 49))\n ((:tag . "JJ") (:stem . "mutual") (:form . "mutual") (:end . 43)\n (:start . 37) (:id . 50))\n ((:tag . "NNS") (:stem . "overlap") (:form . "overlaps") (:end . 52)\n (:start . 44) (:id . 51))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 60)\n (:start . 53) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n (:id . 53))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 68) (:start . 65)\n (:id . 54))\n ((:tag . "NNS") (:stem . "eukaryote") (:form . "eukaryotes") (:end . 79)\n (:start . 69) (:id . 55))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 82) (:start . 80)\n (:id . 56))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 93)\n (:start . 83) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n (:id . 58))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 100) (:start . 98)\n (:id . 59))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 108)\n (:start . 101) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n (:id . 62))\n ((:tag . "NN") (:stem . "prokaryote") (:form . "prokaryote") (:end . 127)\n (:start . 117) (:id . 63))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 130) (:start . 128)\n (:id . 64))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 135) (:start . 131)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s4.144) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101257@unknown@formal@none@1@S@While the eukaryotes share 524 domain pairs, only 158 iPfam domain pairs are shared between S. cerevisiae and E. coli, and only 135 between E. coli and H. sapiens.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "NNS") (:stem . "eukaryote") (:form . "eukaryotes") (:end . 20)\n (:start . 10) (:id . 44))\n ((:tag . "VBP") (:stem . "share") (:form . "share") (:end . 26) (:start . 21)\n (:id . 45))\n ((:tag . "CD") (:stem . "524") (:form . "524") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 37)\n (:start . 31) (:id . 47))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 43) (:start . 38)\n (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n (:id . 49))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 49) (:start . 45)\n (:id . 50))\n ((:tag . "CD") (:stem . "158") (:form . "158") (:end . 53) (:start . 50)\n (:id . 51))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 59) (:start . 54)\n (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 66)\n (:start . 60) (:id . 53))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 72) (:start . 67)\n (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 76) (:start . 73)\n (:id . 55))\n ((:tag . "VBN") (:stem . "share") (:form . "shared") (:end . 83)\n (:start . 77) (:id . 56))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 91)\n (:start . 84) (:id . 57))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 94) (:start . 92)\n (:id . 58))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 105)\n (:start . 95) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n (:id . 60))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 112) (:start . 110)\n (:id . 61))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 117) (:start . 113)\n (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n (:id . 64))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 127) (:start . 123)\n (:id . 65))\n ((:tag . "CD") (:stem . "135") (:form . "135") (:end . 131) (:start . 128)\n (:id . 66))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 139)\n (:start . 132) (:id . 67))\n ((:tag . "NNP") (:stem . "E.") (:form . "E.") (:end . 142) (:start . 140)\n (:id . 68))\n ((:tag . "NNP") (:stem . "coli") (:form . "coli") (:end . 147) (:start . 143)\n (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 151) (:start . 148)\n (:id . 70))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 154) (:start . 152)\n (:id . 71))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 162)\n (:start . 155) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s4.145) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101258@unknown@formal@none@1@S@Remarkably, 53% of the observed iPfam domain pairs in E. coli are also observed in one of the two eukaryotes, and 107 iPfam domain pairs are even conserved amongst all three species.@(((:tag . "RB") (:stem . "remarkably") (:form . "Remarkably") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 43))\n ((:tag . "CD") (:stem . "53") (:form . "53") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 15) (:start . 14)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 47))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 31)\n (:start . 23) (:id . 48))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 37) (:start . 32)\n (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 44)\n (:start . 38) (:id . 50))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 50) (:start . 45)\n (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n (:id . 52))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 56) (:start . 54)\n (:id . 53))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 61) (:start . 57)\n (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 65) (:start . 62)\n (:id . 55))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 70) (:start . 66)\n (:id . 56))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 79)\n (:start . 71) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n (:id . 58))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 86) (:start . 83)\n (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n (:id . 61))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 97) (:start . 94)\n (:id . 62))\n ((:tag . "NNS") (:stem . "eukaryote") (:form . "eukaryotes") (:end . 108)\n (:start . 98) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n (:id . 65))\n ((:tag . "CD") (:stem . "107") (:form . "107") (:end . 117) (:start . 114)\n (:id . 66))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 123)\n (:start . 118) (:id . 67))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 130)\n (:start . 124) (:id . 68))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 136)\n (:start . 131) (:id . 69))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 140) (:start . 137)\n (:id . 70))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 145) (:start . 141)\n (:id . 71))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 155)\n (:start . 146) (:id . 72))\n ((:tag . "IN") (:stem . "amongst") (:form . "amongst") (:end . 163)\n (:start . 156) (:id . 73))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 167) (:start . 164)\n (:id . 74))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 173)\n (:start . 168) (:id . 75))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 181)\n (:start . 174) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s4.146) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101260@unknown@formal@none@1@S@Additional file 3 contains a list of the conserved iPfam domain pairs.@(((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 15) (:start . 11)\n (:id . 43))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 17) (:start . 16)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 26)\n (:start . 18) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n (:id . 46))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n (:id . 49))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 50)\n (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 56) (:start . 51)\n (:id . 51))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 63)\n (:start . 57) (:id . 52))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 69) (:start . 64)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s4.148) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101261@unknown@formal@none@1@S@Venn diagramm showing the fractions of iPfam domain pairs found in the E. coli, S. cerevisiae and H. sapiens binary protein interaction sets@(((:tag . "NNP") (:stem . "Venn") (:form . "Venn") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "diagramm") (:form . "diagramm") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 21)\n (:start . 14) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "NNS") (:stem . "fraction") (:form . "fractions") (:end . 35)\n (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n (:id . 47))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 44) (:start . 39)\n (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 51)\n (:start . 45) (:id . 49))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 57) (:start . 52)\n (:id . 50))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 63) (:start . 58)\n (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n (:id . 53))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 73) (:start . 71)\n (:id . 54))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 78) (:start . 74)\n (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n (:id . 56))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 82) (:start . 80)\n (:id . 57))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 93)\n (:start . 83) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n (:id . 59))\n ((:tag . "FW") (:stem . "h.") (:form . "H.") (:end . 100) (:start . 98)\n (:id . 60))\n ((:tag . "FW") (:stem . "sapiens") (:form . "sapiens") (:end . 108)\n (:start . 101) (:id . 61))\n ((:tag . "JJ") (:stem . "binary") (:form . "binary") (:end . 115)\n (:start . 109) (:id . 62))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 123)\n (:start . 116) (:id . 63))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 135)\n (:start . 124) (:id . 64))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 140) (:start . 136)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.149) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|TableLegend|)))@oe@9-2-2011 5101262@unknown@formal@none@1@S@Venn diagramm showing the fractions of iPfam domain pairs found in the E. coli, S. cerevisiae and H. sapiens binary protein interaction sets.@(((:tag . "NNP") (:stem . "Venn") (:form . "Venn") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "diagramm") (:form . "diagramm") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 21)\n (:start . 14) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "NNS") (:stem . "fraction") (:form . "fractions") (:end . 35)\n (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n (:id . 47))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 44) (:start . 39)\n (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 51)\n (:start . 45) (:id . 49))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 57) (:start . 52)\n (:id . 50))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 63) (:start . 58)\n (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n (:id . 53))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 73) (:start . 71)\n (:id . 54))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 78) (:start . 74)\n (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n (:id . 56))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 82) (:start . 80)\n (:id . 57))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 93)\n (:start . 83) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n (:id . 59))\n ((:tag . "FW") (:stem . "h.") (:form . "H.") (:end . 100) (:start . 98)\n (:id . 60))\n ((:tag . "FW") (:stem . "sapiens") (:form . "sapiens") (:end . 108)\n (:start . 101) (:id . 61))\n ((:tag . "JJ") (:stem . "binary") (:form . "binary") (:end . 115)\n (:start . 109) (:id . 62))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 123)\n (:start . 116) (:id . 63))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 135)\n (:start . 124) (:id . 64))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 140) (:start . 136)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s4.150) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101263@unknown@formal@none@1@S@The three circles represent the iPfam domain pairs observed in the respective species.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "circle") (:form . "circles") (:end . 17)\n (:start . 10) (:id . 44))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 27)\n (:start . 18) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n (:id . 46))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 37) (:start . 32)\n (:id . 47))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 44)\n (:start . 38) (:id . 48))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 50) (:start . 45)\n (:id . 49))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 59)\n (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n (:id . 52))\n ((:tag . "JJ") (:stem . "respective") (:form . "respective") (:end . 77)\n (:start . 67) (:id . 53))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 85)\n (:start . 78) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s4.151) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101264@unknown@formal@none@1@S@The overlaps denote co-observed iPfam domain pairs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "overlap") (:form . "overlaps") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "denote") (:form . "denote") (:end . 19)\n (:start . 13) (:id . 44))\n ((:tag . "VBN") (:stem . "co-observe") (:form . "co-observed") (:end . 31)\n (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 37) (:start . 32)\n (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 44)\n (:start . 38) (:id . 47))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 50) (:start . 45)\n (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 51) (:start . 50)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s4.152) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101265@unknown@formal@none@1@S@The grey set in the background represents iPfam domain pairs not found in the three species.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "grey") (:form . "grey") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 46))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 30)\n (:start . 20) (:id . 47))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 41)\n (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 47) (:start . 42)\n (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 54)\n (:start . 48) (:id . 50))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 60) (:start . 55)\n (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 64) (:start . 61)\n (:id . 52))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 70) (:start . 65)\n (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n (:id . 55))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 83) (:start . 78)\n (:id . 56))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 91)\n (:start . 84) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n (:id . 58)))@@@1@17@((:ncues ((:id . :x4.153.1) (:span 61 64)))\n (:nscopes ((:id . :x4.153.1) (:span 61 91)))\n (:identifiers (:sid . :s4.153) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101266@unknown@formal@none@1@S@We also compared the iPfam domain pair frequencies between H. sapiens and S. cerevisiae directly.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "compare") (:form . "compared") (:end . 16)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 26) (:start . 21)\n (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 33)\n (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 38) (:start . 34)\n (:id . 48))\n ((:tag . "NNS") (:stem . "frequency") (:form . "frequencies") (:end . 50)\n (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 58)\n (:start . 51) (:id . 50))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 61) (:start . 59)\n (:id . 51))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 69)\n (:start . 62) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n (:id . 53))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 76) (:start . 74)\n (:id . 54))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 87)\n (:start . 77) (:id . 55))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 96)\n (:start . 88) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s4.154) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101267@unknown@formal@none@1@S@We derive a Spearman correlation coefficient of 0.50 for the frequencies of all 524 iPfam domain pairs that are conserved between S. cerevisiae and H. sapiens.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "derive") (:form . "derive") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 11) (:start . 10)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Spearman") (:form . "Spearman") (:end . 20)\n (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 32)\n (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "coefficient") (:form . "coefficient") (:end . 44)\n (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n (:id . 48))\n ((:tag . "CD") (:stem . "0.50") (:form . "0.50") (:end . 52) (:start . 48)\n (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 56) (:start . 53)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n (:id . 51))\n ((:tag . "NNS") (:stem . "frequency") (:form . "frequencies") (:end . 72)\n (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n (:id . 53))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 79) (:start . 76)\n (:id . 54))\n ((:tag . "CD") (:stem . "524") (:form . "524") (:end . 83) (:start . 80)\n (:id . 55))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 89) (:start . 84)\n (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 96)\n (:start . 90) (:id . 57))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 102) (:start . 97)\n (:id . 58))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 107) (:start . 103)\n (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 111) (:start . 108)\n (:id . 60))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 121)\n (:start . 112) (:id . 61))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 129)\n (:start . 122) (:id . 62))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 132) (:start . 130)\n (:id . 63))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 143)\n (:start . 133) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 147) (:start . 144)\n (:id . 65))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 150) (:start . 148)\n (:id . 66))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 158)\n (:start . 151) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s4.155) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101268@unknown@formal@none@1@S@To test whether the correlation is an artefact of the distribution of the values, we recalculated the correlation 1000 times, each time shuffling one distribution randomly.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 15)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 31)\n (:start . 20) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 34) (:start . 32)\n (:id . 47))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 37) (:start . 35)\n (:id . 48))\n ((:tag . "NN") (:stem . "artefact") (:form . "artefact") (:end . 46)\n (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n (:id . 51))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 66)\n (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n (:id . 54))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 80)\n (:start . 74) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n (:id . 56))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 84) (:start . 82)\n (:id . 57))\n ((:tag . "VBD") (:stem . "recalculate") (:form . "recalculated") (:end . 97)\n (:start . 85) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n (:id . 59))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 113)\n (:start . 102) (:id . 60))\n ((:tag . "CD") (:stem . "1000") (:form . "1000") (:end . 118) (:start . 114)\n (:id . 61))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 124)\n (:start . 119) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n (:id . 63))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 130) (:start . 126)\n (:id . 64))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 135) (:start . 131)\n (:id . 65))\n ((:tag . "VBG") (:stem . "shuffle") (:form . "shuffling") (:end . 145)\n (:start . 136) (:id . 66))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 149) (:start . 146)\n (:id . 67))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 162)\n (:start . 150) (:id . 68))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 171)\n (:start . 163) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x4.156.1) (:span 8 15)))\n (:hscopes ((:id . :x4.156.1) (:span 8 80)))\n (:identifiers (:sid . :s4.156) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101270@unknown@formal@none@1@S@This suggests that iPfam domain pairs with a large number of occurrences in one species tend also to be more frequent in the other.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 24) (:start . 19)\n (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 31)\n (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 37) (:start . 32)\n (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 42) (:start . 38)\n (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n (:id . 49))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 50) (:start . 45)\n (:id . 50))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 57)\n (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n (:id . 52))\n ((:tag . "NNS") (:stem . "occurrence") (:form . "occurrences") (:end . 72)\n (:start . 61) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 75) (:start . 73)\n (:id . 54))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 79) (:start . 76)\n (:id . 55))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 87)\n (:start . 80) (:id . 56))\n ((:tag . "VBP") (:stem . "tend") (:form . "tend") (:end . 92) (:start . 88)\n (:id . 57))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 97) (:start . 93)\n (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 103) (:start . 101)\n (:id . 60))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 108) (:start . 104)\n (:id . 61))\n ((:tag . "JJ") (:stem . "frequent") (:form . "frequent") (:end . 117)\n (:start . 109) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 120) (:start . 118)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n (:id . 64))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 130)\n (:start . 125) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x4.158.1) (:span 88 92)) ((:id . :x4.158.2) (:span 5 13)))\n (:hscopes ((:id . :x4.158.1) (:span 88 130))\n ((:id . :x4.158.2) (:span 5 130)))\n (:identifiers (:sid . :s4.158) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101271@unknown@formal@none@1@S@Predicting the total number of iPfam domain pairs in nature@(((:tag . "VBG") (:stem . "predict") (:form . "Predicting") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 43))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 20) (:start . 15)\n (:id . 44))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 27)\n (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 36) (:start . 31)\n (:id . 47))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 43)\n (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 49) (:start . 44)\n (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n (:id . 50))\n ((:tag . "NN") (:stem . "nature") (:form . "nature") (:end . 59)\n (:start . 53) (:id . 51)))@@@1@10@((:identifiers (:sid . :s4.159) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101272@unknown@formal@none@1@S@Our analysis allow us to estimate how many iPfam domain pairs would eventually cover all protein interactions.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "allow") (:form . "allow") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 24) (:start . 22)\n (:id . 46))\n ((:tag . "VB") (:stem . "estimate") (:form . "estimate") (:end . 33)\n (:start . 25) (:id . 47))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 37) (:start . 34)\n (:id . 48))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 42) (:start . 38)\n (:id . 49))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 48) (:start . 43)\n (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 55)\n (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 61) (:start . 56)\n (:id . 52))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 67) (:start . 62)\n (:id . 53))\n ((:tag . "RB") (:stem . "eventually") (:form . "eventually") (:end . 78)\n (:start . 68) (:id . 54))\n ((:tag . "VB") (:stem . "cover") (:form . "cover") (:end . 84) (:start . 79)\n (:id . 55))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 88) (:start . 85)\n (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 96)\n (:start . 89) (:id . 57))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 109)\n (:start . 97) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n (:id . 59)))@@@1@18@((:hcues ((:id . :x4.160.1) (:span 62 67)))\n (:hscopes ((:id . :x4.160.1) (:span 62 109)))\n (:identifiers (:sid . :s4.160) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101273@unknown@formal@none@1@S@This corresponds to the predictions made by Aloy and Russel 2.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "correspond") (:form . "corresponds") (:end . 16)\n (:start . 5) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 35)\n (:start . 24) (:id . 46))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 40) (:start . 36)\n (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 43) (:start . 41)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Aloy") (:form . "Aloy") (:end . 48) (:start . 44)\n (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Russel") (:form . "Russel") (:end . 59)\n (:start . 53) (:id . 51))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 61) (:start . 60)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 62) (:start . 61)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s4.161) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101274@unknown@formal@none@1@S@Similar to their approach, we make a linear estimation with the following factors:@(((:tag . "JJ") (:stem . "similar") (:form . "Similar") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 10) (:start . 8)\n (:id . 43))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 16)\n (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 25)\n (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 29) (:start . 27)\n (:id . 47))\n ((:tag . "VBP") (:stem . "make") (:form . "make") (:end . 34) (:start . 30)\n (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 36) (:start . 35)\n (:id . 49))\n ((:tag . "JJ") (:stem . "linear") (:form . "linear") (:end . 43)\n (:start . 37) (:id . 50))\n ((:tag . "NN") (:stem . "estimation") (:form . "estimation") (:end . 54)\n (:start . 44) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 59) (:start . 55)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n (:id . 53))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 73)\n (:start . 64) (:id . 54))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 81)\n (:start . 74) (:id . 55))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 82) (:start . 81)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.162) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101275@unknown@formal@none@1@S@χS The number of iPfam domain pairs observed in species S@(((:tag . "VBZ") (:stem . "χs") (:form . "χS") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 13) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 22) (:start . 17)\n (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 29)\n (:start . 23) (:id . 47))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 35) (:start . 30)\n (:id . 48))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 44)\n (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n (:id . 50))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 55)\n (:start . 48) (:id . 51))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 57) (:start . 56)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s4.163) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101276@unknown@formal@none@1@S@θS The number of observed interactions in species S that contain an iPfam domain pair@(((:tag . "VBZ") (:stem . "θs") (:form . "θS") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 13) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 25)\n (:start . 17) (:id . 46))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 38)\n (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n (:id . 48))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 49)\n (:start . 42) (:id . 49))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 51) (:start . 50)\n (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 56) (:start . 52)\n (:id . 51))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 64)\n (:start . 57) (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 67) (:start . 65)\n (:id . 53))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 73) (:start . 68)\n (:id . 54))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 80)\n (:start . 74) (:id . 55))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 85) (:start . 81)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.164) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101277@unknown@formal@none@1@S@ΘS The total number of observed interactions in species S@(((:tag . "VBZ") (:stem . "θs") (:form . "ΘS") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 12) (:start . 7)\n (:id . 44))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 19)\n (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n (:id . 46))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 31)\n (:start . 23) (:id . 47))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 44)\n (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 55)\n (:start . 48) (:id . 50))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 57) (:start . 56)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s4.165) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101278@unknown@formal@none@1@S@ψS The number of proteins from species S that are seen in an interaction screen@(((:tag . "VBZ") (:stem . "ψs") (:form . "ψS") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 13) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 25)\n (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 30) (:start . 26)\n (:id . 47))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 38)\n (:start . 31) (:id . 48))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 40) (:start . 39)\n (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 45) (:start . 41)\n (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 49) (:start . 46)\n (:id . 51))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 54) (:start . 50)\n (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n (:id . 53))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 60) (:start . 58)\n (:id . 54))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 72)\n (:start . 61) (:id . 55))\n ((:tag . "NN") (:stem . "screen") (:form . "screen") (:end . 79)\n (:start . 73) (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.166) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101280@unknown@formal@none@1@S@ξS The number of Pfam domains observed in all protein of species S@(((:tag . "VBZ") (:stem . "ξs") (:form . "ξS") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 13) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 21) (:start . 17)\n (:id . 46))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 29)\n (:start . 22) (:id . 47))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 38)\n (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n (:id . 49))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 45) (:start . 42)\n (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 53)\n (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n (:id . 52))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 64)\n (:start . 57) (:id . 53))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 66) (:start . 65)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s4.168) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101281@unknown@formal@none@1@S@Ξ The total number of known Pfam domains@(((:tag . "LS") (:stem . "ξ") (:form . "Ξ") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 5) (:start . 2)\n (:id . 43))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 11) (:start . 6)\n (:id . 44))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 18)\n (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 46))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 27) (:start . 22)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 32) (:start . 28)\n (:id . 48))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 40)\n (:start . 33) (:id . 49)))@@@1@8@((:identifiers (:sid . :s4.169) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101282@unknown@formal@none@1@S@We denote the estimated number of iPfam domain pairs in species S with x^S.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "denote") (:form . "denote") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 23)\n (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 30)\n (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n (:id . 47))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 39) (:start . 34)\n (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 46)\n (:start . 40) (:id . 49))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 52) (:start . 47)\n (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n (:id . 51))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 63)\n (:start . 56) (:id . 52))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 65) (:start . 64)\n (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 70) (:start . 66)\n (:id . 54))\n ((:tag . "NN") (:stem . "x^s") (:form . "x^S") (:end . 74) (:start . 71)\n (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.170) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101283@unknown@formal@none@1@S@The formula we apply is x^S=χS⋅ΘSθS⋅ΨSψS@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "formula") (:form . "formula") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "VBP") (:stem . "apply") (:form . "apply") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 23) (:start . 21)\n (:id . 46))\n ((:tag . "NN") (:stem . "x^s=χs⋅θsθs⋅ψsψs") (:form . "x^S=χS⋅ΘSθS⋅ΨSψS")\n (:end . 40) (:start . 24) (:id . 47)))@@@1@6@((:identifiers (:sid . :s4.171) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101284@unknown@formal@none@1@S@This means we scale the observed number of iPfam domain pairs to cover all observed interactions.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "mean") (:form . "means") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "VBP") (:stem . "scale") (:form . "scale") (:end . 19) (:start . 14)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n (:id . 46))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 32)\n (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 39)\n (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n (:id . 49))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 48) (:start . 43)\n (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 55)\n (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 61) (:start . 56)\n (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n (:id . 53))\n ((:tag . "VB") (:stem . "cover") (:form . "cover") (:end . 70) (:start . 65)\n (:id . 54))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 74) (:start . 71)\n (:id . 55))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 83)\n (:start . 75) (:id . 56))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 96)\n (:start . 84) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s4.172) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101285@unknown@formal@none@1@S@We then use the relative proteome coverage to estimate the total number of iPfam domain pairs in all proteins.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBP") (:stem . "use") (:form . "use") (:end . 11) (:start . 8)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n (:id . 45))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 24)\n (:start . 16) (:id . 46))\n ((:tag . "NN") (:stem . "proteome") (:form . "proteome") (:end . 33)\n (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 42)\n (:start . 34) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 45) (:start . 43)\n (:id . 49))\n ((:tag . "VB") (:stem . "estimate") (:form . "estimate") (:end . 54)\n (:start . 46) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n (:id . 51))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 64) (:start . 59)\n (:id . 52))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 71)\n (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n (:id . 54))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 80) (:start . 75)\n (:id . 55))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 87)\n (:start . 81) (:id . 56))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 93) (:start . 88)\n (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 96) (:start . 94)\n (:id . 58))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 100) (:start . 97)\n (:id . 59))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 109)\n (:start . 101) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s4.173) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101286@unknown@formal@none@1@S@Finally, we follow the argument of Aloy and Russel that the number of Pfam families seen in species S indicates the fraction of the protein universe represented in the species.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "VBP") (:stem . "follow") (:form . "follow") (:end . 18)\n (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 46))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 31)\n (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Aloy") (:form . "Aloy") (:end . 39) (:start . 35)\n (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Russel") (:form . "Russel") (:end . 50)\n (:start . 44) (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 55) (:start . 51)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n (:id . 53))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 66)\n (:start . 60) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 74) (:start . 70)\n (:id . 56))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 83)\n (:start . 75) (:id . 57))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 88) (:start . 84)\n (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n (:id . 59))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 99)\n (:start . 92) (:id . 60))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 101) (:start . 100)\n (:id . 61))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 111)\n (:start . 102) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n (:id . 63))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 124)\n (:start . 116) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n (:id . 66))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 139)\n (:start . 132) (:id . 67))\n ((:tag . "NN") (:stem . "universe") (:form . "universe") (:end . 148)\n (:start . 140) (:id . 68))\n ((:tag . "VBN") (:stem . "represent") (:form . "represented") (:end . 160)\n (:start . 149) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 163) (:start . 161)\n (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 167) (:start . 164)\n (:id . 71))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 175)\n (:start . 168) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s4.174) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101287@unknown@formal@none@1@S@We therefore predict the total number of iPfam domain pairs x^ as x^=x^S⋅ΞξS.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . "VBP") (:stem . "predict") (:form . "predict") (:end . 20)\n (:start . 13) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n (:id . 45))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 30) (:start . 25)\n (:id . 46))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 37)\n (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n (:id . 48))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 46) (:start . 41)\n (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 53)\n (:start . 47) (:id . 50))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 59) (:start . 54)\n (:id . 51))\n ((:tag . "VBP") (:stem . "x^") (:form . "x^") (:end . 62) (:start . 60)\n (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 65) (:start . 63)\n (:id . 53))\n ((:tag . "NN") (:stem . "x^=x^s⋅ξξs") (:form . "x^=x^S⋅ΞξS") (:end . 76)\n (:start . 66) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s4.175) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101288@unknown@formal@none@1@S@Both parameters and results of the calculation are shown in Table 3.@(((:tag . "DT") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 15)\n (:start . 5) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 27)\n (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "NN") (:stem . "calculation") (:form . "calculation") (:end . 46)\n (:start . 35) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 50) (:start . 47)\n (:id . 49))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 56) (:start . 51)\n (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n (:id . 51))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 65) (:start . 60)\n (:id . 52))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 67) (:start . 66)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s4.176) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101290@unknown@formal@none@1@S@Prediction of total number of iPfam domain pairs@(((:tag . "NN") (:stem . "prediction") (:form . "Prediction") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 43))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 19) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 26)\n (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 35) (:start . 30)\n (:id . 47))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 42)\n (:start . 36) (:id . 48))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 48) (:start . 43)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s4.178) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|TableLegend|)))@oe@9-2-2011 5101291@unknown@formal@none@1@S@ΘS The total number of observed interactions in species S@(((:tag . "VBZ") (:stem . "θs") (:form . "ΘS") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 12) (:start . 7)\n (:id . 44))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 19)\n (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n (:id . 46))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 31)\n (:start . 23) (:id . 47))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 44)\n (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 55)\n (:start . 48) (:id . 50))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 57) (:start . 56)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s4.179) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101292@unknown@formal@none@1@S@θS The number of observed interactions in species S that contain an iPfam domain pair@(((:tag . "VBZ") (:stem . "θs") (:form . "θS") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 13) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 25)\n (:start . 17) (:id . 46))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 38)\n (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n (:id . 48))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 49)\n (:start . 42) (:id . 49))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 51) (:start . 50)\n (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 56) (:start . 52)\n (:id . 51))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 64)\n (:start . 57) (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 67) (:start . 65)\n (:id . 53))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 73) (:start . 68)\n (:id . 54))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 80)\n (:start . 74) (:id . 55))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 85) (:start . 81)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.180) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101293@unknown@formal@none@1@S@ΨS The proteome size for species S@(((:tag . "VBZ") (:stem . "ψs") (:form . "ΨS") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "proteome") (:form . "proteome") (:end . 15)\n (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 24) (:start . 21)\n (:id . 46))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 32)\n (:start . 25) (:id . 47))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 34) (:start . 33)\n (:id . 48)))@@@1@7@((:identifiers (:sid . :s4.181) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101294@unknown@formal@none@1@S@ψS The number of proteins from species S that are seen in an interaction screen@(((:tag . "VBZ") (:stem . "ψs") (:form . "ψS") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 13) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 25)\n (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 30) (:start . 26)\n (:id . 47))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 38)\n (:start . 31) (:id . 48))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 40) (:start . 39)\n (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 45) (:start . 41)\n (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 49) (:start . 46)\n (:id . 51))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 54) (:start . 50)\n (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n (:id . 53))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 60) (:start . 58)\n (:id . 54))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 72)\n (:start . 61) (:id . 55))\n ((:tag . "NN") (:stem . "screen") (:form . "screen") (:end . 79)\n (:start . 73) (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.182) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101295@unknown@formal@none@1@S@χS The number of iPfam domain pairs observed in species S@(((:tag . "VBZ") (:stem . "χs") (:form . "χS") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 13) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 22) (:start . 17)\n (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 29)\n (:start . 23) (:id . 47))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 35) (:start . 30)\n (:id . 48))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 44)\n (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n (:id . 50))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 55)\n (:start . 48) (:id . 51))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 57) (:start . 56)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s4.183) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101296@unknown@formal@none@1@S@The predicted total number of iPfam domain pairs in species S@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 19) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 26)\n (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 35) (:start . 30)\n (:id . 47))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 42)\n (:start . 36) (:id . 48))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 48) (:start . 43)\n (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n (:id . 50))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 59)\n (:start . 52) (:id . 51))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 61) (:start . 60)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s4.184) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101297@unknown@formal@none@1@S@Ξ The total number of known Pfam domains@(((:tag . "LS") (:stem . "ξ") (:form . "Ξ") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 5) (:start . 2)\n (:id . 43))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 11) (:start . 6)\n (:id . 44))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 18)\n (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 46))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 27) (:start . 22)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 32) (:start . 28)\n (:id . 48))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 40)\n (:start . 33) (:id . 49)))@@@1@8@((:identifiers (:sid . :s4.185) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101298@unknown@formal@none@1@S@ζS The number of Pfam domains observed in all protein of species S@(((:tag . "VBZ") (:stem . "ζs") (:form . "ζS") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 13) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 21) (:start . 17)\n (:id . 46))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 29)\n (:start . 22) (:id . 47))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 38)\n (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n (:id . 49))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 45) (:start . 42)\n (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 53)\n (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n (:id . 52))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 64)\n (:start . 57) (:id . 53))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 66) (:start . 65)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s4.186) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101300@unknown@formal@none@1@S@Prediction results are shown in bold font.@(((:tag . "NN") (:stem . "prediction") (:form . "Prediction") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 18)\n (:start . 11) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 22) (:start . 19)\n (:id . 44))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 28) (:start . 23)\n (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n (:id . 46))\n ((:tag . "JJ") (:stem . "bold") (:form . "bold") (:end . 36) (:start . 32)\n (:id . 47))\n ((:tag . "NN") (:stem . "font") (:form . "font") (:end . 41) (:start . 37)\n (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 42) (:start . 41)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s4.188) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101301@unknown@formal@none@1@S@Discussion@(((:tag . "NN") (:stem . "discussion") (:form . "Discussion") (:end . 10)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.189) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Title|)))@oe@9-2-2011 5101302@unknown@formal@none@1@S@iPfam coverage is low@(((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 14)\n (:start . 6) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 17) (:start . 15)\n (:id . 44))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 21) (:start . 18)\n (:id . 45)))@@@1@4@((:identifiers (:sid . :s4.190) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101303@unknown@formal@none@1@S@The coverage of iPfam on experimentally derived protein interactions is low.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 21) (:start . 16)\n (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 24) (:start . 22)\n (:id . 46))\n ((:tag . "RB") (:stem . "experimentally") (:form . "experimentally")\n (:end . 39) (:start . 25) (:id . 47))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 47)\n (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 55)\n (:start . 48) (:id . 49))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 68)\n (:start . 56) (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 71) (:start . 69)\n (:id . 51))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 75) (:start . 72)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s4.191) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101304@unknown@formal@none@1@S@For S. cerevisiae, the species with the best mapped interactome, only 4.47% of the protein interactions contain an iPfam domain pair.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 6) (:start . 4)\n (:id . 43))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 17)\n (:start . 7) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 46))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 30)\n (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 35) (:start . 31)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 49))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 44) (:start . 40)\n (:id . 50))\n ((:tag . "VBN") (:stem . "map") (:form . "mapped") (:end . 51) (:start . 45)\n (:id . 51))\n ((:tag . "NN") (:stem . "interactome") (:form . "interactome") (:end . 63)\n (:start . 52) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n (:id . 53))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 69) (:start . 65)\n (:id . 54))\n ((:tag . "CD") (:stem . "4.47") (:form . "4.47") (:end . 74) (:start . 70)\n (:id . 55))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 75) (:start . 74)\n (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n (:id . 58))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 90)\n (:start . 83) (:id . 59))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 103)\n (:start . 91) (:id . 60))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 111)\n (:start . 104) (:id . 61))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 114) (:start . 112)\n (:id . 62))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 120)\n (:start . 115) (:id . 63))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 127)\n (:start . 121) (:id . 64))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 132) (:start . 128)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s4.192) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101305@unknown@formal@none@1@S@Even in H. sapiens, where we suspect a positive bias due to the overrepresentation of disease-related proteins in both the PDB and protein interaction databases, 81% of protein interactions do not contain an iPfam domain pair.@(((:tag . "RB") (:stem . "even") (:form . "Even") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 10) (:start . 8)\n (:id . 44))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 18)\n (:start . 11) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n (:id . 46))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 25) (:start . 20)\n (:id . 47))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 28) (:start . 26)\n (:id . 48))\n ((:tag . "VBP") (:stem . "suspect") (:form . "suspect") (:end . 36)\n (:start . 29) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n (:id . 50))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 47)\n (:start . 39) (:id . 51))\n ((:tag . "NN") (:stem . "bias") (:form . "bias") (:end . 52) (:start . 48)\n (:id . 52))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 56) (:start . 53)\n (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n (:id . 55))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n (:end . 82) (:start . 64) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n (:id . 57))\n ((:tag . "JJ") (:stem . "disease-related") (:form . "disease-related")\n (:end . 101) (:start . 86) (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 110)\n (:start . 102) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 113) (:start . 111)\n (:id . 60))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 118) (:start . 114)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n (:id . 62))\n ((:tag . "NN") (:stem . "pdb") (:form . "PDB") (:end . 126) (:start . 123)\n (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n (:id . 64))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 138)\n (:start . 131) (:id . 65))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 150)\n (:start . 139) (:id . 66))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 160)\n (:start . 151) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n (:id . 68))\n ((:tag . "CD") (:stem . "81") (:form . "81") (:end . 164) (:start . 162)\n (:id . 69))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 165) (:start . 164)\n (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 168) (:start . 166)\n (:id . 71))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 176)\n (:start . 169) (:id . 72))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 189)\n (:start . 177) (:id . 73))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 192) (:start . 190)\n (:id . 74))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 196) (:start . 193)\n (:id . 75))\n ((:tag . "VB") (:stem . "contain") (:form . "contain") (:end . 204)\n (:start . 197) (:id . 76))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 207) (:start . 205)\n (:id . 77))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 213)\n (:start . 208) (:id . 78))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 220)\n (:start . 214) (:id . 79))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 225) (:start . 221)\n (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 226) (:start . 225)\n (:id . 81)))@@@1@40@((:hcues ((:id . :x4.193.2) (:span 29 36)))\n (:ncues ((:id . :x4.193.1) (:span 193 196)))\n (:hscopes ((:id . :x4.193.2) (:span 29 160)))\n (:nscopes ((:id . :x4.193.1) (:span 193 225)))\n (:identifiers (:sid . :s4.193) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101306@unknown@formal@none@1@S@This reveals the limits of our understanding of the molecular structure of protein interactions.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "NNS") (:stem . "limit") (:form . "limits") (:end . 23)\n (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 30) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "understanding") (:form . "understanding")\n (:end . 44) (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n (:id . 50))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 61)\n (:start . 52) (:id . 51))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 71)\n (:start . 62) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 82)\n (:start . 75) (:id . 54))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 95)\n (:start . 83) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.194) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101307@unknown@formal@none@1@S@Figure 1 also shows that a majority of protein interactions contains at least one pair of Pfam domains.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 8) (:start . 7)\n (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 19) (:start . 14)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n (:id . 47))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 35)\n (:start . 27) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 46)\n (:start . 39) (:id . 50))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 59)\n (:start . 47) (:id . 51))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 68)\n (:start . 60) (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 71) (:start . 69)\n (:id . 53))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 77) (:start . 72)\n (:id . 54))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 81) (:start . 78)\n (:id . 55))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 86) (:start . 82)\n (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n (:id . 57))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 94) (:start . 90)\n (:id . 58))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 102)\n (:start . 95) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.195) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101308@unknown@formal@none@1@S@ While there is no structural information about putative interactions between these pairs, this fraction can already be analysed using statistical methods to identify putative domain interactions 7910.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 6) (:start . 1)\n (:id . 42))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 12) (:start . 7)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . 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",") (:end . 90) (:start . 89)\n (:id . 54))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 95) (:start . 91)\n (:id . 55))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 104)\n (:start . 96) (:id . 56))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 108) (:start . 105)\n (:id . 57))\n ((:tag . "RB") (:stem . "already") (:form . "already") (:end . 116)\n (:start . 109) (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 119) (:start . 117)\n (:id . 59))\n ((:tag . "VBN") (:stem . "analyse") (:form . "analysed") (:end . 128)\n (:start . 120) (:id . 60))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 134) (:start . 129)\n (:id . 61))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 146)\n (:start . 135) (:id . 62))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 154)\n (:start . 147) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 157) (:start . 155)\n (:id . 64))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 166)\n (:start . 158) (:id . 65))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 175)\n (:start . 167) (:id . 66))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 182)\n (:start . 176) (:id . 67))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 195)\n (:start . 183) (:id . 68))\n ((:tag . "CD") (:stem . "7910") (:form . "7910") (:end . 200) (:start . 196)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n (:id . 70)))@@@1@29@((:ncues ((:id . :x4.196.1) (:span 16 18)))\n (:nscopes ((:id . :x4.196.1) (:span 16 89)))\n (:identifiers (:sid . :s4.196) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101310@unknown@formal@none@1@S@Prioritising these targets according to the number of covered experimental interactions could increase the coverage of databases like iPfam quickly.@(((:tag . "VBG") (:stem . "prioritise") (:form . "Prioritising") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 18) (:start . 13)\n (:id . 43))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 26)\n (:start . 19) (:id . 44))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 36)\n (:start . 27) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n (:id . 47))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 50)\n (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n (:id . 49))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 61)\n (:start . 54) (:id . 50))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 74)\n (:start . 62) (:id . 51))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 87)\n (:start . 75) (:id . 52))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 93) (:start . 88)\n (:id . 53))\n ((:tag . "VB") (:stem . "increase") (:form . "increase") (:end . 102)\n (:start . 94) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n (:id . 55))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 115)\n (:start . 107) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 118) (:start . 116)\n (:id . 57))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 128)\n (:start . 119) (:id . 58))\n ((:tag . "IN") (:stem . "like") (:form . "like") (:end . 133) (:start . 129)\n (:id . 59))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 139)\n (:start . 134) (:id . 60))\n ((:tag . "RB") (:stem . "quickly") (:form . "quickly") (:end . 147)\n (:start . 140) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n (:id . 62)))@@@1@21@((:hcues ((:id . :x4.198.1) (:span 88 93)))\n (:hscopes ((:id . :x4.198.1) (:span 88 147)))\n (:identifiers (:sid . :s4.198) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101311@unknown@formal@none@1@S@We find, however, that iPfam domain pairs occur significantly more often in experimental interactions than would be expected by chance.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 16)\n (:start . 9) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n (:id . 47))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 28) (:start . 23)\n (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 35)\n (:start . 29) (:id . 49))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 41) (:start . 36)\n (:id . 50))\n ((:tag . "VBP") (:stem . "occur") (:form . "occur") (:end . 47) (:start . 42)\n (:id . 51))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 61) (:start . 48) (:id . 52))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 66) (:start . 62)\n (:id . 53))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 72) (:start . 67)\n (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 75) (:start . 73)\n (:id . 55))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 88)\n (:start . 76) (:id . 56))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 101)\n (:start . 89) (:id . 57))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 106) (:start . 102)\n (:id . 58))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 112)\n (:start . 107) (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 115) (:start . 113)\n (:id . 60))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 124)\n (:start . 116) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 127) (:start . 125)\n (:id . 62))\n ((:tag . "NN") (:stem . "chance") (:form . "chance") (:end . 134)\n (:start . 128) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n (:id . 64)))@@@1@23@((:hcues ((:id . :x4.199.1) (:span 107 112)))\n (:hscopes ((:id . :x4.199.1) (:span 107 134)))\n (:identifiers (:sid . :s4.199) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101312@unknown@formal@none@1@S@This requires that at least a subset of the iPfam domain pairs are reused in several experimental interactions.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 27) (:start . 22)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n (:id . 47))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 36)\n (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n (:id . 50))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 49) (:start . 44)\n (:id . 51))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 56)\n (:start . 50) (:id . 52))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 62) (:start . 57)\n (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 66) (:start . 63)\n (:id . 54))\n ((:tag . "VBN") (:stem . "reuse") (:form . "reused") (:end . 73)\n (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n (:id . 56))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 84)\n (:start . 77) (:id . 57))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 97)\n (:start . 85) (:id . 58))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 110)\n (:start . 98) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.200) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101313@unknown@formal@none@1@S@iPfam domain pairs can act as modules@(((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 12) (:start . 6)\n (:id . 43))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "VB") (:stem . "act") (:form . "act") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 29) (:start . 27)\n (:id . 47))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 37)\n (:start . 30) (:id . 48)))@@@1@7@((:identifiers (:sid . :s4.201) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101314@unknown@formal@none@1@S@Despite the low overall coverage, iPfam domain pairs are found in more protein interactions than would be expected by chance (see Table 1).@(((:tag . "IN") (:stem . "despite") (:form . "Despite") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n (:id . 43))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 23)\n (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . 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"interactions") (:end . 91)\n (:start . 79) (:id . 56))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 96) (:start . 92)\n (:id . 57))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 102) (:start . 97)\n (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 105) (:start . 103)\n (:id . 59))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 114)\n (:start . 106) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 117) (:start . 115)\n (:id . 61))\n ((:tag . "NN") (:stem . "chance") (:form . "chance") (:end . 124)\n (:start . 118) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n (:id . 63))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 129) (:start . 126)\n (:id . 64))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 135)\n (:start . 130) (:id . 65))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 137) (:start . 136)\n (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n (:id . 68)))@@@1@27@((:hcues ((:id . :x4.202.1) (:span 97 102)))\n (:hscopes ((:id . :x4.202.1) (:span 97 124)))\n (:identifiers (:sid . :s4.202) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101315@unknown@formal@none@1@S@This statistical overrepresentation suggests that certain iPfam domain pairs constitute modules of molecular recognition which are reused in different protein interactions 2.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 16)\n (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n (:end . 35) (:start . 17) (:id . 44))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 44)\n (:start . 36) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 49) (:start . 45)\n (:id . 46))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 57)\n (:start . 50) (:id . 47))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 63) (:start . 58)\n (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 70)\n (:start . 64) (:id . 49))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 76) (:start . 71)\n (:id . 50))\n ((:tag . "VBP") (:stem . "constitute") (:form . "constitute") (:end . 87)\n (:start . 77) (:id . 51))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 95)\n (:start . 88) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n (:id . 53))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 108)\n (:start . 99) (:id . 54))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 120)\n (:start . 109) (:id . 55))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 126)\n (:start . 121) (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 130) (:start . 127)\n (:id . 57))\n ((:tag . "VBN") (:stem . "reuse") (:form . "reused") (:end . 137)\n (:start . 131) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 140) (:start . 138)\n (:id . 59))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 150)\n (:start . 141) (:id . 60))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 158)\n (:start . 151) (:id . 61))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 171)\n (:start . 159) (:id . 62))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 173) (:start . 172)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n (:id . 64)))@@@1@23@((:hcues ((:id . :x4.203.1) (:span 36 44)))\n (:hscopes ((:id . :x4.203.1) (:span 36 171)))\n (:identifiers (:sid . :s4.203) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101316@unknown@formal@none@1@S@In fact, we find a characteristic power law distribution when we plot the histogram of experimental interactions per iPfam domain pair, see Figure 2.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n (:id . 45))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 16) (:start . 12)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . 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"of") (:end . 86) (:start . 84)\n (:id . 57))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 99)\n (:start . 87) (:id . 58))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 112)\n (:start . 100) (:id . 59))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 116) (:start . 113)\n (:id . 60))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 122)\n (:start . 117) (:id . 61))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 129)\n (:start . 123) (:id . 62))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 134) (:start . 130)\n (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n (:id . 64))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 139) (:start . 136)\n (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 146)\n (:start . 140) (:id . 66))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 148) (:start . 147)\n (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s4.204) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101317@unknown@formal@none@1@S@This underlines that a few promiscuous iPfam domain pairs are responsible for the majority of the iPfam coverage.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "underline") (:form . "underlines") (:end . 15)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 20) (:start . 16)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n (:id . 45))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "JJ") (:stem . "promiscuous") (:form . "promiscuous") (:end . 38)\n (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 44) (:start . 39)\n (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 51)\n (:start . 45) (:id . 49))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 57) (:start . 52)\n (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 61) (:start . 58)\n (:id . 51))\n ((:tag . "JJ") (:stem . "responsible") (:form . "responsible") (:end . 73)\n (:start . 62) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 77) (:start . 74)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n (:id . 54))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 90)\n (:start . 82) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n (:id . 57))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 103) (:start . 98)\n (:id . 58))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 112)\n (:start . 104) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.205) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101318@unknown@formal@none@1@S@These iPfam domain pairs are most likely to be reusable modules.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 18)\n (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 24) (:start . 19)\n (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 40)\n (:start . 34) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 43) (:start . 41)\n (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 46) (:start . 44)\n (:id . 50))\n ((:tag . "JJ") (:stem . "reusable") (:form . "reusable") (:end . 55)\n (:start . 47) (:id . 51))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 63)\n (:start . 56) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 64) (:start . 63)\n (:id . 53)))@@@1@12@((:hcues ((:id . :x4.206.1) (:span 34 40)))\n (:hscopes ((:id . :x4.206.1) (:span 0 63)))\n (:identifiers (:sid . :s4.206) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101320@unknown@formal@none@1@S@Conversely, a large number of iPfam domain pairs are specific to a small number of protein interactions.@(((:tag . "RB") (:stem . "conversely") (:form . "Conversely") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n (:id . 44))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 19) (:start . 14)\n (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 26)\n (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 35) (:start . 30)\n (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 42)\n (:start . 36) (:id . 49))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 48) (:start . 43)\n (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 52) (:start . 49)\n (:id . 51))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 61)\n (:start . 53) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 66) (:start . 65)\n (:id . 54))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 72) (:start . 67)\n (:id . 55))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 79)\n (:start . 73) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n (:id . 57))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 90)\n (:start . 83) (:id . 58))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 103)\n (:start . 91) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.208) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101321@unknown@formal@none@1@S@This implies that recognition specificity amongst proteins is often achieved by maintaining an exclusive interacting domain pair.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "imply") (:form . "implies") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 17) (:start . 13)\n (:id . 44))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 29)\n (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 41)\n (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "amongst") (:form . "amongst") (:end . 49)\n (:start . 42) (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 58)\n (:start . 50) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 61) (:start . 59)\n (:id . 49))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 67) (:start . 62)\n (:id . 50))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 76)\n (:start . 68) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 79) (:start . 77)\n (:id . 52))\n ((:tag . "VBG") (:stem . "maintain") (:form . "maintaining") (:end . 91)\n (:start . 80) (:id . 53))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 94) (:start . 92)\n (:id . 54))\n ((:tag . "JJ") (:stem . "exclusive") (:form . "exclusive") (:end . 104)\n (:start . 95) (:id . 55))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 116)\n (:start . 105) (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 123)\n (:start . 117) (:id . 57))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 128) (:start . 124)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n (:id . 59)))@@@1@18@((:hcues ((:id . :x4.209.1) (:span 5 12)))\n (:hscopes ((:id . :x4.209.1) (:span 5 128)))\n (:identifiers (:sid . :s4.209) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101322@unknown@formal@none@1@S@This could pose a problem for purely statistical approaches to infer domain interactions:: if for many interfaces the real interacting domain pair will only occur once in an interactome, it will be hard to elucidate this on a statistical basis.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "VB") (:stem . "pose") (:form . "pose") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "NN") (:stem . "problem") (:form . "problem") (:end . 25)\n (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 29) (:start . 26)\n (:id . 47))\n ((:tag . "RB") (:stem . "purely") (:form . "purely") (:end . 36)\n (:start . 30) (:id . 48))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 48)\n (:start . 37) (:id . 49))\n ((:tag . "NNS") (:stem . "approach") (:form . "approaches") (:end . 59)\n (:start . 49) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 62) (:start . 60)\n (:id . 51))\n ((:tag . "VB") (:stem . "infer") (:form . "infer") (:end . 68) (:start . 63)\n (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 75)\n (:start . 69) (:id . 53))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 88)\n (:start . 76) (:id . 54))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 89) (:start . 88)\n (:id . 55))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 90) (:start . 89)\n (:id . 56))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 93) (:start . 91)\n (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 97) (:start . 94)\n (:id . 58))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 102) (:start . 98)\n (:id . 59))\n ((:tag . "NNS") (:stem . "interface") (:form . "interfaces") (:end . 113)\n (:start . 103) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n (:id . 61))\n ((:tag . "JJ") (:stem . "real") (:form . "real") (:end . 122) (:start . 118)\n (:id . 62))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 134)\n (:start . 123) (:id . 63))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 141)\n (:start . 135) (:id . 64))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 146) (:start . 142)\n (:id . 65))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 151) (:start . 147)\n (:id . 66))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 156) (:start . 152)\n (:id . 67))\n ((:tag . "VB") (:stem . "occur") (:form . "occur") (:end . 162)\n (:start . 157) (:id . 68))\n ((:tag . "RB") (:stem . "once") (:form . "once") (:end . 167) (:start . 163)\n (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 170) (:start . 168)\n (:id . 70))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 173) (:start . 171)\n (:id . 71))\n ((:tag . "NN") (:stem . "interactome") (:form . "interactome") (:end . 185)\n (:start . 174) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 186) (:start . 185)\n (:id . 73))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 189) (:start . 187)\n (:id . 74))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 194) (:start . 190)\n (:id . 75))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 197) (:start . 195)\n (:id . 76))\n ((:tag . "JJ") (:stem . "hard") (:form . "hard") (:end . 202) (:start . 198)\n (:id . 77))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 205) (:start . 203)\n (:id . 78))\n ((:tag . "VB") (:stem . "elucidate") (:form . "elucidate") (:end . 215)\n (:start . 206) (:id . 79))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 220) (:start . 216)\n (:id . 80))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 223) (:start . 221)\n (:id . 81))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 225) (:start . 224)\n (:id . 82))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 237)\n (:start . 226) (:id . 83))\n ((:tag . "NN") (:stem . "basis") (:form . "basis") (:end . 243)\n (:start . 238) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 244) (:start . 243)\n (:id . 85)))@@@1@44@((:hcues ((:id . :x4.210.1) (:span 5 10)))\n (:hscopes ((:id . :x4.210.1) (:span 5 88)))\n (:identifiers (:sid . :s4.210) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101323@unknown@formal@none@1@S@The concept of modularity of interacting domain pairs is furthermore supported by the positive correlation between the number of protein interactions an iPfam domain pair is seen in and the connectivity of the interacting proteins.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "modularity") (:form . "modularity") (:end . 25)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 40)\n (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 47)\n (:start . 41) (:id . 48))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 53) (:start . 48)\n (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 56) (:start . 54)\n (:id . 50))\n ((:tag . "RB") (:stem . "furthermore") (:form . "furthermore") (:end . 68)\n (:start . 57) (:id . 51))\n ((:tag . "VBN") (:stem . "support") (:form . "supported") (:end . 78)\n (:start . 69) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 81) (:start . 79)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n (:id . 54))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 94)\n (:start . 86) (:id . 55))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 106)\n (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 114)\n (:start . 107) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n (:id . 58))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 125)\n (:start . 119) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 128) (:start . 126)\n (:id . 60))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 136)\n (:start . 129) (:id . 61))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 149)\n (:start . 137) (:id . 62))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 152) (:start . 150)\n (:id . 63))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 158)\n (:start . 153) (:id . 64))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 165)\n (:start . 159) (:id . 65))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 170) (:start . 166)\n (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 173) (:start . 171)\n (:id . 67))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 178) (:start . 174)\n (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 181) (:start . 179)\n (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 185) (:start . 182)\n (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 189) (:start . 186)\n (:id . 71))\n ((:tag . "NN") (:stem . "connectivity") (:form . "connectivity") (:end . 202)\n (:start . 190) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 205) (:start . 203)\n (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 209) (:start . 206)\n (:id . 74))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 221)\n (:start . 210) (:id . 75))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 230)\n (:start . 222) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 231) (:start . 230)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s4.211) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101324@unknown@formal@none@1@S@We hypothesise that if during the course of evolution a protein is duplicated, it is likely to retain connections with other proteins which contain the same domain interaction modules.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "hypothesise") (:form . "hypothesise") (:end . 14)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 22) (:start . 20)\n (:id . 45))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 29)\n (:start . 23) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 47))\n ((:tag . "NN") (:stem . "course") (:form . "course") (:end . 40)\n (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n (:id . 49))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 53)\n (:start . 44) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 55) (:start . 54)\n (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 63)\n (:start . 56) (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 66) (:start . 64)\n (:id . 53))\n ((:tag . "VBN") (:stem . "duplicate") (:form . "duplicated") (:end . 77)\n (:start . 67) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n (:id . 55))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 81) (:start . 79)\n (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 84) (:start . 82)\n (:id . 57))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 91)\n (:start . 85) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n (:id . 59))\n ((:tag . "VB") (:stem . "retain") (:form . "retain") (:end . 101)\n (:start . 95) (:id . 60))\n ((:tag . "NNS") (:stem . "connection") (:form . "connections") (:end . 113)\n (:start . 102) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 118) (:start . 114)\n (:id . 62))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 124)\n (:start . 119) (:id . 63))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 133)\n (:start . 125) (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 139)\n (:start . 134) (:id . 65))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 147)\n (:start . 140) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n (:id . 67))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 156) (:start . 152)\n (:id . 68))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 163)\n (:start . 157) (:id . 69))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 175)\n (:start . 164) (:id . 70))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 183)\n (:start . 176) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n (:id . 72)))@@@1@31@((:hcues ((:id . :x4.212.1) (:span 85 91)) ((:id . :x4.212.2) (:span 3 14)))\n (:hscopes ((:id . :x4.212.1) (:span 79 183))\n ((:id . :x4.212.2) (:span 3 183)))\n (:identifiers (:sid . :s4.212) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101325@unknown@formal@none@1@S@It is clear, however, that even though recognition domains are reused in various proteins, their specificity is bound to be controlled.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 11) (:start . 6)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 45))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 20)\n (:start . 13) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n (:id . 48))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 31) (:start . 27)\n (:id . 49))\n ((:tag . "IN") (:stem . "though") (:form . "though") (:end . 38)\n (:start . 32) (:id . 50))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 50)\n (:start . 39) (:id . 51))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 58)\n (:start . 51) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 62) (:start . 59)\n (:id . 53))\n ((:tag . "VBN") (:stem . "reuse") (:form . "reused") (:end . 69)\n (:start . 63) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n (:id . 55))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 80)\n (:start . 73) (:id . 56))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 89)\n (:start . 81) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n (:id . 58))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 96)\n (:start . 91) (:id . 59))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 108)\n (:start . 97) (:id . 60))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 111) (:start . 109)\n (:id . 61))\n ((:tag . "VBN") (:stem . "bind") (:form . "bound") (:end . 117)\n (:start . 112) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 120) (:start . 118)\n (:id . 63))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 123) (:start . 121)\n (:id . 64))\n ((:tag . "VBN") (:stem . "control") (:form . "controlled") (:end . 134)\n (:start . 124) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s4.213) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101326@unknown@formal@none@1@S@Many domain–domain interfaces remain to be resolved@(((:tag . "JJ") (:stem . "many") (:form . "Many") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "domain–domain") (:form . "domain–domain")\n (:end . 18) (:start . 5) (:id . 43))\n ((:tag . "NNS") (:stem . "interface") (:form . "interfaces") (:end . 29)\n (:start . 19) (:id . 44))\n ((:tag . "VBP") (:stem . "remain") (:form . "remain") (:end . 36)\n (:start . 30) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 42) (:start . 40)\n (:id . 47))\n ((:tag . "VBN") (:stem . "resolve") (:form . "resolved") (:end . 51)\n (:start . 43) (:id . 48)))@@@1@7@((:identifiers (:sid . :s4.214) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101327@unknown@formal@none@1@S@We tried to estimate how many iPfam domain pairs exists in all interactomes.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "try") (:form . "tried") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "VB") (:stem . "estimate") (:form . "estimate") (:end . 20)\n (:start . 12) (:id . 45))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 24) (:start . 21)\n (:id . 46))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 29) (:start . 25)\n (:id . 47))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 35) (:start . 30)\n (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 42)\n (:start . 36) (:id . 49))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 48) (:start . 43)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "exist") (:form . "exists") (:end . 55)\n (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n (:id . 52))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 62) (:start . 59)\n (:id . 53))\n ((:tag . "NNS") (:stem . "interactome") (:form . "interactomes") (:end . 75)\n (:start . 63) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s4.215) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101328@unknown@formal@none@1@S@Our predictions lie almost an order of magnitude higher than the 10000 domain interaction types proposed by Aloy and Russel 2.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "lie") (:form . "lie") (:end . 19) (:start . 16)\n (:id . 44))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 26)\n (:start . 20) (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 35) (:start . 30)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n (:id . 48))\n ((:tag . "NN") (:stem . "magnitude") (:form . "magnitude") (:end . 48)\n (:start . 39) (:id . 49))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 55) (:start . 49)\n (:id . 50))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 60) (:start . 56)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n (:id . 52))\n ((:tag . "CD") (:stem . "10000") (:form . "10000") (:end . 70) (:start . 65)\n (:id . 53))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 77)\n (:start . 71) (:id . 54))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 89)\n (:start . 78) (:id . 55))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 95) (:start . 90)\n (:id . 56))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 104)\n (:start . 96) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 107) (:start . 105)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Aloy") (:form . "Aloy") (:end . 112) (:start . 108)\n (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n (:id . 60))\n ((:tag . "NNP") (:stem . "Russel") (:form . "Russel") (:end . 123)\n (:start . 117) (:id . 61))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 125) (:start . 124)\n (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s4.216) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101330@unknown@formal@none@1@S@The statistical approaches described in the introduction can only cover a small fraction of this domaininteraction space.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "approach") (:form . "approaches") (:end . 26)\n (:start . 16) (:id . 44))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 36)\n (:start . 27) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n (:id . 47))\n ((:tag . "NN") (:stem . "introduction") (:form . "introduction") (:end . 56)\n (:start . 44) (:id . 48))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 60) (:start . 57)\n (:id . 49))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 65) (:start . 61)\n (:id . 50))\n ((:tag . "VB") (:stem . "cover") (:form . "cover") (:end . 71) (:start . 66)\n (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n (:id . 52))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 79) (:start . 74)\n (:id . 53))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 88)\n (:start . 80) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n (:id . 55))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 96) (:start . 92)\n (:id . 56))\n ((:tag . "NN") (:stem . "domaininteraction") (:form . "domaininteraction")\n (:end . 114) (:start . 97) (:id . 57))\n ((:tag . "NN") (:stem . "space") (:form . "space") (:end . 120)\n (:start . 115) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.218) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101331@unknown@formal@none@1@S@Riley et al. for example report only 3005 interacting domain pairs which could be inferred from protein interactions 7.@(((:tag . "NNP") (:stem . "Riley") (:form . "Riley") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 8) (:start . 6)\n (:id . 43))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 24)\n (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 31)\n (:start . 25) (:id . 47))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 36) (:start . 32)\n (:id . 48))\n ((:tag . "CD") (:stem . "3005") (:form . "3005") (:end . 41) (:start . 37)\n (:id . 49))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 53)\n (:start . 42) (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 60)\n (:start . 54) (:id . 51))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 66) (:start . 61)\n (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 72) (:start . 67)\n (:id . 53))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 78) (:start . 73)\n (:id . 54))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 81) (:start . 79)\n (:id . 55))\n ((:tag . "VBN") (:stem . "infer") (:form . "inferred") (:end . 90)\n (:start . 82) (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 95) (:start . 91)\n (:id . 57))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 103)\n (:start . 96) (:id . 58))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 116)\n (:start . 104) (:id . 59))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 118) (:start . 117)\n (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s4.219) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101332@unknown@formal@none@1@S@Even under the assumption that many interactions involve short linear motifs, it seems likely that a large number of domain interactions remain to be resolved.@(((:tag . "RB") (:stem . "even") (:form . "Even") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "assumption") (:form . "assumption") (:end . 25)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n (:id . 46))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 35) (:start . 31)\n (:id . 47))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 48)\n (:start . 36) (:id . 48))\n ((:tag . "VBP") (:stem . "involve") (:form . "involve") (:end . 56)\n (:start . 49) (:id . 49))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 62) (:start . 57)\n (:id . 50))\n ((:tag . "JJ") (:stem . "linear") (:form . "linear") (:end . 69)\n (:start . 63) (:id . 51))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 76)\n (:start . 70) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n (:id . 53))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 80) (:start . 78)\n (:id . 54))\n ((:tag . "VBZ") (:stem . "seem") (:form . "seems") (:end . 86) (:start . 81)\n (:id . 55))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 93)\n (:start . 87) (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 98) (:start . 94)\n (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 100) (:start . 99)\n (:id . 58))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 106)\n (:start . 101) (:id . 59))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 113)\n (:start . 107) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n (:id . 61))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 123)\n (:start . 117) (:id . 62))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 136)\n (:start . 124) (:id . 63))\n ((:tag . "VBP") (:stem . "remain") (:form . "remain") (:end . 143)\n (:start . 137) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 146) (:start . 144)\n (:id . 65))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 149) (:start . 147)\n (:id . 66))\n ((:tag . "VBN") (:stem . "resolve") (:form . "resolved") (:end . 158)\n (:start . 150) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n (:id . 68)))@@@1@27@((:hcues ((:id . :x4.220.1) (:span 87 93)) ((:id . :x4.220.2) (:span 81 86))\n ((:id . :x4.220.3) (:span 15 25)))\n (:hscopes ((:id . :x4.220.1) (:span 87 158))\n ((:id . :x4.220.2) (:span 81 158)) ((:id . :x4.220.3) (:span 15 158)))\n (:identifiers (:sid . :s4.220) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101333@unknown@formal@none@1@S@iPfam domain pairs are conserved during evolution@(((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 12) (:start . 6)\n (:id . 43))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 32)\n (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 39)\n (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 49)\n (:start . 40) (:id . 48)))@@@1@7@((:identifiers (:sid . :s4.221) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101334@unknown@formal@none@1@S@iPfam domain pairs are not only recurrent within the protein interaction network of one species.@(((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 12) (:start . 6)\n (:id . 43))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 31) (:start . 27)\n (:id . 47))\n ((:tag . "JJ") (:stem . "recurrent") (:form . "recurrent") (:end . 41)\n (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 48)\n (:start . 42) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 60)\n (:start . 53) (:id . 51))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 72)\n (:start . 61) (:id . 52))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 80)\n (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n (:id . 54))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 87) (:start . 84)\n (:id . 55))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 95)\n (:start . 88) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s4.222) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101335@unknown@formal@none@1@S@They also appear to be conserved between species.@(((:tag . "PRP") (:stem . "they") (:form . "They") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 16)\n (:start . 10) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 22) (:start . 20)\n (:id . 46))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 32)\n (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 40)\n (:start . 33) (:id . 48))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 48)\n (:start . 41) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n (:id . 50)))@@@1@9@((:hcues ((:id . :x4.223.1) (:span 10 16)))\n (:hscopes ((:id . :x4.223.1) (:span 0 48)))\n (:identifiers (:sid . :s4.223) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101336@unknown@formal@none@1@S@In a small set of protein structures from S. cerevisiae, it has been shown that interacting domain pairs are more conserved than non-interacting domain pairs 10.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 10) (:start . 5)\n (:id . 44))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 14) (:start . 11)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 25)\n (:start . 18) (:id . 47))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 36)\n (:start . 26) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 41) (:start . 37)\n (:id . 49))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 44) (:start . 42)\n (:id . 50))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 55)\n (:start . 45) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n (:id . 52))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 59) (:start . 57)\n (:id . 53))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 63) (:start . 60)\n (:id . 54))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 68) (:start . 64)\n (:id . 55))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 74) (:start . 69)\n (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 79) (:start . 75)\n (:id . 57))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 91)\n (:start . 80) (:id . 58))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 98)\n (:start . 92) (:id . 59))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 104) (:start . 99)\n (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 108) (:start . 105)\n (:id . 61))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 113) (:start . 109)\n (:id . 62))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 123)\n (:start . 114) (:id . 63))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 128) (:start . 124)\n (:id . 64))\n ((:tag . "JJ") (:stem . "non-interacting") (:form . "non-interacting")\n (:end . 144) (:start . 129) (:id . 65))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 151)\n (:start . 145) (:id . 66))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 157)\n (:start . 152) (:id . 67))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 160) (:start . 158)\n (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s4.224) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101337@unknown@formal@none@1@S@Here, we call an iPfam domain pair conserved if there are protein interactions in two species which contain the same iPfam domain pair.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n (:id . 44))\n ((:tag . "VBP") (:stem . "call") (:form . "call") (:end . 13) (:start . 9)\n (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 16) (:start . 14)\n (:id . 46))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 22) (:start . 17)\n (:id . 47))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 29)\n (:start . 23) (:id . 48))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 34) (:start . 30)\n (:id . 49))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 44)\n (:start . 35) (:id . 50))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 47) (:start . 45)\n (:id . 51))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 53) (:start . 48)\n (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 57) (:start . 54)\n (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 65)\n (:start . 58) (:id . 54))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 78)\n (:start . 66) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n (:id . 56))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 85) (:start . 82)\n (:id . 57))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 93)\n (:start . 86) (:id . 58))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 99) (:start . 94)\n (:id . 59))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 107)\n (:start . 100) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n (:id . 61))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 116) (:start . 112)\n (:id . 62))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 122)\n (:start . 117) (:id . 63))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 129)\n (:start . 123) (:id . 64))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 134) (:start . 130)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s4.225) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101338@unknown@formal@none@1@S@In a recent study 31, Gandhi et al. have assessed the conservation of protein interactions as the co-occurrence of orthologous interacting proteins.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 11) (:start . 5)\n (:id . 44))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 17) (:start . 12)\n (:id . 45))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 20) (:start . 18)\n (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Gandhi") (:form . "Gandhi") (:end . 28)\n (:start . 22) (:id . 48))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 31) (:start . 29)\n (:id . 49))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 35) (:start . 32)\n (:id . 50))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 40) (:start . 36)\n (:id . 51))\n ((:tag . "VBN") (:stem . "assess") (:form . "assessed") (:end . 49)\n (:start . 41) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n (:id . 53))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 66)\n (:start . 54) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n (:id . 55))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 77)\n (:start . 70) (:id . 56))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 90)\n (:start . 78) (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 93) (:start . 91)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n (:id . 59))\n ((:tag . "NN") (:stem . "co-occurrence") (:form . "co-occurrence")\n (:end . 111) (:start . 98) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n (:id . 61))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 126)\n (:start . 115) (:id . 62))\n ((:tag . "NN") (:stem . "interacting") (:form . "interacting") (:end . 138)\n (:start . 127) (:id . 63))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 147)\n (:start . 139) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.226) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101340@unknown@formal@none@1@S@Conversely, we find that 71 iPfam domain pairs are conserved in the experimental interactions of these species.@(((:tag . "RB") (:stem . "conversely") (:form . "Conversely") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 19) (:start . 15)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n (:id . 46))\n ((:tag . "CD") (:stem . "71") (:form . "71") (:end . 27) (:start . 25)\n (:id . 47))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 33) (:start . 28)\n (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 40)\n (:start . 34) (:id . 49))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 46) (:start . 41)\n (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 50) (:start . 47)\n (:id . 51))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 60)\n (:start . 51) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n (:id . 54))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 80)\n (:start . 68) (:id . 55))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 93)\n (:start . 81) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n (:id . 57))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 102) (:start . 97)\n (:id . 58))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 110)\n (:start . 103) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.228) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101341@unknown@formal@none@1@S@Even between a prokaryote like E. coli and the two eukaryotes S. cerevisiae and H. sapiens there is a considerable proportion of conserved iPfam domain pairs, to the extent that 53% of the iPfam domain pairs from E. coli are also observed in a eukaryote (Table 2).@(((:tag . "RB") (:stem . "even") (:form . "Even") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 14) (:start . 13)\n (:id . 44))\n ((:tag . "NN") (:stem . "prokaryote") (:form . "prokaryote") (:end . 25)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "like") (:form . "like") (:end . 30) (:start . 26)\n (:id . 46))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 33) (:start . 31)\n (:id . 47))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 38) (:start . 34)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n (:id . 50))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 50) (:start . 47)\n (:id . 51))\n ((:tag . "NNS") (:stem . "eukaryote") (:form . "eukaryotes") (:end . 61)\n (:start . 51) (:id . 52))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 64) (:start . 62)\n (:id . 53))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 75)\n (:start . 65) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 79) (:start . 76)\n (:id . 55))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 82) (:start . 80)\n (:id . 56))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 90)\n (:start . 83) (:id . 57))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 96) (:start . 91)\n (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 99) (:start . 97)\n (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 101) (:start . 100)\n (:id . 60))\n ((:tag . "JJ") (:stem . "considerable") (:form . "considerable") (:end . 114)\n (:start . 102) (:id . 61))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 125)\n (:start . 115) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 128) (:start . 126)\n (:id . 63))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 138)\n (:start . 129) (:id . 64))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 144)\n (:start . 139) (:id . 65))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 151)\n (:start . 145) (:id . 66))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 157)\n (:start . 152) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 161) (:start . 159)\n (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n (:id . 70))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 172)\n (:start . 166) (:id . 71))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 177) (:start . 173)\n (:id . 72))\n ((:tag . "CD") (:stem . "53") (:form . "53") (:end . 180) (:start . 178)\n (:id . 73))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 181) (:start . 180)\n (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 184) (:start . 182)\n (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 188) (:start . 185)\n (:id . 76))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 194)\n (:start . 189) (:id . 77))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 201)\n (:start . 195) (:id . 78))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 207)\n (:start . 202) (:id . 79))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 212) (:start . 208)\n (:id . 80))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 215) (:start . 213)\n (:id . 81))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 220) (:start . 216)\n (:id . 82))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 224) (:start . 221)\n (:id . 83))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 229) (:start . 225)\n (:id . 84))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 238)\n (:start . 230) (:id . 85))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 241) (:start . 239)\n (:id . 86))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 243) (:start . 242)\n (:id . 87))\n ((:tag . "JJ") (:stem . "eukaryote") (:form . "eukaryote") (:end . 253)\n (:start . 244) (:id . 88))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 255) (:start . 254)\n (:id . 89))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 260)\n (:start . 255) (:id . 90))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 262) (:start . 261)\n (:id . 91))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 263) (:start . 262)\n (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 264) (:start . 263)\n (:id . 93)))@@@1@52@((:identifiers (:sid . :s4.229) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101342@unknown@formal@none@1@S@107 domain pairs are shared between E. coli, S. cerevisiae and H. sapiens.@(((:tag . "CD") (:stem . "107") (:form . "107") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 16) (:start . 11)\n (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "VBN") (:stem . "share") (:form . "shared") (:end . 27)\n (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 35)\n (:start . 28) (:id . 47))\n ((:tag . "NNP") (:stem . "E.") (:form . "E.") (:end . 38) (:start . 36)\n (:id . 48))\n ((:tag . "NNP") (:stem . "coli") (:form . "coli") (:end . 43) (:start . 39)\n (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n (:id . 50))\n ((:tag . "NNP") (:stem . "S.") (:form . "S.") (:end . 47) (:start . 45)\n (:id . 51))\n ((:tag . "NNP") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 58)\n (:start . 48) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n (:id . 53))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 65) (:start . 63)\n (:id . 54))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 73)\n (:start . 66) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.230) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101343@unknown@formal@none@1@S@These domains are predominantly related to transcription, translation and other basic essential cellular activities, which is in congruence with the findings of Gandhi et al.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 13)\n (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "RB") (:stem . "predominantly") (:form . "predominantly")\n (:end . 31) (:start . 18) (:id . 45))\n ((:tag . "VBN") (:stem . "relate") (:form . 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"NNS") (:stem . "interaction") (:form . "interactions") (:end . 153)\n (:start . 141) (:id . 66))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 158) (:start . 154)\n (:id . 67))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 161) (:start . 159)\n (:id . 68))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 166) (:start . 162)\n (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 169) (:start . 167)\n (:id . 70))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 172) (:start . 170)\n (:id . 71))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 180)\n (:start . 173) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n (:id . 73)))@@@1@32@((:hcues ((:id . :x4.232.1) (:span 86 94)))\n (:hscopes ((:id . :x4.232.1) (:span 86 180)))\n (:identifiers (:sid . :s4.232) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101345@unknown@formal@none@1@S@While more than half of the iPfam domain pairs in E. coli have been retained throughout evolution, numerous new ones seem to have emerged in eukaryotic development.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "half") (:form . "half") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . 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"eukaryotic") (:end . 151)\n (:start . 141) (:id . 68))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 163)\n (:start . 152) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x4.233.1) (:span 117 121)))\n (:hscopes ((:id . :x4.233.1) (:span 99 163)))\n (:identifiers (:sid . :s4.233) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101346@unknown@formal@none@1@S@The significant positive correlation in the frequency of iPfam domain pairs conserved between S. cerevisiae and H. sapiens also suggests that the binding interfaces are more often kept or even reused rather than lost in the course of evolution.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . 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(:end . 244) (:start . 243)\n (:id . 81)))@@@1@40@((:hcues ((:id . :x4.234.2) (:span 185 187))\n ((:id . :x4.234.3) (:span 128 136)))\n (:ncues ((:id . :x4.234.1) (:span 200 211)))\n (:hscopes ((:id . :x4.234.2) (:span 180 199))\n ((:id . :x4.234.3) (:span 128 243)))\n (:nscopes ((:id . :x4.234.1) (:span 200 216)))\n (:identifiers (:sid . :s4.234) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101347@unknown@formal@none@1@S@Conversely, this also raises the question of whether one could establish a comprehensive set of domain interactions that were present in the last universal common ancestor.@(((:tag . "RB") (:stem . "conversely") (:form . "Conversely") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . 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"comprehensive")\n (:end . 88) (:start . 75) (:id . 55))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 92) (:start . 89)\n (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n (:id . 57))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 102)\n (:start . 96) (:id . 58))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 115)\n (:start . 103) (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 120) (:start . 116)\n (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 125) (:start . 121)\n (:id . 61))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 133)\n (:start . 126) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 136) (:start . 134)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n (:id . 64))\n ((:tag . "JJ") (:stem . "last") (:form . "last") (:end . 145) (:start . 141)\n (:id . 65))\n ((:tag . "JJ") (:stem . "universal") (:form . "universal") (:end . 155)\n (:start . 146) (:id . 66))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 162)\n (:start . 156) (:id . 67))\n ((:tag . "NN") (:stem . "ancestor") (:form . "ancestor") (:end . 171)\n (:start . 163) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n (:id . 69)))@@@1@28@((:hcues ((:id . :x4.235.1) (:span 57 62)) ((:id . :x4.235.2) (:span 45 52))\n ((:id . :x4.235.3) (:span 22 41)))\n (:hscopes ((:id . :x4.235.1) (:span 57 171))\n ((:id . :x4.235.2) (:span 45 171)) ((:id . :x4.235.3) (:span 22 171)))\n (:identifiers (:sid . :s4.235) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101348@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.236) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Title|)))@oe@9-2-2011 5101350@unknown@formal@none@1@S@Disappointingly, only a small fraction of all experimental interactions can be attributed to a known domain interaction.@(((:tag . "RB") (:stem . "disappointingly") (:form . "Disappointingly")\n (:end . 15) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n (:id . 43))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 21) (:start . 17)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n (:id . 45))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 29) (:start . 24)\n (:id . 46))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 38)\n (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . 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"domain") (:end . 107)\n (:start . 101) (:id . 58))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 119)\n (:start . 108) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.238) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101351@unknown@formal@none@1@S@Within this subset of interactions, we nevertheless made several reassuring observations: structural domain pairs are enriched in experimental protein interactions.@(((:tag . "IN") (:stem . "within") (:form . "Within") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 11) (:start . 7)\n (:id . 43))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 18)\n (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "NNS") (:stem . 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"domain") (:end . 107)\n (:start . 101) (:id . 56))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 113)\n (:start . 108) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 117) (:start . 114)\n (:id . 58))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 126)\n (:start . 118) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 129) (:start . 127)\n (:id . 60))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 142)\n (:start . 130) (:id . 61))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 150)\n (:start . 143) (:id . 62))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 163)\n (:start . 151) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s4.239) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101352@unknown@formal@none@1@S@Some of the domain pairs seem to mediate a large number of protein interactions, thus acting as reusable connectors.@(((:tag . "DT") (:stem . "some") (:form . "Some") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n (:id . 44))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 18)\n (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 24) (:start . 19)\n (:id . 46))\n ((:tag . "VBP") (:stem . "seem") (:form . "seem") (:end . 29) (:start . 25)\n (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 32) (:start . 30)\n (:id . 48))\n ((:tag . "VB") (:stem . "mediate") (:form . "mediate") (:end . 40)\n (:start . 33) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 42) (:start . 41)\n (:id . 50))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 48) (:start . 43)\n (:id . 51))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 55)\n (:start . 49) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 66)\n (:start . 59) (:id . 54))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 79)\n (:start . 67) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n (:id . 56))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 85) (:start . 81)\n (:id . 57))\n ((:tag . "VBG") (:stem . "act") (:form . "acting") (:end . 92) (:start . 86)\n (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 95) (:start . 93)\n (:id . 59))\n ((:tag . "JJ") (:stem . "reusable") (:form . "reusable") (:end . 104)\n (:start . 96) (:id . 60))\n ((:tag . "NNS") (:stem . "connector") (:form . "connectors") (:end . 115)\n (:start . 105) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n (:id . 62)))@@@1@21@((:hcues ((:id . :x4.240.1) (:span 25 29)))\n (:hscopes ((:id . :x4.240.1) (:span 25 115)))\n (:identifiers (:sid . :s4.240) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101353@unknown@formal@none@1@S@This property is also conserved between species.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "property") (:form . "property") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 21) (:start . 17)\n (:id . 45))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 31)\n (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 39)\n (:start . 32) (:id . 47))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 47)\n (:start . 40) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 48) (:start . 47)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s4.241) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101354@unknown@formal@none@1@S@Taken as a whole, this further underlines that solving structures of protein complexes should be an important focus for future structural genomics projects.@(((:tag . "VBN") (:stem . "take") (:form . "Taken") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 8) (:start . 6)\n (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . 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"projects") (:end . 155)\n (:start . 147) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s4.242) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101355@unknown@formal@none@1@S@Targeting the most frequent domain pairs would increase the coverage of databases such as iPfam, shedding more light onto the molecular mechanisms underpinning cellular networks.@(((:tag . "VBG") (:stem . "target") (:form . "Targeting") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n (:id . 43))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "JJ") (:stem . "frequent") (:form . "frequent") (:end . 27)\n (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 34)\n (:start . 28) (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 40) (:start . 35)\n (:id . 47))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 46) (:start . 41)\n (:id . 48))\n ((:tag . "VB") (:stem . "increase") (:form . "increase") (:end . 55)\n (:start . 47) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n (:id . 50))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 68)\n (:start . 60) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n (:id . 52))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 81)\n (:start . 72) (:id . 53))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 86) (:start . 82)\n (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 89) (:start . 87)\n (:id . 55))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 95) (:start . 90)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n (:id . 57))\n ((:tag . "VBG") (:stem . "shed") (:form . "shedding") (:end . 105)\n (:start . 97) (:id . 58))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 110) (:start . 106)\n (:id . 59))\n ((:tag . "NN") (:stem . "light") (:form . "light") (:end . 116)\n (:start . 111) (:id . 60))\n ((:tag . "IN") (:stem . "onto") (:form . "onto") (:end . 121) (:start . 117)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n (:id . 62))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 135)\n (:start . 126) (:id . 63))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 146)\n (:start . 136) (:id . 64))\n ((:tag . "VBG") (:stem . "underpin") (:form . "underpinning") (:end . 159)\n (:start . 147) (:id . 65))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 168)\n (:start . 160) (:id . 66))\n ((:tag . "NNS") (:stem . "network") (:form . "networks") (:end . 177)\n (:start . 169) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n (:id . 68)))@@@1@27@((:hcues ((:id . :x4.243.1) (:span 41 46)))\n (:hscopes ((:id . :x4.243.1) (:span 41 177)))\n (:identifiers (:sid . :s4.243) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101356@unknown@formal@none@1@S@Methods@(((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 7)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.244) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Title|)))@oe@9-2-2011 5101357@unknown@formal@none@1@S@Protein interaction data@(((:tag . "NN") (:stem . "protein") (:form . "Protein") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 19)\n (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 24) (:start . 20)\n (:id . 44)))@@@1@3@((:identifiers (:sid . :s4.245) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101358@unknown@formal@none@1@S@The complete interaction sets from BioGRID 20, DIP 21, HPRD 22, IntAct 23 and MPact 24 were downloaded.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 24)\n (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 29) (:start . 25)\n (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 34) (:start . 30)\n (:id . 46))\n ((:tag . "NNP") (:stem . "BioGRID") (:form . "BioGRID") (:end . 42)\n (:start . 35) (:id . 47))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 45) (:start . 43)\n (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n (:id . 49))\n ((:tag . "NNP") (:stem . "DIP") (:form . "DIP") (:end . 50) (:start . 47)\n (:id . 50))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 53) (:start . 51)\n (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n (:id . 52))\n ((:tag . "NNP") (:stem . "HPRD") (:form . "HPRD") (:end . 59) (:start . 55)\n (:id . 53))\n ((:tag . "CD") (:stem . "22") (:form . "22") (:end . 62) (:start . 60)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n (:id . 55))\n ((:tag . "NNP") (:stem . "IntAct") (:form . "IntAct") (:end . 70)\n (:start . 64) (:id . 56))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 73) (:start . 71)\n (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n (:id . 58))\n ((:tag . "NNP") (:stem . "MPact") (:form . "MPact") (:end . 83) (:start . 78)\n (:id . 59))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 86) (:start . 84)\n (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 91) (:start . 87)\n (:id . 61))\n ((:tag . "VBN") (:stem . "downloade") (:form . "downloaded") (:end . 102)\n (:start . 92) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s4.246) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101360@unknown@formal@none@1@S@BioGRID for example contains a large manually curated set of protein interactions for S. cerevisiae 19.@(((:tag . "NN") (:stem . "biogrid") (:form . "BioGRID") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 11) (:start . 8)\n (:id . 43))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 19)\n (:start . 12) (:id . 44))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 28)\n (:start . 20) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n (:id . 46))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 36) (:start . 31)\n (:id . 47))\n ((:tag . "RB") (:stem . "manually") (:form . "manually") (:end . 45)\n (:start . 37) (:id . 48))\n ((:tag . "VBN") (:stem . "curate") (:form . "curated") (:end . 53)\n (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 57) (:start . 54)\n (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 68)\n (:start . 61) (:id . 52))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 81)\n (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 85) (:start . 82)\n (:id . 54))\n ((:tag . "NNP") (:stem . "S.") (:form . "S.") (:end . 88) (:start . 86)\n (:id . 55))\n ((:tag . "NNP") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 99)\n (:start . 89) (:id . 56))\n ((:tag . "CD") (:stem . "19") (:form . "19") (:end . 102) (:start . 100)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s4.248) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101361@unknown@formal@none@1@S@Similarily, HPRD hosts a set of manually curated protein interactions for H. sapiens.@(((:tag . "RB") (:stem . "similarily") (:form . "Similarily") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 43))\n ((:tag . "NNP") (:stem . "HPRD") (:form . "HPRD") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "host") (:form . "hosts") (:end . 22) (:start . 17)\n (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 24) (:start . 23)\n (:id . 46))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 28) (:start . 25)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n (:id . 48))\n ((:tag . "RB") (:stem . "manually") (:form . "manually") (:end . 40)\n (:start . 32) (:id . 49))\n ((:tag . "VBN") (:stem . "curate") (:form . "curated") (:end . 48)\n (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 56)\n (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 69)\n (:start . 57) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 73) (:start . 70)\n (:id . 53))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 76) (:start . 74)\n (:id . 54))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 84)\n (:start . 77) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.249) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101362@unknown@formal@none@1@S@IntAct on the other hand contains results from high-throughput screens and integrates data from other protein interaction databases as part of the IMEx collaboration.@(((:tag . "NN") (:stem . "intact") (:form . "IntAct") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 9) (:start . 7)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 19) (:start . 14)\n (:id . 45))\n ((:tag . "NN") (:stem . "hand") (:form . "hand") (:end . 24) (:start . 20)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 33)\n (:start . 25) (:id . 47))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 41)\n (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 46) (:start . 42)\n (:id . 49))\n ((:tag . "JJ") (:stem . "high-throughput") (:form . "high-throughput")\n (:end . 62) (:start . 47) (:id . 50))\n ((:tag . "NNS") (:stem . "screen") (:form . "screens") (:end . 70)\n (:start . 63) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n (:id . 52))\n ((:tag . "VBZ") (:stem . "integrate") (:form . "integrates") (:end . 85)\n (:start . 75) (:id . 53))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 90) (:start . 86)\n (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 95) (:start . 91)\n (:id . 55))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 101) (:start . 96)\n (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 109)\n (:start . 102) (:id . 57))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 121)\n (:start . 110) (:id . 58))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 131)\n (:start . 122) (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 134) (:start . 132)\n (:id . 60))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 139) (:start . 135)\n (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n (:id . 63))\n ((:tag . "NNP") (:stem . "IMEx") (:form . "IMEx") (:end . 151) (:start . 147)\n (:id . 64))\n ((:tag . "NN") (:stem . "collaboration") (:form . "collaboration")\n (:end . 165) (:start . 152) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s4.250) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101363@unknown@formal@none@1@S@The MPact database combines the manually curated S. cerevisiae protein complexes data set formerly known as the MIPS complexes with other high-throughput interaction experiments data.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "MPact") (:form . "MPact") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 18)\n (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "combine") (:form . "combines") (:end . 27)\n (:start . 19) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n (:id . 46))\n ((:tag . "RB") (:stem . "manually") (:form . "manually") (:end . 40)\n (:start . 32) (:id . 47))\n ((:tag . "VBN") (:stem . "curate") (:form . "curated") (:end . 48)\n (:start . 41) (:id . 48))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 51) (:start . 49)\n (:id . 49))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 62)\n (:start . 52) (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 70)\n (:start . 63) (:id . 51))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 80)\n (:start . 71) (:id . 52))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 85) (:start . 81)\n (:id . 53))\n ((:tag . "VBD") (:stem . "set") (:form . "set") (:end . 89) (:start . 86)\n (:id . 54))\n ((:tag . "RB") (:stem . "formerly") (:form . "formerly") (:end . 98)\n (:start . 90) (:id . 55))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 104) (:start . 99)\n (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 107) (:start . 105)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n (:id . 58))\n ((:tag . "NNP") (:stem . "MIPS") (:form . "MIPS") (:end . 116) (:start . 112)\n (:id . 59))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 126)\n (:start . 117) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 131) (:start . 127)\n (:id . 61))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 137)\n (:start . 132) (:id . 62))\n ((:tag . "JJ") (:stem . "high-throughput") (:form . "high-throughput")\n (:end . 153) (:start . 138) (:id . 63))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 165)\n (:start . 154) (:id . 64))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 177)\n (:start . 166) (:id . 65))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 182)\n (:start . 178) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.251) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101364@unknown@formal@none@1@S@Taken together, these databases represent most of the protein interactions currently stored in machine-accessible form.@(((:tag . "VBN") (:stem . "take") (:form . "Taken") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 14)\n (:start . 6) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 21) (:start . 16)\n (:id . 45))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 31)\n (:start . 22) (:id . 46))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 41)\n (:start . 32) (:id . 47))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 46) (:start . 42)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 61)\n (:start . 54) (:id . 51))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 74)\n (:start . 62) (:id . 52))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 84)\n (:start . 75) (:id . 53))\n ((:tag . "VBN") (:stem . "store") (:form . "stored") (:end . 91)\n (:start . 85) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 94) (:start . 92)\n (:id . 55))\n ((:tag . "JJ") (:stem . "machine-accessible") (:form . "machine-accessible")\n (:end . 113) (:start . 95) (:id . 56))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 118) (:start . 114)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s4.252) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101365@unknown@formal@none@1@S@Despite great efforts to unify access to protein interaction data 32, acquiring large data sets from diverse sources is still far from trivial and error prone.@(((:tag . "IN") (:stem . "despite") (:form . "Despite") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "great") (:form . "great") (:end . 13) (:start . 8)\n (:id . 43))\n ((:tag . "NNS") (:stem . "effort") (:form . "efforts") (:end . 21)\n (:start . 14) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 24) (:start . 22)\n (:id . 45))\n ((:tag . "VB") (:stem . "unify") (:form . "unify") (:end . 30) (:start . 25)\n (:id . 46))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 37)\n (:start . 31) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 48)\n (:start . 41) (:id . 49))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 60)\n (:start . 49) (:id . 50))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 65) (:start . 61)\n (:id . 51))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 68) (:start . 66)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n (:id . 53))\n ((:tag . "VBG") (:stem . "acquire") (:form . "acquiring") (:end . 79)\n (:start . 70) (:id . 54))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 85) (:start . 80)\n (:id . 55))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 90) (:start . 86)\n (:id . 56))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 95) (:start . 91)\n (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 100) (:start . 96)\n (:id . 58))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 108)\n (:start . 101) (:id . 59))\n ((:tag . "NNS") (:stem . "source") (:form . "sources") (:end . 116)\n (:start . 109) (:id . 60))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 119) (:start . 117)\n (:id . 61))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 125)\n (:start . 120) (:id . 62))\n ((:tag . "RB") (:stem . "far") (:form . "far") (:end . 129) (:start . 126)\n (:id . 63))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 134) (:start . 130)\n (:id . 64))\n ((:tag . "JJ") (:stem . "trivial") (:form . "trivial") (:end . 142)\n (:start . 135) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 146) (:start . 143)\n (:id . 66))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 152)\n (:start . 147) (:id . 67))\n ((:tag . "NN") (:stem . "prone") (:form . "prone") (:end . 158)\n (:start . 153) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s4.253) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101366@unknown@formal@none@1@S@The PSI-MI XML data exchange format provided by the aforementioned databases was used to generate a local relational database of protein interactions.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "PSI-MI") (:form . "PSI-MI") (:end . 10)\n (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "XML") (:form . "XML") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 19) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "exchange") (:form . "exchange") (:end . 28)\n (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "format") (:form . "format") (:end . 35)\n (:start . 29) (:id . 47))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 44)\n (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n (:id . 50))\n ((:tag . "JJ") (:stem . "aforementioned") (:form . "aforementioned")\n (:end . 66) (:start . 52) (:id . 51))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 76)\n (:start . 67) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 80) (:start . 77)\n (:id . 53))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 85) (:start . 81)\n (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n (:id . 55))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 97)\n (:start . 89) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 99) (:start . 98)\n (:id . 57))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 105)\n (:start . 100) (:id . 58))\n ((:tag . "JJ") (:stem . "relational") (:form . "relational") (:end . 116)\n (:start . 106) (:id . 59))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 125)\n (:start . 117) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 128) (:start . 126)\n (:id . 61))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 136)\n (:start . 129) (:id . 62))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 149)\n (:start . 137) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s4.254) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101367@unknown@formal@none@1@S@All entries were mapped to UniProt 33 by either relying on existing annotations from the source databases or by pair-wise sequence alignment to all UniProt proteins from the same species as the query protein.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "entry") (:form . "entries") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "VBN") (:stem . "map") (:form . "mapped") (:end . 23) (:start . 17)\n (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "NNP") (:stem . "UniProt") (:form . "UniProt") (:end . 34)\n (:start . 27) (:id . 47))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 37) (:start . 35)\n (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 40) (:start . 38)\n (:id . 49))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 47)\n (:start . 41) (:id . 50))\n ((:tag . "VBG") (:stem . "rely") (:form . "relying") (:end . 55)\n (:start . 48) (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 58) (:start . 56)\n (:id . 52))\n ((:tag . "VBG") (:stem . "exist") (:form . "existing") (:end . 67)\n (:start . 59) (:id . 53))\n ((:tag . "NNS") (:stem . "annotation") (:form . "annotations") (:end . 79)\n (:start . 68) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 84) (:start . 80)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n (:id . 56))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 95)\n (:start . 89) (:id . 57))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 105)\n (:start . 96) (:id . 58))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 108) (:start . 106)\n (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 111) (:start . 109)\n (:id . 60))\n ((:tag . "JJ") (:stem . "pair-wise") (:form . "pair-wise") (:end . 121)\n (:start . 112) (:id . 61))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 130)\n (:start . 122) (:id . 62))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 140)\n (:start . 131) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 143) (:start . 141)\n (:id . 64))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 147) (:start . 144)\n (:id . 65))\n ((:tag . "NNP") (:stem . "UniProt") (:form . "UniProt") (:end . 155)\n (:start . 148) (:id . 66))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 164)\n (:start . 156) (:id . 67))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 169) (:start . 165)\n (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 173) (:start . 170)\n (:id . 69))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 178) (:start . 174)\n (:id . 70))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 186)\n (:start . 179) (:id . 71))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 189) (:start . 187)\n (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 193) (:start . 190)\n (:id . 73))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 199)\n (:start . 194) (:id . 74))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 207)\n (:start . 200) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s4.255) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101368@unknown@formal@none@1@S@The direct sequence comparison was performed using pmatch, a very fast pairwise alignment algorithm developed by Richard Durbin (unpublished, source code available 34).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 19)\n (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 30)\n (:start . 20) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 34) (:start . 31)\n (:id . 46))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 44)\n (:start . 35) (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 50) (:start . 45)\n (:id . 48))\n ((:tag . "NN") (:stem . "pmatch") (:form . "pmatch") (:end . 57)\n (:start . 51) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 60) (:start . 59)\n (:id . 51))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 65) (:start . 61)\n (:id . 52))\n ((:tag . "JJ") (:stem . "fast") (:form . "fast") (:end . 70) (:start . 66)\n (:id . 53))\n ((:tag . "JJ") (:stem . "pairwise") (:form . "pairwise") (:end . 79)\n (:start . 71) (:id . 54))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 89)\n (:start . 80) (:id . 55))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 99)\n (:start . 90) (:id . 56))\n ((:tag . "VBN") (:stem . "develop") (:form . "developed") (:end . 109)\n (:start . 100) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 112) (:start . 110)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Richard") (:form . "Richard") (:end . 120)\n (:start . 113) (:id . 59))\n ((:tag . "NNP") (:stem . "Durbin") (:form . "Durbin") (:end . 127)\n (:start . 121) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 129) (:start . 128)\n (:id . 61))\n ((:tag . "JJ") (:stem . "unpublished") (:form . "unpublished") (:end . 140)\n (:start . 129) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n (:id . 63))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 148)\n (:start . 142) (:id . 64))\n ((:tag . "VBP") (:stem . "code") (:form . "code") (:end . 153) (:start . 149)\n (:id . 65))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 163)\n (:start . 154) (:id . 66))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 166) (:start . 164)\n (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s4.256) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101370@unknown@formal@none@1@S@To allow cross-species comparisons, the data were split into five distinct species sets: E. coli, S. cerevisiae, C. elegans, D. melanogaster and H. sapiens.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "allow") (:form . "allow") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "cross-species") (:form . "cross-species")\n (:end . 22) (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 34)\n (:start . 23) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 47))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 44) (:start . 40)\n (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 49) (:start . 45)\n (:id . 49))\n ((:tag . "VBN") (:stem . "split") (:form . "split") (:end . 55) (:start . 50)\n (:id . 50))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 60) (:start . 56)\n (:id . 51))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 65) (:start . 61)\n (:id . 52))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 74)\n (:start . 66) (:id . 53))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 82)\n (:start . 75) (:id . 54))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 87) (:start . 83)\n (:id . 55))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 88) (:start . 87)\n (:id . 56))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 91) (:start . 89)\n (:id . 57))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 96) (:start . 92)\n (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n (:id . 59))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 100) (:start . 98)\n (:id . 60))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 111)\n (:start . 101) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n (:id . 62))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 115) (:start . 113)\n (:id . 63))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 123)\n (:start . 116) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n (:id . 65))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 127) (:start . 125)\n (:id . 66))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n (:end . 140) (:start . 128) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 144) (:start . 141)\n (:id . 68))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 147) (:start . 145)\n (:id . 69))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 155)\n (:start . 148) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s4.258) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101371@unknown@formal@none@1@S@It should be noted that the proportion of proteins for which an interaction is known varies greatly between the species, see Table 1.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 12) (:start . 10)\n (:id . 44))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 38)\n (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n (:id . 49))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 50)\n (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 54) (:start . 51)\n (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 60) (:start . 55)\n (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 63) (:start . 61)\n (:id . 53))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 75)\n (:start . 64) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 78) (:start . 76)\n (:id . 55))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 84) (:start . 79)\n (:id . 56))\n ((:tag . "VBZ") (:stem . "vary") (:form . "varies") (:end . 91) (:start . 85)\n (:id . 57))\n ((:tag . "RB") (:stem . "greatly") (:form . "greatly") (:end . 99)\n (:start . 92) (:id . 58))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 107)\n (:start . 100) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n (:id . 60))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 119)\n (:start . 112) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n (:id . 62))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 124) (:start . 121)\n (:id . 63))\n ((:tag . "NNP") (:stem . "Table") (:form . "Table") (:end . 130)\n (:start . 125) (:id . 64))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 132) (:start . 131)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s4.259) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101372@unknown@formal@none@1@S@This might affect the results if there is a systematic bias on the composition of a protein interaction set.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "VB") (:stem . "affect") (:form . "affect") (:end . 17)\n (:start . 11) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n (:id . 45))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 29)\n (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 32) (:start . 30)\n (:id . 47))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 38) (:start . 33)\n (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 41) (:start . 39)\n (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 43) (:start . 42)\n (:id . 50))\n ((:tag . "JJ") (:stem . "systematic") (:form . "systematic") (:end . 54)\n (:start . 44) (:id . 51))\n ((:tag . "NN") (:stem . "bias") (:form . "bias") (:end . 59) (:start . 55)\n (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 62) (:start . 60)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n (:id . 54))\n ((:tag . "NN") (:stem . "composition") (:form . "composition") (:end . 78)\n (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 83) (:start . 82)\n (:id . 57))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 91)\n (:start . 84) (:id . 58))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 103)\n (:start . 92) (:id . 59))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 107) (:start . 104)\n (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n (:id . 61)))@@@1@20@((:hcues ((:id . :x4.260.1) (:span 5 10)))\n (:hscopes ((:id . :x4.260.1) (:span 5 29)))\n (:identifiers (:sid . :s4.260) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101373@unknown@formal@none@1@S@To prevent bias from multiple alternative versions of the same protein, all interacting proteins were mapped to reference proteomes as defined by Integr8 35, again using pmatch.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "prevent") (:form . "prevent") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "bias") (:form . "bias") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 29)\n (:start . 21) (:id . 46))\n ((:tag . "JJ") (:stem . "alternative") (:form . "alternative") (:end . 41)\n (:start . 30) (:id . 47))\n ((:tag . "NNS") (:stem . "version") (:form . "versions") (:end . 50)\n (:start . 42) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n (:id . 50))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 62) (:start . 58)\n (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 70)\n (:start . 63) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n (:id . 53))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 75) (:start . 72)\n (:id . 54))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 87)\n (:start . 76) (:id . 55))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 96)\n (:start . 88) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 101) (:start . 97)\n (:id . 57))\n ((:tag . "VBN") (:stem . "map") (:form . "mapped") (:end . 108)\n (:start . 102) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 111) (:start . 109)\n (:id . 59))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 121)\n (:start . 112) (:id . 60))\n ((:tag . "NNS") (:stem . "proteome") (:form . "proteomes") (:end . 131)\n (:start . 122) (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 134) (:start . 132)\n (:id . 62))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 142)\n (:start . 135) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 145) (:start . 143)\n (:id . 64))\n ((:tag . "NN") (:stem . "integr8") (:form . "Integr8") (:end . 153)\n (:start . 146) (:id . 65))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 156) (:start . 154)\n (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 157) (:start . 156)\n (:id . 67))\n ((:tag . "RB") (:stem . "again") (:form . "again") (:end . 163)\n (:start . 158) (:id . 68))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 169) (:start . 164)\n (:id . 69))\n ((:tag . "NN") (:stem . "pmatch") (:form . "pmatch") (:end . 176)\n (:start . 170) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s4.261) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101374@unknown@formal@none@1@S@An average of ≈ 16% of interaction entries were lost in the mapping process, either if no sequence was provided with the original entry or if no significant matching sequence could be found in Integr8.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "average") (:form . "average") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "≈") (:form . "≈") (:end . 15) (:start . 14)\n (:id . 45))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 18) (:start . 16)\n (:id . 46))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 19) (:start . 18)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n (:id . 48))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 34)\n (:start . 23) (:id . 49))\n ((:tag . "NNS") (:stem . "entry") (:form . "entries") (:end . 42)\n (:start . 35) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 47) (:start . 43)\n (:id . 51))\n ((:tag . "VBN") (:stem . "lose") (:form . "lost") (:end . 52) (:start . 48)\n (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n (:id . 54))\n ((:tag . "NN") (:stem . "mapping") (:form . "mapping") (:end . 67)\n (:start . 60) (:id . 55))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 75)\n (:start . 68) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n (:id . 57))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 83)\n (:start . 77) (:id . 58))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 86) (:start . 84)\n (:id . 59))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 89) (:start . 87)\n (:id . 60))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 98)\n (:start . 90) (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 102) (:start . 99)\n (:id . 62))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 111)\n (:start . 103) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 116) (:start . 112)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n (:id . 65))\n ((:tag . "JJ") (:stem . "original") (:form . "original") (:end . 129)\n (:start . 121) (:id . 66))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 135)\n (:start . 130) (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 138) (:start . 136)\n (:id . 68))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 141) (:start . 139)\n (:id . 69))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 144) (:start . 142)\n (:id . 70))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 156)\n (:start . 145) (:id . 71))\n ((:tag . "NN") (:stem . "matching") (:form . "matching") (:end . 165)\n (:start . 157) (:id . 72))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 174)\n (:start . 166) (:id . 73))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 180)\n (:start . 175) (:id . 74))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 183) (:start . 181)\n (:id . 75))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 189)\n (:start . 184) (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 192) (:start . 190)\n (:id . 77))\n ((:tag . "NN") (:stem . "integr8") (:form . "Integr8") (:end . 200)\n (:start . 193) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n (:id . 79)))@@@1@38@((:ncues ((:id . :x4.262.1) (:span 142 144))\n ((:id . :x4.262.2) (:span 87 89)))\n (:nscopes ((:id . :x4.262.1) (:span 142 200))\n ((:id . :x4.262.2) (:span 87 135)))\n (:identifiers (:sid . :s4.262) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101375@unknown@formal@none@1@S@The total number of missing proteins will be lower, as several entries from different databases refer to the same sequence.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 16)\n (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . "VBG") (:stem . "miss") (:form . "missing") (:end . 27)\n (:start . 20) (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 36)\n (:start . 28) (:id . 47))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 41) (:start . 37)\n (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 44) (:start . 42)\n (:id . 49))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 50) (:start . 45)\n (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 54) (:start . 52)\n (:id . 52))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 62)\n (:start . 55) (:id . 53))\n ((:tag . "NNS") (:stem . "entry") (:form . "entries") (:end . 70)\n (:start . 63) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 75) (:start . 71)\n (:id . 55))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 85)\n (:start . 76) (:id . 56))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 95)\n (:start . 86) (:id . 57))\n ((:tag . "VBP") (:stem . "refer") (:form . "refer") (:end . 101)\n (:start . 96) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 104) (:start . 102)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n (:id . 60))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 113) (:start . 109)\n (:id . 61))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 122)\n (:start . 114) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s4.263) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101376@unknown@formal@none@1@S@iPfam@(((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 5) (:start . 0)\n (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.264) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101377@unknown@formal@none@1@S@The iPfam database is derived from protein structures deposited in the PDB.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 18)\n (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 29)\n (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 34) (:start . 30)\n (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 42)\n (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 53)\n (:start . 43) (:id . 49))\n ((:tag . "VBN") (:stem . "deposit") (:form . "deposited") (:end . 63)\n (:start . 54) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n (:id . 52))\n ((:tag . "NN") (:stem . "pdb") (:form . "PDB") (:end . 74) (:start . 71)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s4.265) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101378@unknown@formal@none@1@S@Regions in every protein structure that match a Pfam domain are scanned for interactions with residues in another Pfam domain.@(((:tag . "NNS") (:stem . "region") (:form . "Regions") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 10) (:start . 8)\n (:id . 43))\n ((:tag . "DT") (:stem . "every") (:form . "every") (:end . 16) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 24)\n (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 34)\n (:start . 25) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 39) (:start . 35)\n (:id . 47))\n ((:tag . "VBP") (:stem . "match") (:form . "match") (:end . 45) (:start . 40)\n (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 47) (:start . 46)\n (:id . 49))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 52) (:start . 48)\n (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 59)\n (:start . 53) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 63) (:start . 60)\n (:id . 52))\n ((:tag . "VBN") (:stem . "scan") (:form . "scanned") (:end . 71)\n (:start . 64) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 75) (:start . 72)\n (:id . 54))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 88)\n (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 93) (:start . 89)\n (:id . 56))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 102)\n (:start . 94) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 105) (:start . 103)\n (:id . 58))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 113)\n (:start . 106) (:id . 59))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 118) (:start . 114)\n (:id . 60))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 125)\n (:start . 119) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.266) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101380@unknown@formal@none@1@S@Every pair of Pfam families that are found to interact in a PDB structure are called an iPfam domain pair throughout the text.@(((:tag . "DT") (:stem . "every") (:form . "Every") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 18) (:start . 14)\n (:id . 45))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 27)\n (:start . 19) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 36) (:start . 33)\n (:id . 48))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 42) (:start . 37)\n (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 45) (:start . 43)\n (:id . 50))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 54)\n (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 59) (:start . 58)\n (:id . 53))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 63) (:start . 60)\n (:id . 54))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 73)\n (:start . 64) (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 77) (:start . 74)\n (:id . 56))\n ((:tag . "VBN") (:stem . "call") (:form . "called") (:end . 84) (:start . 78)\n (:id . 57))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 87) (:start . 85)\n (:id . 58))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 93) (:start . 88)\n (:id . 59))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 100)\n (:start . 94) (:id . 60))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 105) (:start . 101)\n (:id . 61))\n ((:tag . "IN") (:stem . "throughout") (:form . "throughout") (:end . 116)\n (:start . 106) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n (:id . 63))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 125) (:start . 121)\n (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.268) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101381@unknown@formal@none@1@S@Single Pfam families that are part of an iPfam domain pair are then called iPfam domains.@(((:tag . "JJ") (:stem . "single") (:form . "Single") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 11) (:start . 7)\n (:id . 43))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 20)\n (:start . 12) (:id . 44))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n (:id . 46))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 34) (:start . 30)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 40) (:start . 38)\n (:id . 49))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 46) (:start . 41)\n (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 53)\n (:start . 47) (:id . 51))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 58) (:start . 54)\n (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 62) (:start . 59)\n (:id . 53))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 67) (:start . 63)\n (:id . 54))\n ((:tag . "VBN") (:stem . "call") (:form . "called") (:end . 74) (:start . 68)\n (:id . 55))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 80) (:start . 75)\n (:id . 56))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 88)\n (:start . 81) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s4.269) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101382@unknown@formal@none@1@S@For example, in PDB entry 1k9a the two iPfam domains SH2 (Pfam accession PF00017) and Pkinase_Tyr (PF07714) interact, therefore they form an iPfam domain pair.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 19) (:start . 16)\n (:id . 46))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 25) (:start . 20)\n (:id . 47))\n ((:tag . "NN") (:stem . "1k9a") (:form . "1k9a") (:end . 30) (:start . 26)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 49))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 38) (:start . 35)\n (:id . 50))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 44) (:start . 39)\n (:id . 51))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 52)\n (:start . 45) (:id . 52))\n ((:tag . "NN") (:stem . "sh2") (:form . "SH2") (:end . 56) (:start . 53)\n (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 62) (:start . 58)\n (:id . 55))\n ((:tag . "NN") (:stem . "accession") (:form . "accession") (:end . 72)\n (:start . 63) (:id . 56))\n ((:tag . "NN") (:stem . "pf00017") (:form . "PF00017") (:end . 80)\n (:start . 73) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n (:id . 59))\n ((:tag . "NNP") (:stem . "Pkinase_Tyr") (:form . "Pkinase_Tyr") (:end . 97)\n (:start . 86) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 99) (:start . 98)\n (:id . 61))\n ((:tag . "NN") (:stem . "pf07714") (:form . "PF07714") (:end . 106)\n (:start . 99) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n (:id . 63))\n ((:tag . "VBP") (:stem . "interact") (:form . "interact") (:end . 116)\n (:start . 108) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n (:id . 65))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 127)\n (:start . 118) (:id . 66))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 132) (:start . 128)\n (:id . 67))\n ((:tag . "VBP") (:stem . "form") (:form . "form") (:end . 137) (:start . 133)\n (:id . 68))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 140) (:start . 138)\n (:id . 69))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 146)\n (:start . 141) (:id . 70))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 153)\n (:start . 147) (:id . 71))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 158) (:start . 154)\n (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s4.270) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101383@unknown@formal@none@1@S@In this study, iPfam version 21 was employed, containing 2837 iPfam domains, forming 4030 iPfam domain pairs.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 45))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 20) (:start . 15)\n (:id . 46))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 28)\n (:start . 21) (:id . 47))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 31) (:start . 29)\n (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 35) (:start . 32)\n (:id . 49))\n ((:tag . "VBN") (:stem . "employ") (:form . "employed") (:end . 44)\n (:start . 36) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n (:id . 51))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 56)\n (:start . 46) (:id . 52))\n ((:tag . "CD") (:stem . "2837") (:form . "2837") (:end . 61) (:start . 57)\n (:id . 53))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 67) (:start . 62)\n (:id . 54))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 75)\n (:start . 68) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n (:id . 56))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 84)\n (:start . 77) (:id . 57))\n ((:tag . "CD") (:stem . "4030") (:form . "4030") (:end . 89) (:start . 85)\n (:id . 58))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 95) (:start . 90)\n (:id . 59))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 102)\n (:start . 96) (:id . 60))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 108)\n (:start . 103) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.271) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101384@unknown@formal@none@1@S@Figure 5 shows the species distribution of iPfam domain pairs.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 8) (:start . 7)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 26)\n (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 39)\n (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n (:id . 48))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 48) (:start . 43)\n (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 55)\n (:start . 49) (:id . 50))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 61) (:start . 56)\n (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 62) (:start . 61)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s4.272) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101385@unknown@formal@none@1@S@H. sapiens, E. coli and S. cerevisiae are clearly over-represented compared to the other 1113 species with less than 179 complex structures.@(((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 44))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 14) (:start . 12)\n (:id . 45))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 19) (:start . 15)\n (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n (:id . 47))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 26) (:start . 24)\n (:id . 48))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 37)\n (:start . 27) (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 41) (:start . 38)\n (:id . 50))\n ((:tag . "RB") (:stem . "clearly") (:form . "clearly") (:end . 49)\n (:start . 42) (:id . 51))\n ((:tag . "JJ") (:stem . "over-represented") (:form . "over-represented")\n (:end . 66) (:start . 50) (:id . 52))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 75)\n (:start . 67) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n (:id . 55))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 88) (:start . 83)\n (:id . 56))\n ((:tag . "CD") (:stem . "1113") (:form . "1113") (:end . 93) (:start . 89)\n (:id . 57))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 101)\n (:start . 94) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 106) (:start . 102)\n (:id . 59))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 111) (:start . 107)\n (:id . 60))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 116) (:start . 112)\n (:id . 61))\n ((:tag . "CD") (:stem . "179") (:form . "179") (:end . 120) (:start . 117)\n (:id . 62))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 128)\n (:start . 121) (:id . 63))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 139)\n (:start . 129) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.273) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101386@unknown@formal@none@1@S@Some iPfam domain pairs are seen to form interactions between distinct peptide chains in the structure (interchain), while others form an interaction between two distinct domains within the same chain (intrachain).@(((:tag . "DT") (:stem . "some") (:form . "Some") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 17)\n (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 23) (:start . 18)\n (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 27) (:start . 24)\n (:id . 46))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 32) (:start . 28)\n (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n (:id . 48))\n ((:tag . "VB") (:stem . "form") (:form . "form") (:end . 40) (:start . 36)\n (:id . 49))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 53)\n (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 61)\n (:start . 54) (:id . 51))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 70)\n (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 78)\n (:start . 71) (:id . 53))\n ((:tag . "NNS") (:stem . "chain") (:form . "chains") (:end . 85)\n (:start . 79) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n (:id . 56))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 102)\n (:start . 93) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n (:id . 58))\n ((:tag . "NN") (:stem . "interchain") (:form . "interchain") (:end . 114)\n (:start . 104) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n (:id . 61))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 122)\n (:start . 117) (:id . 62))\n ((:tag . "NNS") (:stem . "other") (:form . "others") (:end . 129)\n (:start . 123) (:id . 63))\n ((:tag . "VBP") (:stem . "form") (:form . "form") (:end . 134) (:start . 130)\n (:id . 64))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 137) (:start . 135)\n (:id . 65))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 149)\n (:start . 138) (:id . 66))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 157)\n (:start . 150) (:id . 67))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 161) (:start . 158)\n (:id . 68))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 170)\n (:start . 162) (:id . 69))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 178)\n (:start . 171) (:id . 70))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 185)\n (:start . 179) (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 189) (:start . 186)\n (:id . 72))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 194) (:start . 190)\n (:id . 73))\n ((:tag . "NN") (:stem . "chain") (:form . "chain") (:end . 200)\n (:start . 195) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 202) (:start . 201)\n (:id . 75))\n ((:tag . "NN") (:stem . "intrachain") (:form . "intrachain") (:end . 212)\n (:start . 202) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 213) (:start . 212)\n (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n (:id . 78)))@@@1@37@((:identifiers (:sid . :s4.274) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101387@unknown@formal@none@1@S@In iPfam version 21, there are 3407 interchain and 1171 intrachain domain pairs, which means that 548 domain pairs mediate both inter- and intrachain interactions.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 16)\n (:start . 9) (:id . 44))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n (:id . 46))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 26) (:start . 21)\n (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 30) (:start . 27)\n (:id . 48))\n ((:tag . "CD") (:stem . "3407") (:form . "3407") (:end . 35) (:start . 31)\n (:id . 49))\n ((:tag . "NN") (:stem . "interchain") (:form . "interchain") (:end . 46)\n (:start . 36) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n (:id . 51))\n ((:tag . "CD") (:stem . "1171") (:form . "1171") (:end . 55) (:start . 51)\n (:id . 52))\n ((:tag . "JJ") (:stem . "intrachain") (:form . "intrachain") (:end . 66)\n (:start . 56) (:id . 53))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 73)\n (:start . 67) (:id . 54))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 79) (:start . 74)\n (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 86) (:start . 81)\n (:id . 57))\n ((:tag . "VBZ") (:stem . "mean") (:form . "means") (:end . 92) (:start . 87)\n (:id . 58))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 97) (:start . 93)\n (:id . 59))\n ((:tag . "CD") (:stem . "548") (:form . "548") (:end . 101) (:start . 98)\n (:id . 60))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 108)\n (:start . 102) (:id . 61))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 114)\n (:start . 109) (:id . 62))\n ((:tag . "VBP") (:stem . "mediate") (:form . "mediate") (:end . 122)\n (:start . 115) (:id . 63))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 127) (:start . 123)\n (:id . 64))\n ((:tag . "JJ") (:stem . "inter-") (:form . "inter-") (:end . 134)\n (:start . 128) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 138) (:start . 135)\n (:id . 66))\n ((:tag . "JJ") (:stem . "intrachain") (:form . "intrachain") (:end . 149)\n (:start . 139) (:id . 67))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 162)\n (:start . 150) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s4.275) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101388@unknown@formal@none@1@S@In this analysis, both types of domain interactions were used equivalently, assuming that intrachain interactions can become interchain interactions and vice-versa as a result of a gene-fission/fusion events.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 16)\n (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 22) (:start . 18)\n (:id . 46))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 28) (:start . 23)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 38)\n (:start . 32) (:id . 49))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 51)\n (:start . 39) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 56) (:start . 52)\n (:id . 51))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 61) (:start . 57)\n (:id . 52))\n ((:tag . "RB") (:stem . "equivalently") (:form . "equivalently") (:end . 74)\n (:start . 62) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n (:id . 54))\n ((:tag . "VBG") (:stem . "assume") (:form . "assuming") (:end . 84)\n (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 89) (:start . 85)\n (:id . 56))\n ((:tag . "JJ") (:stem . "intrachain") (:form . "intrachain") (:end . 100)\n (:start . 90) (:id . 57))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 113)\n (:start . 101) (:id . 58))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 117) (:start . 114)\n (:id . 59))\n ((:tag . "VB") (:stem . "become") (:form . "become") (:end . 124)\n (:start . 118) (:id . 60))\n ((:tag . "JJ") (:stem . "interchain") (:form . "interchain") (:end . 135)\n (:start . 125) (:id . 61))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 148)\n (:start . 136) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 152) (:start . 149)\n (:id . 63))\n ((:tag . "NN") (:stem . "vice-versa") (:form . "vice-versa") (:end . 163)\n (:start . 153) (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 166) (:start . 164)\n (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 168) (:start . 167)\n (:id . 66))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 175)\n (:start . 169) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 178) (:start . 176)\n (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 180) (:start . 179)\n (:id . 69))\n ((:tag . "NN") (:stem . "gene-fission/fusion")\n (:form . "gene-fission/fusion") (:end . 200) (:start . 181) (:id . 70))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 207)\n (:start . 201) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n (:id . 72)))@@@1@31@((:hcues ((:id . :x4.276.1) (:span 114 117))\n ((:id . :x4.276.2) (:span 76 84)))\n (:hscopes ((:id . :x4.276.1) (:span 114 207))\n ((:id . :x4.276.2) (:span 76 207)))\n (:identifiers (:sid . :s4.276) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101390@unknown@formal@none@1@S@Species distribution of iPfam domain pairs.@(((:tag . "NNP") (:stem . "Species") (:form . "Species") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 20)\n (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 44))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 29) (:start . 24)\n (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 36)\n (:start . 30) (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 42) (:start . 37)\n (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 43) (:start . 42)\n (:id . 48)))@@@1@7@((:identifiers (:sid . :s4.278) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101391@unknown@formal@none@1@S@This pie chart shows how many iPfam domain pairs were found in PDB structures from each species.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "pie") (:form . "pie") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "chart") (:form . "chart") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 24) (:start . 21)\n (:id . 46))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 29) (:start . 25)\n (:id . 47))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 35) (:start . 30)\n (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 42)\n (:start . 36) (:id . 49))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 48) (:start . 43)\n (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 53) (:start . 49)\n (:id . 51))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 59) (:start . 54)\n (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n (:id . 53))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 66) (:start . 63)\n (:id . 54))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 77)\n (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 82) (:start . 78)\n (:id . 56))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 87) (:start . 83)\n (:id . 57))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 95)\n (:start . 88) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.279) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101392@unknown@formal@none@1@S@The total number is larger than the 4030 unique iPfam pairs in the database because an iPfam pair can be found in structures from several species.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 16)\n (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . "JJR") (:stem . "large") (:form . "larger") (:end . 26)\n (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 31) (:start . 27)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n (:id . 48))\n ((:tag . "CD") (:stem . "4030") (:form . "4030") (:end . 40) (:start . 36)\n (:id . 49))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 47)\n (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 53) (:start . 48)\n (:id . 51))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 59) (:start . 54)\n (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n (:id . 54))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 75)\n (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 83)\n (:start . 76) (:id . 56))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 86) (:start . 84)\n (:id . 57))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 92) (:start . 87)\n (:id . 58))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 97) (:start . 93)\n (:id . 59))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 101) (:start . 98)\n (:id . 60))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 104) (:start . 102)\n (:id . 61))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 110)\n (:start . 105) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 113) (:start . 111)\n (:id . 63))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 124)\n (:start . 114) (:id . 64))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 129) (:start . 125)\n (:id . 65))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 137)\n (:start . 130) (:id . 66))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 145)\n (:start . 138) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s4.280) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101393@unknown@formal@none@1@S@Filtering@(((:tag . "NNP") (:stem . "Filtering") (:form . "Filtering") (:end . 9)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.281) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101394@unknown@formal@none@1@S@There are many types of experiments used to derive protein interactions, with different properties and error rates.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 46))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 35)\n (:start . 24) (:id . 47))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 40) (:start . 36)\n (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 43) (:start . 41)\n (:id . 49))\n ((:tag . "VB") (:stem . "derive") (:form . "derive") (:end . 50)\n (:start . 44) (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 58)\n (:start . 51) (:id . 51))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 71)\n (:start . 59) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 77) (:start . 73)\n (:id . 54))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 87)\n (:start . 78) (:id . 55))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 98)\n (:start . 88) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n (:id . 57))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 108)\n (:start . 103) (:id . 58))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 114)\n (:start . 109) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.282) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101395@unknown@formal@none@1@S@For this analysis, solely the properties of physically interacting proteins is of interest.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 17)\n (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n (:id . 45))\n ((:tag . "RB") (:stem . "solely") (:form . "solely") (:end . 25)\n (:start . 19) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n (:id . 47))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 40)\n (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n (:id . 49))\n ((:tag . "RB") (:stem . "physically") (:form . "physically") (:end . 54)\n (:start . 44) (:id . 50))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 66)\n (:start . 55) (:id . 51))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 75)\n (:start . 67) (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 78) (:start . 76)\n (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n (:id . 54))\n ((:tag . "NN") (:stem . "interest") (:form . "interest") (:end . 90)\n (:start . 82) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.283) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101396@unknown@formal@none@1@S@Therefore, only interactions between exactly two proteins per experiment were considered.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 28)\n (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 36)\n (:start . 29) (:id . 46))\n ((:tag . "RB") (:stem . "exactly") (:form . "exactly") (:end . 44)\n (:start . 37) (:id . 47))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 48) (:start . 45)\n (:id . 48))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 57)\n (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 61) (:start . 58)\n (:id . 50))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 72)\n (:start . 62) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 77) (:start . 73)\n (:id . 52))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 88)\n (:start . 78) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s4.284) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101397@unknown@formal@none@1@S@That means all protein complex data that were derived by co-purification methods were removed, unless a particular experiment had identified exactly two binding partners.@(((:tag . "DT") (:stem . "that") (:form . "That") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "mean") (:form . "means") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 22)\n (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 30)\n (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 35) (:start . 31)\n (:id . 47))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 40) (:start . 36)\n (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 45) (:start . 41)\n (:id . 49))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 53)\n (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 56) (:start . 54)\n (:id . 51))\n ((:tag . "NN") (:stem . "co-purification") (:form . "co-purification")\n (:end . 72) (:start . 57) (:id . 52))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 80)\n (:start . 73) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 85) (:start . 81)\n (:id . 54))\n ((:tag . "VBN") (:stem . "remove") (:form . "removed") (:end . 93)\n (:start . 86) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n (:id . 56))\n ((:tag . "IN") (:stem . "unless") (:form . "unless") (:end . 101)\n (:start . 95) (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 103) (:start . 102)\n (:id . 58))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 114)\n (:start . 104) (:id . 59))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 125)\n (:start . 115) (:id . 60))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 129) (:start . 126)\n (:id . 61))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 140)\n (:start . 130) (:id . 62))\n ((:tag . "RB") (:stem . "exactly") (:form . "exactly") (:end . 148)\n (:start . 141) (:id . 63))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 152) (:start . 149)\n (:id . 64))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 160)\n (:start . 153) (:id . 65))\n ((:tag . "NNS") (:stem . "partner") (:form . "partners") (:end . 169)\n (:start . 161) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.285) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101398@unknown@formal@none@1@S@All genetic interactions were also removed.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 24)\n (:start . 12) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 29) (:start . 25)\n (:id . 45))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 34) (:start . 30)\n (:id . 46))\n ((:tag . "VBN") (:stem . "remove") (:form . "removed") (:end . 42)\n (:start . 35) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 43) (:start . 42)\n (:id . 48)))@@@1@7@((:identifiers (:sid . :s4.286) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101400@unknown@formal@none@1@S@Randomised protein interaction networks with identical degree distributions were generated from the original filtered experimental interaction data for each species.@(((:tag . "VBN") (:stem . "randomise") (:form . "Randomised") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 18)\n (:start . 11) (:id . 43))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 30)\n (:start . 19) (:id . 44))\n ((:tag . "NNS") (:stem . "network") (:form . "networks") (:end . 39)\n (:start . 31) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 44) (:start . 40)\n (:id . 46))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 54)\n (:start . 45) (:id . 47))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 61)\n (:start . 55) (:id . 48))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n (:end . 75) (:start . 62) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 80) (:start . 76)\n (:id . 50))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 90)\n (:start . 81) (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 95) (:start . 91)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n (:id . 53))\n ((:tag . "JJ") (:stem . "original") (:form . "original") (:end . 108)\n (:start . 100) (:id . 54))\n ((:tag . "VBN") (:stem . "filter") (:form . "filtered") (:end . 117)\n (:start . 109) (:id . 55))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 130)\n (:start . 118) (:id . 56))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 142)\n (:start . 131) (:id . 57))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 147)\n (:start . 143) (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 151) (:start . 148)\n (:id . 59))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 156) (:start . 152)\n (:id . 60))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 164)\n (:start . 157) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.288) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101401@unknown@formal@none@1@S@In each randomisation step, a mapping is created that assigns every node a randomly chosen replacement node.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "randomisation") (:form . "randomisation")\n (:end . 21) (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 26) (:start . 22)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n (:id . 47))\n ((:tag . "NN") (:stem . "mapping") (:form . "mapping") (:end . 37)\n (:start . 30) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 40) (:start . 38)\n (:id . 49))\n ((:tag . "VBN") (:stem . "create") (:form . "created") (:end . 48)\n (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 53) (:start . 49)\n (:id . 51))\n ((:tag . "NNS") (:stem . "assign") (:form . "assigns") (:end . 61)\n (:start . 54) (:id . 52))\n ((:tag . "DT") (:stem . "every") (:form . "every") (:end . 67) (:start . 62)\n (:id . 53))\n ((:tag . "NN") (:stem . "node") (:form . "node") (:end . 72) (:start . 68)\n (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 74) (:start . 73)\n (:id . 55))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 83)\n (:start . 75) (:id . 56))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 90)\n (:start . 84) (:id . 57))\n ((:tag . "NN") (:stem . "replacement") (:form . "replacement") (:end . 102)\n (:start . 91) (:id . 58))\n ((:tag . "NN") (:stem . "node") (:form . "node") (:end . 107) (:start . 103)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.289) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101402@unknown@formal@none@1@S@In this way the edges of the network remain in place, while the nodes are shuffled randomly.@(((:tag . "IN") (:stem . "in") (:form . 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",") (:end . 53) (:start . 52)\n (:id . 53))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 59) (:start . 54)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n (:id . 55))\n ((:tag . "NNS") (:stem . "node") (:form . "nodes") (:end . 69) (:start . 64)\n (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 73) (:start . 70)\n (:id . 57))\n ((:tag . "VBN") (:stem . "shuffle") (:form . "shuffled") (:end . 82)\n (:start . 74) (:id . 58))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 91)\n (:start . 83) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.290) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101403@unknown@formal@none@1@S@It should be noted that the degree distribution per node is not maintained.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 12) (:start . 10)\n (:id . 44))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 34)\n (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 47)\n (:start . 35) (:id . 49))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 51) (:start . 48)\n (:id . 50))\n ((:tag . "NN") (:stem . "node") (:form . "node") (:end . 56) (:start . 52)\n (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 59) (:start . 57)\n (:id . 52))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 63) (:start . 60)\n (:id . 53))\n ((:tag . "VBN") (:stem . "maintain") (:form . "maintained") (:end . 74)\n (:start . 64) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n (:id . 55)))@@@1@14@((:ncues ((:id . :x4.291.1) (:span 60 63)))\n (:nscopes ((:id . :x4.291.1) (:span 60 74)))\n (:identifiers (:sid . :s4.291) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101404@unknown@formal@none@1@S@Instead, this behaviour simulates a network with a high false positive rate.@(((:tag . "RB") (:stem . "instead") (:form . "Instead") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "behaviour") (:form . 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(:end . 76) (:start . 75)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s4.292) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101405@unknown@formal@none@1@S@P values@(((:tag . "NN") (:stem . "p") (:form . "P") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 8) (:start . 2)\n (:id . 43)))@@@1@2@((:identifiers (:sid . :s4.293) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101406@unknown@formal@none@1@S@P values for observations x were calculated as P(X ≥ x) = f(x; μ, σ), where f(x; μ, σ) is the probability density function of the normal distribution with mean μ and standard deviation σ.@(((:tag . "NN") (:stem . "p") (:form . "P") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 8) (:start . 2)\n (:id . 43))\n ((:tag . 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(:end . 187) (:start . 186)\n (:id . 85)))@@@1@44@((:identifiers (:sid . :s4.294) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101407@unknown@formal@none@1@S@μ and σ are estimated through the randomisation experiments.@(((:tag . "NNP") (:stem . "μ") (:form . "μ") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 5) (:start . 2)\n (:id . 43))\n ((:tag . "NNP") (:stem . "σ") (:form . "σ") (:end . 7) (:start . 6)\n (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 11) (:start . 8)\n (:id . 45))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 21)\n (:start . 12) (:id . 46))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 29)\n (:start . 22) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 48))\n ((:tag . "NN") (:stem . "randomisation") (:form . 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"RB") (:stem . "yet") (:form . "yet") (:end . 130) (:start . 127)\n (:id . 64))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 135) (:start . 131)\n (:id . 65))\n ((:tag . "VBN") (:stem . "examine") (:form . "examined") (:end . 144)\n (:start . 136) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n (:id . 67)))@@@1@26@((:ncues ((:id . :x5.5.1) (:span 123 126)))\n (:nscopes ((:id . :x5.5.1) (:span 59 144)))\n (:identifiers (:sid . :s5.5) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101415@unknown@formal@none@1@S@We show here that the Drosophila mind bomb (D-mib) gene regulates a subset of Notch signaling events, including wing margin specification, leg segmentation, and vein determination, that are distinct from those events requiring neur activity.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . 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(:end . 241) (:start . 240)\n (:id . 83)))@@@1@42@((:identifiers (:sid . :s5.6) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101416@unknown@formal@none@1@S@D-mib also modulates lateral inhibition, a neur- and Dl-dependent signaling event, suggesting that D-mib regulates Dl signaling.@(((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "modulate") (:form . "modulates") (:end . 20)\n (:start . 11) (:id . 44))\n ((:tag . "JJ") (:stem . "lateral") (:form . "lateral") (:end . 28)\n (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 39)\n (:start . 29) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . 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(:end . 182) (:start . 181)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x5.8.1) (:span 131 146)) ((:id . :x5.8.2) (:span 61 68)))\n (:hscopes ((:id . :x5.8.1) (:span 131 181)) ((:id . :x5.8.2) (:span 25 129)))\n (:identifiers (:sid . :s5.8) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101418@unknown@formal@none@1@S@Moreover, the activity of the D-mib gene is required for the endocytosis of Ser in wing imaginal disc cells.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 22)\n (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . 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(:end . 161) (:start . 160)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s5.11) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101421@unknown@formal@none@1@S@Introduction@(((:tag . "NN") (:stem . "introduction") (:form . "Introduction") (:end . 12)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s5.12) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101422@unknown@formal@none@1@S@Cell-to-cell signaling mediated by receptors of the Notch (N) family has been implicated in various developmental decisions in organisms ranging from nematodes to mammals [1].@(((:tag . "JJ") (:stem . "cell-to-cell") (:form . "Cell-to-cell") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 22)\n (:start . 13) (:id . 43))\n ((:tag . "VBN") (:stem . "mediate") (:form . 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(:end . 275) (:start . 274)\n (:id . 94)))@@@1@53@((:hcues ((:id . :x5.23.1) (:span 58 66)))\n (:hscopes ((:id . :x5.23.1) (:span 37 144)))\n (:identifiers (:sid . :s5.23) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101433@unknown@formal@none@1@S@Furthermore, Dl and Ser appear to be partially interchangeable because the forced expression of Ser can partially rescue the Dl neurogenic phenotype [13].@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 23) (:start . 20)\n (:id . 46))\n ((:tag . "VBP") (:stem . "appear") (:form . 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".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n (:id . 68)))@@@1@27@((:hcues ((:id . :x5.24.1) (:span 24 30)))\n (:hscopes ((:id . :x5.24.1) (:span 13 62)))\n (:identifiers (:sid . :s5.24) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101434@unknown@formal@none@1@S@Additionally, the ectopic expression of Dl can partially rescue the Ser wing phenotype [14].@(((:tag . "RB") (:stem . "additionally") (:form . "Additionally") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "JJ") (:stem . "ectopic") (:form . "ectopic") (:end . 25)\n (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 36)\n (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . 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"]") (:end . 91) (:start . 90)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s5.25) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101435@unknown@formal@none@1@S@The notion that Dl and Ser have similar signaling properties has, however, recently been challenged by the observation that human homologs of Dl and Ser have distinct instructive signaling activity [15].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "notion") (:form . "notion") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 18) (:start . 16)\n (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n (:id . 46))\n ((:tag . "NNP") (:stem . 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"and") (:end . 148) (:start . 145)\n (:id . 67))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 152) (:start . 149)\n (:id . 68))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 157) (:start . 153)\n (:id . 69))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 166)\n (:start . 158) (:id . 70))\n ((:tag . "JJ") (:stem . "instructive") (:form . "instructive") (:end . 178)\n (:start . 167) (:id . 71))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 188)\n (:start . 179) (:id . 72))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 197)\n (:start . 189) (:id . 73))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 199) (:start . 198)\n (:id . 74))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 201) (:start . 199)\n (:id . 75))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 202) (:start . 201)\n (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s5.26) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101436@unknown@formal@none@1@S@Endocytosis has recently emerged as a key mechanism regulating the signaling activity of Dl.@(((:tag . "NNP") (:stem . "Endocytosis") (:form . "Endocytosis") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 15) (:start . 12)\n (:id . 43))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 24)\n (:start . 16) (:id . 44))\n ((:tag . "VBN") (:stem . "emerge") (:form . "emerged") (:end . 32)\n (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 35) (:start . 33)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n (:id . 47))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 41) (:start . 38)\n (:id . 48))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 51)\n (:start . 42) (:id . 49))\n ((:tag . "VBG") (:stem . "regulate") (:form . "regulating") (:end . 62)\n (:start . 52) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n (:id . 51))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 76)\n (:start . 67) (:id . 52))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 85)\n (:start . 77) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 91) (:start . 89)\n (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s5.27) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101437@unknown@formal@none@1@S@First, clonal analysis in Drosophila has suggested that dynamin-dependent endocytosis is required not only in signal-receiving cells but also in signal-sending cells to promote N activation [16].@(((:tag . "RB") (:stem . "first") (:form . "First") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "JJ") (:stem . "clonal") (:form . "clonal") (:end . 13) (:start . 7)\n (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 22)\n (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 25) (:start . 23)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 36)\n (:start . 26) (:id . 47))\n ((:tag . 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"signal-receiving") (:form . "signal-receiving")\n (:end . 126) (:start . 110) (:id . 58))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 132)\n (:start . 127) (:id . 59))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 136) (:start . 133)\n (:id . 60))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 141) (:start . 137)\n (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 144) (:start . 142)\n (:id . 62))\n ((:tag . "JJ") (:stem . "signal-sending") (:form . "signal-sending")\n (:end . 159) (:start . 145) (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 165)\n (:start . 160) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 168) (:start . 166)\n (:id . 65))\n ((:tag . "VB") (:stem . "promote") (:form . "promote") (:end . 176)\n (:start . 169) (:id . 66))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 178) (:start . 177)\n (:id . 67))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 189)\n (:start . 179) (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 191) (:start . 190)\n (:id . 69))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 193) (:start . 191)\n (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 194) (:start . 193)\n (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n (:id . 72)))@@@1@31@((:hcues ((:id . :x5.28.1) (:span 41 50)))\n (:hscopes ((:id . :x5.28.1) (:span 41 189)))\n (:identifiers (:sid . :s5.28) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101438@unknown@formal@none@1@S@Second, mutant Dl proteins that are endocytosis defective exhibit reduced signaling activity [17].@(((:tag . "JJ") (:stem . "second") (:form . "Second") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 14) (:start . 8)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 17) (:start . 15)\n (:id . 45))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 26)\n (:start . 18) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 31) (:start . 27)\n (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n (:id . 48))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 47)\n (:start . 36) (:id . 49))\n ((:tag . "JJ") (:stem . "defective") (:form . "defective") (:end . 57)\n (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "exhibit") (:form . "exhibit") (:end . 65)\n (:start . 58) (:id . 51))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 73)\n (:start . 66) (:id . 52))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 83)\n (:start . 74) (:id . 53))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 92)\n (:start . 84) (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 94) (:start . 93)\n (:id . 55))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 96) (:start . 94)\n (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 97) (:start . 96)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s5.29) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101440@unknown@formal@none@1@S@Ubiquitin is a 76-amino-acid polypeptide that is covalently linked to substrates in a multi-step process that involves a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and a ubiquitin–protein ligase (E3).@(((:tag . "NNP") (:stem . "Ubiquitin") (:form . "Ubiquitin") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . 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"E1") (:end . 152) (:start . 150)\n (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 153) (:start . 152)\n (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 154) (:start . 153)\n (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 156) (:start . 155)\n (:id . 66))\n ((:tag . "JJ") (:stem . "ubiquitin-conjugating")\n (:form . "ubiquitin-conjugating") (:end . 178) (:start . 157) (:id . 67))\n ((:tag . "NN") (:stem . "enzyme") (:form . "enzyme") (:end . 185)\n (:start . 179) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 187) (:start . 186)\n (:id . 69))\n ((:tag . "NNP") (:stem . "E2") (:form . "E2") (:end . 189) (:start . 187)\n (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 190) (:start . 189)\n (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 191) (:start . 190)\n (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 195) (:start . 192)\n (:id . 73))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 197) (:start . 196)\n (:id . 74))\n ((:tag . "NN") (:stem . "ubiquitin–protein") (:form . "ubiquitin–protein")\n (:end . 215) (:start . 198) (:id . 75))\n ((:tag . "NN") (:stem . "ligase") (:form . "ligase") (:end . 222)\n (:start . 216) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 224) (:start . 223)\n (:id . 77))\n ((:tag . "NNP") (:stem . "E3") (:form . "E3") (:end . 226) (:start . 224)\n (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 227) (:start . 226)\n (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 228) (:start . 227)\n (:id . 80)))@@@1@39@((:identifiers (:sid . :s5.31) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101441@unknown@formal@none@1@S@E3s recognize specific substrates and catalyze the transfer of ubiquitin to the protein substrate.@(((:tag . "NNS") (:stem . "e3") (:form . "E3s") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "recognize") (:form . "recognize") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 22)\n (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "substrate") (:form . "substrates") (:end . 33)\n (:start . 23) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n (:id . 46))\n ((:tag . "VB") (:stem . "catalyze") (:form . "catalyze") (:end . 46)\n (:start . 38) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n (:id . 48))\n ((:tag . "NN") (:stem . "transfer") (:form . "transfer") (:end . 59)\n (:start . 51) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n (:id . 50))\n ((:tag . "NN") (:stem . "ubiquitin") (:form . "ubiquitin") (:end . 72)\n (:start . 63) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 75) (:start . 73)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 87)\n (:start . 80) (:id . 54))\n ((:tag . "NN") (:stem . "substrate") (:form . "substrate") (:end . 97)\n (:start . 88) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s5.32) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101442@unknown@formal@none@1@S@Ubiquitin was first identified as a tag for proteins destined for degradation.@(((:tag . "NNP") (:stem . "Ubiquitin") (:form . "Ubiquitin") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 13) (:start . 10)\n (:id . 43))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 19) (:start . 14)\n (:id . 44))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 30)\n (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 33) (:start . 31)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 35) (:start . 34)\n (:id . 47))\n ((:tag . "NN") (:stem . "tag") (:form . "tag") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n (:id . 49))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 52)\n (:start . 44) (:id . 50))\n ((:tag . "VBN") (:stem . "destine") (:form . "destined") (:end . 61)\n (:start . 53) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 65) (:start . 62)\n (:id . 52))\n ((:tag . "NN") (:stem . "degradation") (:form . "degradation") (:end . 77)\n (:start . 66) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s5.33) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101443@unknown@formal@none@1@S@More recently, ubiquitin has also been shown to serve as a signal for endocytosis [26,27].@(((:tag . "RBR") (:stem . "more") (:form . "More") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 44))\n ((:tag . "NN") (:stem . "ubiquitin") (:form . "ubiquitin") (:end . 24)\n (:start . 15) (:id . 45))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 38) (:start . 34)\n (:id . 48))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 44) (:start . 39)\n (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n (:id . 50))\n ((:tag . "VB") (:stem . "serve") (:form . "serve") (:end . 53) (:start . 48)\n (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 56) (:start . 54)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 58) (:start . 57)\n (:id . 53))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 65)\n (:start . 59) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 69) (:start . 66)\n (:id . 55))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 81)\n (:start . 70) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 83) (:start . 82)\n (:id . 57))\n ((:tag . "CD") (:stem . "26,27") (:form . "26,27") (:end . 88) (:start . 83)\n (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 89) (:start . 88)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s5.34) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101444@unknown@formal@none@1@S@Mib in D. rerio and Neur in Drosophila and Xenopus have been shown to associate with Dl, regulate Dl ubiquitination, and promote its endocytosis [18,19,20,22,25,28].@(((:tag . "NNP") (:stem . "Mib") (:form . "Mib") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 6) (:start . 4)\n (:id . 43))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 9) (:start . 7)\n (:id . 44))\n ((:tag . "NN") (:stem . "rerio") (:form . "rerio") (:end . 15) (:start . 10)\n (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 24) (:start . 20)\n (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 38)\n (:start . 28) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Xenopus") (:form . "Xenopus") (:end . 50)\n (:start . 43) (:id . 51))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 55) (:start . 51)\n (:id . 52))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 60) (:start . 56)\n (:id . 53))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 66) (:start . 61)\n (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 69) (:start . 67)\n (:id . 55))\n ((:tag . "VB") (:stem . "associate") (:form . "associate") (:end . 79)\n (:start . 70) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 84) (:start . 80)\n (:id . 57))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 87) (:start . 85)\n (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n (:id . 59))\n ((:tag . "VBP") (:stem . "regulate") (:form . "regulate") (:end . 97)\n (:start . 89) (:id . 60))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 100) (:start . 98)\n (:id . 61))\n ((:tag . "NN") (:stem . "ubiquitination") (:form . "ubiquitination")\n (:end . 115) (:start . 101) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n (:id . 64))\n ((:tag . "VB") (:stem . "promote") (:form . "promote") (:end . 128)\n (:start . 121) (:id . 65))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 132) (:start . 129)\n (:id . 66))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 144)\n (:start . 133) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 146) (:start . 145)\n (:id . 68))\n ((:tag . "CD") (:stem . "18,19,20,22,25,28") (:form . 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"that") (:end . 151) (:start . 147)\n (:id . 65))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 163)\n (:start . 152) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 166) (:start . 164)\n (:id . 67))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 169) (:start . 167)\n (:id . 68))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 172) (:start . 170)\n (:id . 69))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 183)\n (:start . 173) (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 188) (:start . 184)\n (:id . 71))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 198)\n (:start . 189) (:id . 72))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 201) (:start . 199)\n (:id . 73))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 211)\n (:start . 202) (:id . 74))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 220)\n (:start . 212) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 221) (:start . 220)\n (:id . 76)))@@@1@35@((:hcues ((:id . :x5.36.1) (:span 136 151)) ((:id . :x5.36.2) (:span 51 65)))\n (:hscopes ((:id . :x5.36.1) (:span 136 220))\n ((:id . :x5.36.2) (:span 51 220)))\n (:identifiers (:sid . :s5.36) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101446@unknown@formal@none@1@S@Finally, epsin, a regulator of endocytosis that contains a ubiquitin-interacting motif and that is known in Drosophila as Liquid facet, is essential for Dl signaling [30,31].@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "epsin") (:form . "epsin") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . 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"and") (:end . 90) (:start . 87)\n (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 95) (:start . 91)\n (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 98) (:start . 96)\n (:id . 57))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 104) (:start . 99)\n (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n (:id . 59))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 118)\n (:start . 108) (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 121) (:start . 119)\n (:id . 61))\n ((:tag . "NNP") (:stem . "Liquid") (:form . "Liquid") (:end . 128)\n (:start . 122) (:id . 62))\n ((:tag . "NN") (:stem . "facet") (:form . "facet") (:end . 134)\n (:start . 129) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 138) (:start . 136)\n (:id . 65))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 148)\n (:start . 139) (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 152) (:start . 149)\n (:id . 67))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 155) (:start . 153)\n (:id . 68))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 165)\n (:start . 156) (:id . 69))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 167) (:start . 166)\n (:id . 70))\n ((:tag . "CD") (:stem . "30,31") (:form . "30,31") (:end . 172)\n (:start . 167) (:id . 71))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 173) (:start . 172)\n (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s5.37) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101447@unknown@formal@none@1@S@In one study, Liquid facet was proposed to target Dl to an endocytic recycling compartment, suggesting that recycling of Dl may be required for signaling.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 12) (:start . 7)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Liquid") (:form . "Liquid") (:end . 20)\n (:start . 14) (:id . 46))\n ((:tag . "NN") (:stem . "facet") (:form . "facet") (:end . 26) (:start . 21)\n (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . 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(:end . 154) (:start . 153)\n (:id . 69)))@@@1@28@((:hcues ((:id . :x5.38.1) (:span 124 127)) ((:id . :x5.38.2) (:span 92 102))\n ((:id . :x5.38.3) (:span 31 39)))\n (:hscopes ((:id . :x5.38.1) (:span 108 153))\n ((:id . :x5.38.2) (:span 92 153)) ((:id . :x5.38.3) (:span 14 153)))\n (:identifiers (:sid . :s5.38) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101448@unknown@formal@none@1@S@Accordingly, signaling would not be linked directly to endocytosis, but endocytosis would be prerequisite for signaling [30].@(((:tag . "RB") (:stem . "accordingly") (:form . "Accordingly") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 43))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 22)\n (:start . 13) (:id . 44))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 28) (:start . 23)\n (:id . 45))\n ((:tag . "RB") (:stem . 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"be") (:end . 92) (:start . 90)\n (:id . 56))\n ((:tag . "JJ") (:stem . "prerequisite") (:form . "prerequisite") (:end . 105)\n (:start . 93) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 109) (:start . 106)\n (:id . 58))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 119)\n (:start . 110) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 121) (:start . 120)\n (:id . 60))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 123) (:start . 121)\n (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 124) (:start . 123)\n (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n (:id . 63)))@@@1@22@((:hcues ((:id . :x5.39.1) (:span 84 89)) ((:id . :x5.39.2) (:span 23 28)))\n (:ncues ((:id . :x5.39.3) (:span 29 32)))\n (:hscopes ((:id . :x5.39.1) (:span 84 119)) ((:id . :x5.39.2) (:span 13 66)))\n (:nscopes ((:id . :x5.39.3) (:span 13 66)))\n (:identifiers (:sid . :s5.39) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101450@unknown@formal@none@1@S@Also, whether the signaling activity of Ser is similarly regulated by endocytosis is not known.@(((:tag . "RB") (:stem . "also") (:form . "Also") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 13)\n (:start . 6) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 45))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 27)\n (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 36)\n (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 43) (:start . 40)\n (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 46) (:start . 44)\n (:id . 50))\n ((:tag . "RB") (:stem . "similarly") (:form . "similarly") (:end . 56)\n (:start . 47) (:id . 51))\n ((:tag . "VBN") (:stem . "regulate") (:form . "regulated") (:end . 66)\n (:start . 57) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 69) (:start . 67)\n (:id . 53))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 81)\n (:start . 70) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 84) (:start . 82)\n (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 88) (:start . 85)\n (:id . 56))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 94) (:start . 89)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n (:id . 58)))@@@1@17@((:hcues ((:id . :x5.41.2) (:span 85 94)) ((:id . :x5.41.1) (:span 6 13)))\n (:hscopes ((:id . :x5.41.2) (:span 6 81)) ((:id . :x5.41.1) (:span 6 94)))\n (:identifiers (:sid . :s5.41) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101451@unknown@formal@none@1@S@Neur and Mib proteins completely differ in primary structure.@(((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Mib") (:form . "Mib") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 21)\n (:start . 13) (:id . 45))\n ((:tag . "RB") (:stem . "completely") (:form . "completely") (:end . 32)\n (:start . 22) (:id . 46))\n ((:tag . "VBP") (:stem . "differ") (:form . "differ") (:end . 39)\n (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n (:id . 48))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 50)\n (:start . 43) (:id . 49))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 60)\n (:start . 51) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 61) (:start . 60)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s5.42) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101452@unknown@formal@none@1@S@Drosophila Neur is a 754-amino-acid protein that contains two conserved Neur homology repeats of unknown function and one C-terminal catalytic really interesting new gene (RING) domain.@(((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 15) (:start . 11)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n (:id . 45))\n ((:tag . "JJ") (:stem . "754-amino-acid") (:form . "754-amino-acid")\n (:end . 35) (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 43)\n (:start . 36) (:id . 47))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 48) (:start . 44)\n (:id . 48))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 57)\n (:start . 49) (:id . 49))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 61) (:start . 58)\n (:id . 50))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 71)\n (:start . 62) (:id . 51))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 76) (:start . 72)\n (:id . 52))\n ((:tag . "NN") (:stem . "homology") (:form . "homology") (:end . 85)\n (:start . 77) (:id . 53))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 93)\n (:start . 86) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n (:id . 55))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 104)\n (:start . 97) (:id . 56))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 113)\n (:start . 105) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n (:id . 58))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 121) (:start . 118)\n (:id . 59))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 132)\n (:start . 122) (:id . 60))\n ((:tag . "JJ") (:stem . "catalytic") (:form . "catalytic") (:end . 142)\n (:start . 133) (:id . 61))\n ((:tag . "RB") (:stem . "really") (:form . "really") (:end . 149)\n (:start . 143) (:id . 62))\n ((:tag . "JJ") (:stem . "interesting") (:form . "interesting") (:end . 161)\n (:start . 150) (:id . 63))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 165) (:start . 162)\n (:id . 64))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 170) (:start . 166)\n (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 172) (:start . 171)\n (:id . 66))\n ((:tag . "NN") (:stem . "ring") (:form . "RING") (:end . 176) (:start . 172)\n (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 177) (:start . 176)\n (:id . 68))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 184)\n (:start . 178) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s5.43) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101453@unknown@formal@none@1@S@D. rerio Mib (also known as DIP-1 in the mouse [32]) is a 1,030-amino-acid protein with one ZZ zinc finger domain surrounded by two Mib/HERC2 domains, two Mib repeats, eight ankyrin repeats, two atypical RING domains, and one C-terminal catalytic RING domain.@(((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "rerio") (:form . "rerio") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Mib") (:form . "Mib") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 14) (:start . 13)\n (:id . 45))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 18) (:start . 14)\n (:id . 46))\n ((:tag . "VBN") (:stem . "know") (:form . 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"a") (:end . 57) (:start . 56)\n (:id . 58))\n ((:tag . "JJ") (:stem . "1,030-amino-acid") (:form . "1,030-amino-acid")\n (:end . 74) (:start . 58) (:id . 59))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 82)\n (:start . 75) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 87) (:start . 83)\n (:id . 61))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 91) (:start . 88)\n (:id . 62))\n ((:tag . "NNP") (:stem . "ZZ") (:form . "ZZ") (:end . 94) (:start . 92)\n (:id . 63))\n ((:tag . "NN") (:stem . "zinc") (:form . "zinc") (:end . 99) (:start . 95)\n (:id . 64))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 106)\n (:start . 100) (:id . 65))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 113)\n (:start . 107) (:id . 66))\n ((:tag . "VBN") (:stem . "surround") (:form . "surrounded") (:end . 124)\n (:start . 114) (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 127) (:start . 125)\n (:id . 68))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 131) (:start . 128)\n (:id . 69))\n ((:tag . "NN") (:stem . "mib/herc2") (:form . "Mib/HERC2") (:end . 141)\n (:start . 132) (:id . 70))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 149)\n (:start . 142) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n (:id . 72))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 154) (:start . 151)\n (:id . 73))\n ((:tag . "NNP") (:stem . "Mib") (:form . "Mib") (:end . 158) (:start . 155)\n (:id . 74))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 166)\n (:start . 159) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n (:id . 76))\n ((:tag . "CD") (:stem . "eight") (:form . "eight") (:end . 173)\n (:start . 168) (:id . 77))\n ((:tag . "NN") (:stem . "ankyrin") (:form . "ankyrin") (:end . 181)\n (:start . 174) (:id . 78))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 189)\n (:start . 182) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 190) (:start . 189)\n (:id . 80))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 194) (:start . 191)\n (:id . 81))\n ((:tag . "JJ") (:stem . "atypical") (:form . "atypical") (:end . 203)\n (:start . 195) (:id . 82))\n ((:tag . "NN") (:stem . "ring") (:form . "RING") (:end . 208) (:start . 204)\n (:id . 83))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 216)\n (:start . 209) (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 217) (:start . 216)\n (:id . 85))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 221) (:start . 218)\n (:id . 86))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 225) (:start . 222)\n (:id . 87))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 236)\n (:start . 226) (:id . 88))\n ((:tag . "JJ") (:stem . "catalytic") (:form . "catalytic") (:end . 246)\n (:start . 237) (:id . 89))\n ((:tag . "NN") (:stem . "ring") (:form . "RING") (:end . 251) (:start . 247)\n (:id . 90))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 258)\n (:start . 252) (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 259) (:start . 258)\n (:id . 92)))@@@1@51@((:identifiers (:sid . :s5.44) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101454@unknown@formal@none@1@S@Both genes have been conserved from flies to mammals [18,19,33,34].@(((:tag . "DT") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 30)\n (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 35) (:start . 31)\n (:id . 47))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 41) (:start . 36)\n (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n (:id . 49))\n ((:tag . "NNS") (:stem . "mammal") (:form . "mammals") (:end . 52)\n (:start . 45) (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 54) (:start . 53)\n (:id . 51))\n ((:tag . "CD") (:stem . "18,19,33,34") (:form . "18,19,33,34") (:end . 65)\n (:start . 54) (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 66) (:start . 65)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s5.45) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101455@unknown@formal@none@1@S@While genetic analysis has revealed that neur in Drosophila and mib in D. rerio are strictly required for N signaling, knockout studies of mouse Neur1 has indicated that NEUR1 is not strictly required for N signaling [33,34].@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 13)\n (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 22)\n (:start . 14) (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 26) (:start . 23)\n (:id . 45))\n ((:tag . "VBN") (:stem . "reveal") (:form . "revealed") (:end . 35)\n (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 40) (:start . 36)\n (:id . 47))\n ((:tag . "NN") (:stem . "neur") (:form . "neur") (:end . 45) (:start . 41)\n (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n (:id . 49))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 59)\n (:start . 49) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n (:id . 51))\n ((:tag . "NN") (:stem . "mib") (:form . "mib") (:end . 67) (:start . 64)\n (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 70) (:start . 68)\n (:id . 53))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 73) (:start . 71)\n (:id . 54))\n ((:tag . "NN") (:stem . "rerio") (:form . "rerio") (:end . 79) (:start . 74)\n (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 83) (:start . 80)\n (:id . 56))\n ((:tag . "RB") (:stem . "strictly") (:form . "strictly") (:end . 92)\n (:start . 84) (:id . 57))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 101)\n (:start . 93) (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 105) (:start . 102)\n (:id . 59))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 107) (:start . 106)\n (:id . 60))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 117)\n (:start . 108) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n (:id . 62))\n ((:tag . "JJ") (:stem . "knockout") (:form . "knockout") (:end . 127)\n (:start . 119) (:id . 63))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 135)\n (:start . 128) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n (:id . 65))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 144)\n (:start . 139) (:id . 66))\n ((:tag . "NN") (:stem . "neur1") (:form . "Neur1") (:end . 150)\n (:start . 145) (:id . 67))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 154) (:start . 151)\n (:id . 68))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 164)\n (:start . 155) (:id . 69))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 169) (:start . 165)\n (:id . 70))\n ((:tag . "NN") (:stem . "neur1") (:form . "NEUR1") (:end . 175)\n (:start . 170) (:id . 71))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 178) (:start . 176)\n (:id . 72))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 182) (:start . 179)\n (:id . 73))\n ((:tag . "RB") (:stem . "strictly") (:form . "strictly") (:end . 191)\n (:start . 183) (:id . 74))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 200)\n (:start . 192) (:id . 75))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 204) (:start . 201)\n (:id . 76))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 206) (:start . 205)\n (:id . 77))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 216)\n (:start . 207) (:id . 78))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 218) (:start . 217)\n (:id . 79))\n ((:tag . "CD") (:stem . "33,34") (:form . "33,34") (:end . 223)\n (:start . 218) (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 224) (:start . 223)\n (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n (:id . 82)))@@@1@41@((:hcues ((:id . :x5.46.1) (:span 155 169)))\n (:hscopes ((:id . :x5.46.1) (:span 155 216)))\n (:identifiers (:sid . :s5.46) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101456@unknown@formal@none@1@S@One possible explanation is functional redundancy with the mouse Neur2 gene.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "explanation") (:form . "explanation") (:end . 24)\n (:start . 13) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n (:id . 45))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 38)\n (:start . 28) (:id . 46))\n ((:tag . "NN") (:stem . "redundancy") (:form . "redundancy") (:end . 49)\n (:start . 39) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 54) (:start . 50)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n (:id . 49))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 64) (:start . 59)\n (:id . 50))\n ((:tag . "NN") (:stem . "neur2") (:form . "Neur2") (:end . 70) (:start . 65)\n (:id . 51))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 75) (:start . 71)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n (:id . 53)))@@@1@12@((:hcues ((:id . :x5.47.1) (:span 4 12)))\n (:hscopes ((:id . :x5.47.1) (:span 4 75)))\n (:identifiers (:sid . :s5.47) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101457@unknown@formal@none@1@S@Conversely, the function of Drosophila mib (D-mib), the homolog of D. rerio mib gene, is not known.@(((:tag . "RB") (:stem . "conversely") (:form . "Conversely") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 24)\n (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 38)\n (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "mib") (:form . "mib") (:end . 42) (:start . 39)\n (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 44) (:start . 43)\n (:id . 49))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 49) (:start . 44)\n (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 50) (:start . 49)\n (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n (:id . 53))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 63)\n (:start . 56) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n (:id . 55))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 69) (:start . 67)\n (:id . 56))\n ((:tag . "NN") (:stem . "rerio") (:form . "rerio") (:end . 75) (:start . 70)\n (:id . 57))\n ((:tag . "NN") (:stem . "mib") (:form . "mib") (:end . 79) (:start . 76)\n (:id . 58))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 84) (:start . 80)\n (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n (:id . 60))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 88) (:start . 86)\n (:id . 61))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 92) (:start . 89)\n (:id . 62))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 98) (:start . 93)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 64)))@@@1@23@((:hcues ((:id . :x5.48.1) (:span 89 98)))\n (:hscopes ((:id . :x5.48.1) (:span 12 98)))\n (:identifiers (:sid . :s5.48) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101458@unknown@formal@none@1@S@To establish the respective roles of these two distinct E3 ligases in the context of a single model organism, we have studied the function of the Drosophila D-mib gene.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "establish") (:form . "establish") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "respective") (:form . "respective") (:end . 27)\n (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 33) (:start . 28)\n (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n (:id . 47))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 42) (:start . 37)\n (:id . 48))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 46) (:start . 43)\n (:id . 49))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 55)\n (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "e3") (:form . "E3") (:end . 58) (:start . 56)\n (:id . 51))\n ((:tag . "NNS") (:stem . "ligas") (:form . "ligases") (:end . 66)\n (:start . 59) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 69) (:start . 67)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n (:id . 54))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 81)\n (:start . 74) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 86) (:start . 85)\n (:id . 57))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 93)\n (:start . 87) (:id . 58))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 99) (:start . 94)\n (:id . 59))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 108)\n (:start . 100) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n (:id . 61))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 112) (:start . 110)\n (:id . 62))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 117) (:start . 113)\n (:id . 63))\n ((:tag . "VBN") (:stem . "study") (:form . "studied") (:end . 125)\n (:start . 118) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n (:id . 65))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 138)\n (:start . 130) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 141) (:start . 139)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n (:id . 68))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 156)\n (:start . 146) (:id . 69))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 162)\n (:start . 157) (:id . 70))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 167) (:start . 163)\n (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n (:id . 72)))@@@1@31@((:identifiers (:sid . :s5.49) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101460@unknown@formal@none@1@S@We further show that D-mib is specifically required for Ser endocytosis and signaling during wing development, indicating for the first time, to our knowledge, that endocytosis regulates Ser signaling.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "further") (:form . "further") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 26) (:start . 21)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n (:id . 47))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 42)\n (:start . 30) (:id . 48))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 51)\n (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 55) (:start . 52)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 59) (:start . 56)\n (:id . 51))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 71)\n (:start . 60) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n (:id . 53))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 85)\n (:start . 76) (:id . 54))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 92)\n (:start . 86) (:id . 55))\n ((:tag . "VBG") (:stem . "wing") (:form . "wing") (:end . 97) (:start . 93)\n (:id . 56))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 109)\n (:start . 98) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n (:id . 58))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 121)\n (:start . 111) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 125) (:start . 122)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n (:id . 61))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 135)\n (:start . 130) (:id . 62))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 140) (:start . 136)\n (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 144) (:start . 142)\n (:id . 65))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 148) (:start . 145)\n (:id . 66))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 158)\n (:start . 149) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 159) (:start . 158)\n (:id . 68))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 164) (:start . 160)\n (:id . 69))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 176)\n (:start . 165) (:id . 70))\n ((:tag . "VBZ") (:stem . "regulate") (:form . "regulates") (:end . 186)\n (:start . 177) (:id . 71))\n ((:tag . "NN") (:stem . "ser") (:form . "Ser") (:end . 190) (:start . 187)\n (:id . 72))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 200)\n (:start . 191) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n (:id . 74)))@@@1@33@((:hcues ((:id . :x5.51.1) (:span 111 121)))\n (:hscopes ((:id . :x5.51.1) (:span 111 200)))\n (:identifiers (:sid . :s5.51) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101461@unknown@formal@none@1@S@Interestingly, the D-mib activity was found necessary for a subset of N signaling events that are distinct from those requiring the activity of the neur gene.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 44))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 24) (:start . 19)\n (:id . 45))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 33)\n (:start . 25) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 37) (:start . 34)\n (:id . 47))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 43) (:start . 38)\n (:id . 48))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 53)\n (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 57) (:start . 54)\n (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 59) (:start . 58)\n (:id . 51))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 66)\n (:start . 60) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n (:id . 53))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 71) (:start . 70)\n (:id . 54))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 81)\n (:start . 72) (:id . 55))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 88)\n (:start . 82) (:id . 56))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 93) (:start . 89)\n (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 97) (:start . 94)\n (:id . 58))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 106)\n (:start . 98) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 111) (:start . 107)\n (:id . 60))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 117)\n (:start . 112) (:id . 61))\n ((:tag . "VBG") (:stem . "require") (:form . "requiring") (:end . 127)\n (:start . 118) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n (:id . 63))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 140)\n (:start . 132) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 143) (:start . 141)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 147) (:start . 144)\n (:id . 66))\n ((:tag . "NN") (:stem . "neur") (:form . "neur") (:end . 152) (:start . 148)\n (:id . 67))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 157) (:start . 153)\n (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s5.52) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101462@unknown@formal@none@1@S@Nevertheless, the ectopic expression of Neur compensates for the loss of D-mib activity in the wing, indicating that Neur and D-mib have overlapping functions.@(((:tag . "RB") (:stem . "nevertheless") (:form . "Nevertheless") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "JJ") (:stem . "ectopic") (:form . "ectopic") (:end . 25)\n (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 36)\n (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 44) (:start . 40)\n (:id . 48))\n ((:tag . "NNS") (:stem . "compensate") (:form . "compensates") (:end . 56)\n (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 60) (:start . 57)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n (:id . 51))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 69) (:start . 65)\n (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n (:id . 53))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 78) (:start . 73)\n (:id . 54))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 87)\n (:start . 79) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n (:id . 57))\n ((:tag . "NN") (:stem . "wing") (:form . "wing") (:end . 99) (:start . 95)\n (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n (:id . 59))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 111)\n (:start . 101) (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 116) (:start . 112)\n (:id . 61))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 121) (:start . 117)\n (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n (:id . 63))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 131)\n (:start . 126) (:id . 64))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 136) (:start . 132)\n (:id . 65))\n ((:tag . "VBG") (:stem . "overlap") (:form . "overlapping") (:end . 148)\n (:start . 137) (:id . 66))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 158)\n (:start . 149) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n (:id . 68)))@@@1@27@((:hcues ((:id . :x5.53.1) (:span 101 116)))\n (:hscopes ((:id . :x5.53.1) (:span 101 158)))\n (:identifiers (:sid . :s5.53) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101463@unknown@formal@none@1@S@We conclude that D-mib and Neur are two structurally distinct proteins with similar molecular activities but distinct and complementary functions in Drosophila.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "conclude") (:form . "conclude") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 22) (:start . 17)\n (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 31) (:start . 27)\n (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n (:id . 48))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 39) (:start . 36)\n (:id . 49))\n ((:tag . "RB") (:stem . "structurally") (:form . "structurally") (:end . 52)\n (:start . 40) (:id . 50))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 61)\n (:start . 53) (:id . 51))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 70)\n (:start . 62) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 75) (:start . 71)\n (:id . 53))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 83)\n (:start . 76) (:id . 54))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 93)\n (:start . 84) (:id . 55))\n ((:tag . "NNS") (:stem . "activity") (:form . "activities") (:end . 104)\n (:start . 94) (:id . 56))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 108) (:start . 105)\n (:id . 57))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 117)\n (:start . 109) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 121) (:start . 118)\n (:id . 59))\n ((:tag . "JJ") (:stem . "complementary") (:form . "complementary")\n (:end . 135) (:start . 122) (:id . 60))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 145)\n (:start . 136) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 148) (:start . 146)\n (:id . 62))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 159)\n (:start . 149) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s5.54) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101464@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s5.55) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101465@unknown@formal@none@1@S@Isolation of D-mib Mutations@(((:tag . "NN") (:stem . "isolation") (:form . "Isolation") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n (:id . 43))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "NNPS") (:stem . "Mutation") (:form . "Mutations") (:end . 28)\n (:start . 19) (:id . 45)))@@@1@4@((:identifiers (:sid . :s5.56) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101466@unknown@formal@none@1@S@The closest Drosophila homolog of the vertebrate mib gene is the predicted gene CG5841, D-mib [18].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJS") (:stem . "close") (:form . "closest") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 22)\n (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 30)\n (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n (:id . 47))\n ((:tag . "NN") (:stem . "vertebrate") (:form . "vertebrate") (:end . 48)\n (:start . 38) (:id . 48))\n ((:tag . "NN") (:stem . "mib") (:form . "mib") (:end . 52) (:start . 49)\n (:id . 49))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 57) (:start . 53)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 60) (:start . 58)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n (:id . 52))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 74)\n (:start . 65) (:id . 53))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 79) (:start . 75)\n (:id . 54))\n ((:tag . "NN") (:stem . "cg5841") (:form . "CG5841") (:end . 86)\n (:start . 80) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n (:id . 56))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 93) (:start . 88)\n (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 95) (:start . 94)\n (:id . 58))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 97) (:start . 95)\n (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 98) (:start . 97)\n (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s5.57) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101467@unknown@formal@none@1@S@The D-mib mutations identified are shown in Figure 1.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "d-mib") (:form . "D-mib") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 19)\n (:start . 10) (:id . 44))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 30)\n (:start . 20) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 34) (:start . 31)\n (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 40) (:start . 35)\n (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 50)\n (:start . 44) (:id . 49))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 52) (:start . 51)\n (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 53) (:start . 52)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s5.58) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101468@unknown@formal@none@1@S@A P-element inserted into the 5? untranslated region of the D-mib gene was recently isolated (http://flypush.imgen.bcm.tmc.edu/pscreen/) (Figure 1A).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "p-element") (:form . "P-element") (:end . 11)\n (:start . 2) (:id . 43))\n ((:tag . "VBN") (:stem . "insert") (:form . "inserted") (:end . 20)\n (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 25) (:start . 21)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n (:id . 46))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 31) (:start . 30)\n (:id . 47))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 32) (:start . 31)\n (:id . 48))\n ((:tag . "JJ") (:stem . "untranslated") (:form . "untranslated") (:end . 45)\n (:start . 33) (:id . 49))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 52)\n (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n (:id . 52))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 65) (:start . 60)\n (:id . 53))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 70) (:start . 66)\n (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 74) (:start . 71)\n (:id . 55))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 83)\n (:start . 75) (:id . 56))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 92)\n (:start . 84) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 94) (:start . 93)\n (:id . 58))\n ((:tag . "NNP") (:stem . "http://flypush.imgen.bcm.tmc.edu/pscreen/")\n (:form . "http://flypush.imgen.bcm.tmc.edu/pscreen/") (:end . 135)\n (:start . 94) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 138) (:start . 137)\n (:id . 61))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 144)\n (:start . 138) (:id . 62))\n ((:tag . "NN") (:stem . "1a") (:form . "1A") (:end . 147) (:start . 145)\n (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s5.59) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101470@unknown@formal@none@1@S@Lethality was reverted by precise excision of the P-element, suggesting that insertion of this P-element is a D-mib mutation, referred to as D-mib1.@(((:tag . "NNP") (:stem . "Lethality") (:form . "Lethality") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 13) (:start . 10)\n (:id . 43))\n ((:tag . "VBN") (:stem . "revert") (:form . "reverted") (:end . 22)\n (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 25) (:start . 23)\n (:id . 45))\n ((:tag . "JJ") (:stem . "precise") (:form . "precise") (:end . 33)\n (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . "excision") (:form . "excision") (:end . 42)\n (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "NNP") (:stem . "P-element") (:form . "P-element") (:end . 59)\n (:start . 50) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n (:id . 51))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 71)\n (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 76) (:start . 72)\n (:id . 53))\n ((:tag . "NN") (:stem . "insertion") (:form . "insertion") (:end . 86)\n (:start . 77) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n (:id . 55))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 94) (:start . 90)\n (:id . 56))\n ((:tag . "NNP") (:stem . "P-element") (:form . "P-element") (:end . 104)\n (:start . 95) (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 107) (:start . 105)\n (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 109) (:start . 108)\n (:id . 59))\n ((:tag . "JJ") (:stem . "d-mib") (:form . "D-mib") (:end . 115)\n (:start . 110) (:id . 60))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 124)\n (:start . 116) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n (:id . 62))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 134)\n (:start . 126) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 137) (:start . 135)\n (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 140) (:start . 138)\n (:id . 65))\n ((:tag . "NN") (:stem . "d-mib1") (:form . "D-mib1") (:end . 147)\n (:start . 141) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n (:id . 67)))@@@1@26@((:hcues ((:id . :x5.61.1) (:span 61 71)))\n (:hscopes ((:id . :x5.61.1) (:span 61 147)))\n (:identifiers (:sid . :s5.61) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101471@unknown@formal@none@1@S@A 13.6-kb deletion that removes the entire D-mib coding region was selected by imprecise excision of this P-element.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "13.6-kb") (:form . "13.6-kb") (:end . 9)\n (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 18)\n (:start . 10) (:id . 44))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "remove") (:form . "removes") (:end . 31)\n (:start . 24) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n (:id . 47))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 42)\n (:start . 36) (:id . 48))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 48) (:start . 43)\n (:id . 49))\n ((:tag . "VBG") (:stem . "cod") (:form . "coding") (:end . 55) (:start . 49)\n (:id . 50))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 62)\n (:start . 56) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 66) (:start . 63)\n (:id . 52))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 75)\n (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 78) (:start . 76)\n (:id . 54))\n ((:tag . "JJ") (:stem . "imprecise") (:form . "imprecise") (:end . 88)\n (:start . 79) (:id . 55))\n ((:tag . "NN") (:stem . "excision") (:form . "excision") (:end . 97)\n (:start . 89) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n (:id . 57))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 105) (:start . 101)\n (:id . 58))\n ((:tag . "NNP") (:stem . "P-element") (:form . "P-element") (:end . 115)\n (:start . 106) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s5.62) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101472@unknown@formal@none@1@S@This deletion represents a null allele of D-mib and was named D-mib2.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 24)\n (:start . 14) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n (:id . 45))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 31) (:start . 27)\n (:id . 46))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 38)\n (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n (:id . 48))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 47) (:start . 42)\n (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 55) (:start . 52)\n (:id . 51))\n ((:tag . "VBN") (:stem . "name") (:form . "named") (:end . 61) (:start . 56)\n (:id . 52))\n ((:tag . "NN") (:stem . "d-mib2") (:form . "D-mib2") (:end . 68)\n (:start . 62) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s5.63) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101473@unknown@formal@none@1@S@This deletion also deletes the 3? flanking RpS31 gene (Figure 1A).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "delete") (:form . "deletes") (:end . 26)\n (:start . 19) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 32) (:start . 31)\n (:id . 47))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 33) (:start . 32)\n (:id . 48))\n ((:tag . "VBG") (:stem . "flank") (:form . "flanking") (:end . 42)\n (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "rps31") (:form . "RpS31") (:end . 48) (:start . 43)\n (:id . 50))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 53) (:start . 49)\n (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n (:id . 52))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 61)\n (:start . 55) (:id . 53))\n ((:tag . "NN") (:stem . "1a") (:form . "1A") (:end . 64) (:start . 62)\n (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 65) (:start . 64)\n (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s5.64) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101474@unknown@formal@none@1@S@The D-mib1 and D-mib2mutant alleles did not complement the l(3)72CdaJ12 and l(3)72CdaI5 lethal mutations that have been mapped to the same cytological interval as the D-mib gene [35].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "d-mib1") (:form . "D-mib1") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "JJ") (:stem . "d-mib2mutant") (:form . "D-mib2mutant") (:end . 27)\n (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "allele") (:form . "alleles") (:end . 35)\n (:start . 28) (:id . 46))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 39) (:start . 36)\n (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 43) (:start . 40)\n (:id . 48))\n ((:tag . "VB") (:stem . "complement") (:form . "complement") (:end . 54)\n (:start . 44) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n (:id . 50))\n ((:tag . "CD") (:stem . "l(3)72CdaJ12") (:form . "l(3)72CdaJ12") (:end . 71)\n (:start . 59) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n (:id . 52))\n ((:tag . "CD") (:stem . "l(3)72CdaI5") (:form . "l(3)72CdaI5") (:end . 87)\n (:start . 76) (:id . 53))\n ((:tag . "JJ") (:stem . "lethal") (:form . "lethal") (:end . 94)\n (:start . 88) (:id . 54))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 104)\n (:start . 95) (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 109) (:start . 105)\n (:id . 56))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 114) (:start . 110)\n (:id . 57))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 119) (:start . 115)\n (:id . 58))\n ((:tag . "VBN") (:stem . "map") (:form . "mapped") (:end . 126)\n (:start . 120) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 129) (:start . 127)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n (:id . 61))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 138) (:start . 134)\n (:id . 62))\n ((:tag . "JJ") (:stem . "cytological") (:form . "cytological") (:end . 150)\n (:start . 139) (:id . 63))\n ((:tag . "NN") (:stem . "interval") (:form . "interval") (:end . 159)\n (:start . 151) (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 162) (:start . 160)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n (:id . 66))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 172)\n (:start . 167) (:id . 67))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 177) (:start . 173)\n (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 179) (:start . 178)\n (:id . 69))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 181) (:start . 179)\n (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 182) (:start . 181)\n (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n (:id . 72)))@@@1@31@((:ncues ((:id . :x5.65.1) (:span 40 43)))\n (:nscopes ((:id . :x5.65.1) (:span 40 182)))\n (:identifiers (:sid . :s5.65) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101475@unknown@formal@none@1@S@This indicates that these two lethal mutations are D-mib mutant alleles, and they were therefore renamed D-mib3 and D-mib4, respectively.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 14)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 25) (:start . 20)\n (:id . 45))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 29) (:start . 26)\n (:id . 46))\n ((:tag . "JJ") (:stem . "lethal") (:form . "lethal") (:end . 36)\n (:start . 30) (:id . 47))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 46)\n (:start . 37) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 50) (:start . 47)\n (:id . 49))\n ((:tag . "JJ") (:stem . "d-mib") (:form . "D-mib") (:end . 56) (:start . 51)\n (:id . 50))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 63)\n (:start . 57) (:id . 51))\n ((:tag . "NNS") (:stem . "allele") (:form . "alleles") (:end . 71)\n (:start . 64) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n (:id . 54))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 81) (:start . 77)\n (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 86) (:start . 82)\n (:id . 56))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 96)\n (:start . 87) (:id . 57))\n ((:tag . "VBN") (:stem . "rename") (:form . "renamed") (:end . 104)\n (:start . 97) (:id . 58))\n ((:tag . "NN") (:stem . "d-mib3") (:form . "D-mib3") (:end . 111)\n (:start . 105) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n (:id . 60))\n ((:tag . "NN") (:stem . "d-mib4") (:form . "D-mib4") (:end . 122)\n (:start . 116) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n (:id . 62))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 136)\n (:start . 124) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n (:id . 64)))@@@1@23@((:hcues ((:id . :x5.66.1) (:span 5 19)))\n (:hscopes ((:id . :x5.66.1) (:span 5 71)))\n (:identifiers (:sid . :s5.66) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101476@unknown@formal@none@1@S@The D-mib1 and D-mib3 mutations behave as genetic null alleles (see Materials and Methods).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "d-mib1") (:form . "D-mib1") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "d-mib3") (:form . "D-mib3") (:end . 21)\n (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 31)\n (:start . 22) (:id . 46))\n ((:tag . "VBP") (:stem . "behave") (:form . "behave") (:end . 38)\n (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 41) (:start . 39)\n (:id . 48))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 49)\n (:start . 42) (:id . 49))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 54) (:start . 50)\n (:id . 50))\n ((:tag . "NNS") (:stem . "allele") (:form . "alleles") (:end . 62)\n (:start . 55) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 64) (:start . 63)\n (:id . 52))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 67) (:start . 64)\n (:id . 53))\n ((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 77)\n (:start . 68) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n (:id . 55))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 89)\n (:start . 82) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 90) (:start . 89)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s5.67) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101477@unknown@formal@none@1@S@In contrast, D-mib4 is a partial loss-of-function allele because flies trans-heterozygous for D-mib4 and any other D-mib null alleles are viable.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "NNP") (:stem . "D-mib4") (:form . "D-mib4") (:end . 19)\n (:start . 13) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 22) (:start . 20)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 24) (:start . 23)\n (:id . 47))\n ((:tag . "JJ") (:stem . "partial") (:form . "partial") (:end . 32)\n (:start . 25) (:id . 48))\n ((:tag . "JJ") (:stem . "loss-of-function") (:form . "loss-of-function")\n (:end . 49) (:start . 33) (:id . 49))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 56)\n (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 64)\n (:start . 57) (:id . 51))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 70) (:start . 65)\n (:id . 52))\n ((:tag . "JJ") (:stem . "trans-heterozygous") (:form . "trans-heterozygous")\n (:end . 89) (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 93) (:start . 90)\n (:id . 54))\n ((:tag . "NN") (:stem . "d-mib4") (:form . "D-mib4") (:end . 100)\n (:start . 94) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 104) (:start . 101)\n (:id . 56))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 108) (:start . 105)\n (:id . 57))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 114)\n (:start . 109) (:id . 58))\n ((:tag . "JJ") (:stem . "d-mib") (:form . "D-mib") (:end . 120)\n (:start . 115) (:id . 59))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 125) (:start . 121)\n (:id . 60))\n ((:tag . "NNS") (:stem . "allele") (:form . "alleles") (:end . 133)\n (:start . 126) (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 137) (:start . 134)\n (:id . 62))\n ((:tag . "JJ") (:stem . "viable") (:form . "viable") (:end . 144)\n (:start . 138) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s5.68) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101478@unknown@formal@none@1@S@These four mutations identify the CG5841 gene as D-mib by the following evidence.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . 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"following") (:end . 71)\n (:start . 62) (:id . 53))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 80)\n (:start . 72) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s5.69) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101480@unknown@formal@none@1@S@Second, genomic sequencing of the D-mib3 allele revealed the presence of a stop codon at position 258 (Figure 1B).@(((:tag . "JJ") (:stem . "second") (:form . "Second") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 15)\n (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "sequencing") (:form . "sequencing") (:end . 26)\n (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . 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"at") (:form . "at") (:end . 88) (:start . 86)\n (:id . 57))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 97)\n (:start . 89) (:id . 58))\n ((:tag . "CD") (:stem . "258") (:form . "258") (:end . 101) (:start . 98)\n (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n (:id . 60))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 109)\n (:start . 103) (:id . 61))\n ((:tag . "NN") (:stem . "1b") (:form . "1B") (:end . 112) (:start . 110)\n (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s5.71) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101481@unknown@formal@none@1@S@This allele is therefore predicted to produce a truncated protein devoid of the catalytic RING domain, consistent with D-mib3 being a null allele.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 24)\n (:start . 15) (:id . 45))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 34)\n (:start . 25) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n (:id . 47))\n ((:tag . "VB") (:stem . "produce") (:form . "produce") (:end . 45)\n (:start . 38) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 47) (:start . 46)\n (:id . 49))\n ((:tag . "VBN") (:stem . "truncate") (:form . "truncated") (:end . 57)\n (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 65)\n (:start . 58) (:id . 51))\n ((:tag . "JJ") (:stem . "devoid") (:form . "devoid") (:end . 72)\n (:start . 66) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n (:id . 54))\n ((:tag . "JJ") (:stem . "catalytic") (:form . "catalytic") (:end . 89)\n (:start . 80) (:id . 55))\n ((:tag . "NN") (:stem . "ring") (:form . "RING") (:end . 94) (:start . 90)\n (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 101)\n (:start . 95) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n (:id . 58))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 113)\n (:start . 103) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 118) (:start . 114)\n (:id . 60))\n ((:tag . "NNP") (:stem . "D-mib3") (:form . "D-mib3") (:end . 125)\n (:start . 119) (:id . 61))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 131) (:start . 126)\n (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 133) (:start . 132)\n (:id . 63))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 138) (:start . 134)\n (:id . 64))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 145)\n (:start . 139) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x5.72.1) (:span 25 34)))\n (:hscopes ((:id . :x5.72.1) (:span 0 145)))\n (:identifiers (:sid . :s5.72) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101482@unknown@formal@none@1@S@Genomic sequencing of the D-mib4 allele showed that this mutation is associated with a valine-to-methionine substitution at a conserved position in the second Mib repeat (Figure 1B).@(((:tag . "JJ") (:stem . "genomic") (:form . "Genomic") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "sequencing") (:form . "sequencing") (:end . 18)\n (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "NN") (:stem . "d-mib4") (:form . "D-mib4") (:end . 32)\n (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . 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"(") (:end . 171) (:start . 170)\n (:id . 67))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 177)\n (:start . 171) (:id . 68))\n ((:tag . "NN") (:stem . "1b") (:form . "1B") (:end . 180) (:start . 178)\n (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 181) (:start . 180)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s5.73) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101483@unknown@formal@none@1@S@Third, Western blot analysis showed that the D-mib protein was not detectable in imaginal disc and brain complex extracts prepared from homozygous D-mib1 and D-mib1/D-mib2 larvae (Figure 1C and C?).@(((:tag . "JJ") (:stem . "third") (:form . "Third") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "JJ") (:stem . 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(:end . 196) (:start . 195)\n (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 197) (:start . 196)\n (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n (:id . 76)))@@@1@35@((:ncues ((:id . :x5.74.1) (:span 63 66)))\n (:nscopes ((:id . :x5.74.1) (:span 63 178)))\n (:identifiers (:sid . :s5.74) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101484@unknown@formal@none@1@S@Fourth, the leaky, GAL4-independent expression of a UAS-D-mib transgene fully rescued the lethality of D-mib1/D-mib2 flies (data not shown; see also Figure 1H).@(((:tag . "NNP") (:stem . "Fourth") (:form . "Fourth") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n (:id . 44))\n ((:tag . "JJ") (:stem . "leaky") (:form . 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"the") (:end . 89) (:start . 86)\n (:id . 55))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 99)\n (:start . 90) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n (:id . 57))\n ((:tag . "NN") (:stem . "d-mib1/d-mib2") (:form . "D-mib1/D-mib2")\n (:end . 116) (:start . 103) (:id . 58))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 122) (:start . 117)\n (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 124) (:start . 123)\n (:id . 60))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 128)\n (:start . 124) (:id . 61))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 132) (:start . 129)\n (:id . 62))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 138)\n (:start . 133) (:id . 63))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 139) (:start . 138)\n (:id . 64))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 143) (:start . 140)\n (:id . 65))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 148) (:start . 144)\n (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 155)\n (:start . 149) (:id . 67))\n ((:tag . "NN") (:stem . "1h") (:form . "1H") (:end . 158) (:start . 156)\n (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 159) (:start . 158)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n (:id . 70)))@@@1@29@((:ncues ((:id . :x5.75.1) (:span 129 132)))\n (:nscopes ((:id . :x5.75.1) (:span 123 138)))\n (:identifiers (:sid . :s5.75) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101485@unknown@formal@none@1@S@Thus, our analysis identified both complete and partial D-mib loss-of-function alleles.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 9) (:start . 6)\n (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 18)\n (:start . 10) (:id . 45))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 29)\n (:start . 19) (:id . 46))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 34) (:start . 30)\n (:id . 47))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 43)\n (:start . 35) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n (:id . 49))\n ((:tag . "JJ") (:stem . "partial") (:form . "partial") (:end . 55)\n (:start . 48) (:id . 50))\n ((:tag . "JJ") (:stem . "d-mib") (:form . "D-mib") (:end . 61) (:start . 56)\n (:id . 51))\n ((:tag . "NN") (:stem . "loss-of-function") (:form . "loss-of-function")\n (:end . 78) (:start . 62) (:id . 52))\n ((:tag . "NNS") (:stem . "allele") (:form . "alleles") (:end . 86)\n (:start . 79) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s5.76) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101486@unknown@formal@none@1@S@Molecular and Genetic Characterization of D-mib Mutations@(((:tag . "JJ") (:stem . "molecular") (:form . "Molecular") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 13) (:start . 10)\n (:id . 43))\n ((:tag . "JJ") (:stem . "genetic") (:form . "Genetic") (:end . 21)\n (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "characterization") (:form . "Characterization")\n (:end . 38) (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n (:id . 46))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 47) (:start . 42)\n (:id . 47))\n ((:tag . "NNPS") (:stem . "Mutation") (:form . "Mutations") (:end . 57)\n (:start . 48) (:id . 48)))@@@1@7@((:identifiers (:sid . :s5.77) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5101487@unknown@formal@none@1@S@(A) Molecular map of the D-mib locus showing the position of the P-element inserted into the 5? untranslated region (allele D-mib1) and the 13.6 kb deletion that removes the D-mib and the RpS31 genes (allele D-mib2).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "molecular") (:form . "Molecular") (:end . 13)\n (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "map") (:form . "map") (:end . 17) (:start . 14)\n (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n (:id . 48))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 30) (:start . 25)\n (:id . 49))\n ((:tag . "NN") (:stem . "locus") (:form . "locus") (:end . 36) (:start . 31)\n (:id . 50))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 44)\n (:start . 37) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n (:id . 52))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 57)\n (:start . 49) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n (:id . 55))\n ((:tag . "NN") (:stem . "p-element") (:form . "P-element") (:end . 74)\n (:start . 65) (:id . 56))\n ((:tag . "VBN") (:stem . "insert") (:form . "inserted") (:end . 83)\n (:start . 75) (:id . 57))\n ((:tag . "IN") (:stem . "into") (:form . 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"the") (:form . "the") (:end . 139) (:start . 136)\n (:id . 69))\n ((:tag . "CD") (:stem . "13.6") (:form . "13.6") (:end . 144) (:start . 140)\n (:id . 70))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 147) (:start . 145)\n (:id . 71))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 156)\n (:start . 148) (:id . 72))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 161) (:start . 157)\n (:id . 73))\n ((:tag . "VBZ") (:stem . "remove") (:form . "removes") (:end . 169)\n (:start . 162) (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 173) (:start . 170)\n (:id . 75))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 179)\n (:start . 174) (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 183) (:start . 180)\n (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 187) (:start . 184)\n (:id . 78))\n ((:tag . "NN") (:stem . "rps31") (:form . "RpS31") (:end . 193)\n (:start . 188) (:id . 79))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 199)\n (:start . 194) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 201) (:start . 200)\n (:id . 81))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 207)\n (:start . 201) (:id . 82))\n ((:tag . "NN") (:stem . "d-mib2") (:form . "D-mib2") (:end . 214)\n (:start . 208) (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 215) (:start . 214)\n (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n (:id . 85)))@@@1@44@((:identifiers (:sid . :s5.78) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101488@unknown@formal@none@1@S@Transcribed regions are indicated with arrows, and exons are indicated with boxes.@(((:tag . "VBN") (:stem . "transcribe") (:form . "Transcribed") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 19)\n (:start . 12) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 23) (:start . 20)\n (:id . 44))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 33)\n (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 38) (:start . 34)\n (:id . 46))\n ((:tag . "NNS") (:stem . "arrow") (:form . "arrows") (:end . 45)\n (:start . 39) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n (:id . 49))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 56) (:start . 51)\n (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 60) (:start . 57)\n (:id . 51))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 70)\n (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 75) (:start . 71)\n (:id . 53))\n ((:tag . "NNS") (:stem . "box") (:form . "boxes") (:end . 81) (:start . 76)\n (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s5.79) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101490@unknown@formal@none@1@S@(B) Domain composition of D-mib and D. rerio Mib.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Domain") (:form . "Domain") (:end . 10)\n (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "composition") (:form . "composition") (:end . 22)\n (:start . 11) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n (:id . 47))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 31) (:start . 26)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n (:id . 49))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 38) (:start . 36)\n (:id . 50))\n ((:tag . "NNP") (:stem . "rerio") (:form . "rerio") (:end . 44) (:start . 39)\n (:id . 51))\n ((:tag . "NNP") (:stem . "Mib") (:form . "Mib") (:end . 48) (:start . 45)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s5.81) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101491@unknown@formal@none@1@S@Both proteins show identical domain organization.@(((:tag . "DT") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 28)\n (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 35)\n (:start . 29) (:id . 46))\n ((:tag . "NN") (:stem . "organization") (:form . "organization") (:end . 48)\n (:start . 36) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n (:id . 48)))@@@1@7@((:identifiers (:sid . :s5.82) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101492@unknown@formal@none@1@S@D-mib has an N-terminal ZZ zinc finger flanked on either side by a Mib/HERC2 (M-H) domain, followed by two Mib repeats, six ankyrin repeats, two atypical RING domains, and a C-terminal protypical RING that has been associated with catalytic E3 ubiquitin ligase activity.@(((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 12) (:start . 10)\n (:id . 44))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 23)\n (:start . 13) (:id . 45))\n ((:tag . "NNP") (:stem . "ZZ") (:form . "ZZ") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "NN") (:stem . "zinc") (:form . "zinc") (:end . 31) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 38)\n (:start . 32) (:id . 48))\n ((:tag . "VBN") (:stem . "flank") (:form . "flanked") (:end . 46)\n (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 49) (:start . 47)\n (:id . 50))\n ((:tag . "DT") (:stem . "either") (:form . "either") (:end . 56)\n (:start . 50) (:id . 51))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 61) (:start . 57)\n (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 64) (:start . 62)\n (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 66) (:start . 65)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Mib/HERC2") (:form . "Mib/HERC2") (:end . 76)\n (:start . 67) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n (:id . 56))\n ((:tag . "NNP") (:stem . "M-H") (:form . "M-H") (:end . 81) (:start . 78)\n (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 82) (:start . 81)\n (:id . 58))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 89)\n (:start . 83) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n (:id . 60))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 99)\n (:start . 91) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 102) (:start . 100)\n (:id . 62))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 106) (:start . 103)\n (:id . 63))\n ((:tag . "NNP") (:stem . "Mib") (:form . "Mib") (:end . 110) (:start . 107)\n (:id . 64))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 118)\n (:start . 111) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n (:id . 66))\n ((:tag . "CD") (:stem . "six") (:form . "six") (:end . 123) (:start . 120)\n (:id . 67))\n ((:tag . "NN") (:stem . "ankyrin") (:form . "ankyrin") (:end . 131)\n (:start . 124) (:id . 68))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 139)\n (:start . 132) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n (:id . 70))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 144) (:start . 141)\n (:id . 71))\n ((:tag . "JJ") (:stem . "atypical") (:form . "atypical") (:end . 153)\n (:start . 145) (:id . 72))\n ((:tag . "NN") (:stem . "ring") (:form . "RING") (:end . 158) (:start . 154)\n (:id . 73))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 166)\n (:start . 159) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 171) (:start . 168)\n (:id . 76))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 173) (:start . 172)\n (:id . 77))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 184)\n (:start . 174) (:id . 78))\n ((:tag . "JJ") (:stem . "protypical") (:form . "protypical") (:end . 195)\n (:start . 185) (:id . 79))\n ((:tag . "NN") (:stem . "ring") (:form . "RING") (:end . 200) (:start . 196)\n (:id . 80))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 205) (:start . 201)\n (:id . 81))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 209) (:start . 206)\n (:id . 82))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 214) (:start . 210)\n (:id . 83))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 225)\n (:start . 215) (:id . 84))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 230) (:start . 226)\n (:id . 85))\n ((:tag . "JJ") (:stem . "catalytic") (:form . "catalytic") (:end . 240)\n (:start . 231) (:id . 86))\n ((:tag . "NN") (:stem . "e3") (:form . "E3") (:end . 243) (:start . 241)\n (:id . 87))\n ((:tag . "NN") (:stem . "ubiquitin") (:form . "ubiquitin") (:end . 253)\n (:start . 244) (:id . 88))\n ((:tag . "NN") (:stem . "ligase") (:form . "ligase") (:end . 260)\n (:start . 254) (:id . 89))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 269)\n (:start . 261) (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 270) (:start . 269)\n (:id . 91)))@@@1@50@((:identifiers (:sid . :s5.83) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101493@unknown@formal@none@1@S@The D-mib3 mutant allele is predicted to produce a truncated protein devoid of E3 ubiquitin ligase activity whereas the D-mib4 protein carries a mutation at a conserved position in the second Mib repeat.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "d-mib3") (:form . "D-mib3") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 17)\n (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 24)\n (:start . 18) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 37)\n (:start . 28) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n (:id . 48))\n ((:tag . "VB") (:stem . "produce") (:form . "produce") (:end . 48)\n (:start . 41) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 50) (:start . 49)\n (:id . 50))\n ((:tag . "VBN") (:stem . "truncate") (:form . "truncated") (:end . 60)\n (:start . 51) (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 68)\n (:start . 61) (:id . 52))\n ((:tag . "JJ") (:stem . "devoid") (:form . "devoid") (:end . 75)\n (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n (:id . 54))\n ((:tag . "NN") (:stem . "e3") (:form . "E3") (:end . 81) (:start . 79)\n (:id . 55))\n ((:tag . "NN") (:stem . "ubiquitin") (:form . "ubiquitin") (:end . 91)\n (:start . 82) (:id . 56))\n ((:tag . "NN") (:stem . "ligase") (:form . "ligase") (:end . 98)\n (:start . 92) (:id . 57))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 107)\n (:start . 99) (:id . 58))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 115)\n (:start . 108) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n (:id . 60))\n ((:tag . "NN") (:stem . "d-mib4") (:form . "D-mib4") (:end . 126)\n (:start . 120) (:id . 61))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 134)\n (:start . 127) (:id . 62))\n ((:tag . "VBZ") (:stem . "carry") (:form . "carries") (:end . 142)\n (:start . 135) (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 144) (:start . 143)\n (:id . 64))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 153)\n (:start . 145) (:id . 65))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 156) (:start . 154)\n (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 158) (:start . 157)\n (:id . 67))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 168)\n (:start . 159) (:id . 68))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 177)\n (:start . 169) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 180) (:start . 178)\n (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 184) (:start . 181)\n (:id . 71))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 191)\n (:start . 185) (:id . 72))\n ((:tag . "NNP") (:stem . "Mib") (:form . "Mib") (:end . 195) (:start . 192)\n (:id . 73))\n ((:tag . "NN") (:stem . "repeat") (:form . "repeat") (:end . 202)\n (:start . 196) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n (:id . 75)))@@@1@34@((:hcues ((:id . :x5.84.1) (:span 28 37)))\n (:hscopes ((:id . :x5.84.1) (:span 0 107)))\n (:identifiers (:sid . :s5.84) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101494@unknown@formal@none@1@S@(C and C?) Western blot analysis of D-mib (C).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 6) (:start . 3)\n (:id . 44))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 8) (:start . 7)\n (:id . 45))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 9) (:start . 8) (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 10) (:start . 9)\n (:id . 47))\n ((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 18)\n (:start . 11) (:id . 48))\n ((:tag . "NN") (:stem . "blot") (:form . "blot") (:end . 23) (:start . 19)\n (:id . 49))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 32)\n (:start . 24) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n (:id . 51))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 41) (:start . 36)\n (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 43) (:start . 42)\n (:id . 53))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 44) (:start . 43)\n (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 46) (:start . 45)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s5.85) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101495@unknown@formal@none@1@S@The endogenous D-mib protein (predicted size: 130 kDa) was detected in S2 cells (lane 2) and in imaginal discs from wild-type larvae (lane 3) but was not detectable in homozygous D-mib1 (lane 4) and D-mib1/D-mib3 (lane 5) third instar larvae.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 20) (:start . 15)\n (:id . 44))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 28)\n (:start . 21) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n (:id . 46))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 39)\n (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 44) (:start . 40)\n (:id . 48))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 45) (:start . 44)\n (:id . 49))\n ((:tag . "CD") (:stem . "130") (:form . "130") (:end . 49) (:start . 46)\n (:id . 50))\n ((:tag . "NN") (:stem . "kda") (:form . "kDa") (:end . 53) (:start . 50)\n (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 54) (:start . 53)\n (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 58) (:start . 55)\n (:id . 53))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 67)\n (:start . 59) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 70) (:start . 68)\n (:id . 55))\n ((:tag . "NN") (:stem . "s2") (:form . "S2") (:end . 73) (:start . 71)\n (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 79) (:start . 74)\n (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 81) (:start . 80)\n (:id . 58))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 85) (:start . 81)\n (:id . 59))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 87) (:start . 86)\n (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 88) (:start . 87)\n (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 95) (:start . 93)\n (:id . 63))\n ((:tag . "JJ") (:stem . "imaginal") (:form . "imaginal") (:end . 104)\n (:start . 96) (:id . 64))\n ((:tag . "NNS") (:stem . "disc") (:form . "discs") (:end . 110)\n (:start . 105) (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 115) (:start . 111)\n (:id . 66))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 125)\n (:start . 116) (:id . 67))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 132)\n (:start . 126) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n (:id . 69))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 138) (:start . 134)\n (:id . 70))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 140) (:start . 139)\n (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 141) (:start . 140)\n (:id . 72))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 145) (:start . 142)\n (:id . 73))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 149) (:start . 146)\n (:id . 74))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 153) (:start . 150)\n (:id . 75))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 164)\n (:start . 154) (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 167) (:start . 165)\n (:id . 77))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 178)\n (:start . 168) (:id . 78))\n ((:tag . "NN") (:stem . "d-mib1") (:form . "D-mib1") (:end . 185)\n (:start . 179) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 187) (:start . 186)\n (:id . 80))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 191) (:start . 187)\n (:id . 81))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 193) (:start . 192)\n (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 194) (:start . 193)\n (:id . 83))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 198) (:start . 195)\n (:id . 84))\n ((:tag . "NNP") (:stem . "D-mib1/D-mib3") (:form . "D-mib1/D-mib3")\n (:end . 212) (:start . 199) (:id . 85))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 214) (:start . 213)\n (:id . 86))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 218) (:start . 214)\n (:id . 87))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 220) (:start . 219)\n (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 221) (:start . 220)\n (:id . 89))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 227)\n (:start . 222) (:id . 90))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 234)\n (:start . 228) (:id . 91))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 241)\n (:start . 235) (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 242) (:start . 241)\n (:id . 93)))@@@1@52@((:ncues ((:id . :x5.86.1) (:span 150 153)))\n (:nscopes ((:id . :x5.86.1) (:span 150 241)))\n (:identifiers (:sid . :s5.86) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101496@unknown@formal@none@1@S@The D-mib protein produced in transfected S2 cells from the cDNA used in this study (lane 1) runs exactly as endogenous D-mib (lane 2).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "d-mib") (:form . "D-mib") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 17)\n (:start . 10) (:id . 44))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 26)\n (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 41)\n (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "s2") (:form . "S2") (:end . 44) (:start . 42)\n (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 50) (:start . 45)\n (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 55) (:start . 51)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n (:id . 51))\n ((:tag . "NN") (:stem . "cdna") (:form . "cDNA") (:end . 64) (:start . 60)\n (:id . 52))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 69) (:start . 65)\n (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n (:id . 54))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 77) (:start . 73)\n (:id . 55))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 83) (:start . 78)\n (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n (:id . 57))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 89) (:start . 85)\n (:id . 58))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 91) (:start . 90)\n (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 92) (:start . 91)\n (:id . 60))\n ((:tag . "VBZ") (:stem . "run") (:form . "runs") (:end . 97) (:start . 93)\n (:id . 61))\n ((:tag . "RB") (:stem . "exactly") (:form . "exactly") (:end . 105)\n (:start . 98) (:id . 62))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 108) (:start . 106)\n (:id . 63))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 119)\n (:start . 109) (:id . 64))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 125)\n (:start . 120) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 127) (:start . 126)\n (:id . 66))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 131) (:start . 127)\n (:id . 67))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 133) (:start . 132)\n (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 134) (:start . 133)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s5.87) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101497@unknown@formal@none@1@S@Panel C? shows a Red Ponceau staining of the gel with the same protein samples as in panel C.@(((:tag . "NNP") (:stem . "Panel") (:form . "Panel") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 7) (:start . 6)\n (:id . 43))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Red") (:form . "Red") (:end . 20) (:start . 17)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Ponceau") (:form . "Ponceau") (:end . 28)\n (:start . 21) (:id . 48))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 37)\n (:start . 29) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n (:id . 51))\n ((:tag . "NN") (:stem . "gel") (:form . "gel") (:end . 48) (:start . 45)\n (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 53) (:start . 49)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n (:id . 54))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 62) (:start . 58)\n (:id . 55))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 70)\n (:start . 63) (:id . 56))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 78)\n (:start . 71) (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n (:id . 59))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 90) (:start . 85)\n (:id . 60))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 92) (:start . 91)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s5.88) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101498@unknown@formal@none@1@S@(D–H) Wings from wild-type (D), D-mib1 (E), SerRX82/Serrev6.1 (F), D-mib2/D-mib4 (G), and UAS-D-mib2/+; D-mib1/D-mib2 flies (H).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D–H") (:form . "D–H") (:end . 4) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NNS") (:stem . "wing") (:form . "Wings") (:end . 11) (:start . 6)\n (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 16) (:start . 12)\n (:id . 46))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 26)\n (:start . 17) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 28) (:start . 27)\n (:id . 48))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 29) (:start . 28)\n (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 30) (:start . 29)\n (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n (:id . 51))\n ((:tag . "NNP") (:stem . "D-mib1") (:form . "D-mib1") (:end . 38)\n (:start . 32) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n (:id . 53))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 41) (:start . 40)\n (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 42) (:start . 41)\n (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n (:id . 56))\n ((:tag . "NNP") (:stem . 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(:end . 141) (:start . 140)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s5.107) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101517@unknown@formal@none@1@S@In contrast, a complete loss of Ser signaling had no effect on bristle density (Figure 1K).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 14) (:start . 13)\n (:id . 45))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 23)\n (:start . 15) (:id . 46))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 28) (:start . 24)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Ser") (:form . 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(:end . 268) (:start . 267)\n (:id . 96)))@@@1@55@((:identifiers (:sid . :s5.109) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101520@unknown@formal@none@1@S@Together, these observations suggest that D-mib regulates Dl signaling in several developmental contexts.@(((:tag . "RB") (:stem . "together") (:form . "Together") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 15) (:start . 10)\n (:id . 44))\n ((:tag . "NNS") (:stem . "observation") (:form . "observations") (:end . 28)\n (:start . 16) (:id . 45))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 36)\n (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 41) (:start . 37)\n (:id . 47))\n ((:tag . "NNP") (:stem . "D-mib") (:form . 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(:end . 105) (:start . 104)\n (:id . 56)))@@@1@15@((:hcues ((:id . :x5.111.1) (:span 29 36)))\n (:hscopes ((:id . :x5.111.1) (:span 29 104)))\n (:identifiers (:sid . :s5.111) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101521@unknown@formal@none@1@S@Consistent with this conclusion, we have shown that D-mib binds Dl and promotes Dl signaling and that overexpression of D-mib down-regulates the accumulation of Dl at the cell surface (E. C. Lai, F. Roegiers, X. Qin, R. Le Borgne, F. Schweisguth, et al., unpublished data).@(((:tag . "JJ") (:stem . "consistent") (:form . "Consistent") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 15) (:start . 11)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 20) (:start . 16)\n (:id . 44))\n ((:tag . "NN") (:stem . "conclusion") (:form . "conclusion") (:end . 31)\n (:start . 21) (:id . 45))\n ((:tag . 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"[") (:end . 120) (:start . 119)\n (:id . 63))\n ((:tag . "CD") (:stem . "8,9,42,43") (:form . "8,9,42,43") (:end . 129)\n (:start . 120) (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 130) (:start . 129)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s5.125) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101535@unknown@formal@none@1@S@N then regulates the expression of the vestigial and wingless (wg) genes that cooperate to promote growth of the wing pouch.@(((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 6) (:start . 2)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "regulate") (:form . "regulates") (:end . 16)\n (:start . 7) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . 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(:end . 124) (:start . 123)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s5.126) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101536@unknown@formal@none@1@S@N also regulates expression of the cut gene in margin cells [44].@(((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 6) (:start . 2)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "regulate") (:form . "regulates") (:end . 16)\n (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 27)\n (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "NN") (:stem . "cut") (:form . "cut") (:end . 38) (:start . 35)\n (:id . 48))\n ((:tag . "NN") (:stem . "gene") (:form . 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(:end . 65) (:start . 64)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s5.127) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101537@unknown@formal@none@1@S@Thus, loss of N signaling results in a reduction in size of the wing pouch accompanied by the loss of cut and wg expression along the D-V boundary.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 10) (:start . 6)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 45))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 15) (:start . 14)\n (:id . 46))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 25)\n (:start . 16) (:id . 47))\n ((:tag . "VBZ") (:stem . "result") (:form . 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"growth") (:end . 119)\n (:start . 113) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n (:id . 66))\n ((:tag . "NN") (:stem . "wing") (:form . "wing") (:end . 131) (:start . 127)\n (:id . 67))\n ((:tag . "NN") (:stem . "pouch") (:form . "pouch") (:end . 137)\n (:start . 132) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s5.131) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101541@unknown@formal@none@1@S@Interestingly, wing margin formation and expression of Cut are not affected by the complete loss of neur activity (Figure 2F and 2F?) [45].@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . 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"and") (:end . 128) (:start . 125)\n (:id . 64))\n ((:tag . "NN") (:stem . "2f") (:form . "2F") (:end . 131) (:start . 129)\n (:id . 65))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 132) (:start . 131)\n (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 135) (:start . 134)\n (:id . 68))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 137) (:start . 135)\n (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 138) (:start . 137)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n (:id . 71)))@@@1@30@((:ncues ((:id . :x5.132.1) (:span 63 66)))\n (:nscopes ((:id . :x5.132.1) (:span 15 113)))\n (:identifiers (:sid . :s5.132) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101542@unknown@formal@none@1@S@Similarly, loss of neur activity had no detectable effect on leg segmentation (data not shown) and vein determination [45], two processes shown here to depend on D-mib gene activity.@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n (:id . 45))\n ((:tag . "NN") (:stem . "neur") (:form . "neur") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "NN") (:stem . 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(:end . 182) (:start . 181)\n (:id . 77)))@@@1@36@((:ncues ((:id . :x5.133.1) (:span 84 87)) ((:id . :x5.133.2) (:span 37 39)))\n (:nscopes ((:id . :x5.133.1) (:span 78 94))\n ((:id . :x5.133.2) (:span 37 77)))\n (:identifiers (:sid . :s5.133) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101543@unknown@formal@none@1@S@We therefore conclude that D-mib and neur have distinct and complementary functions in Drosophila.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . "VBP") (:stem . "conclude") (:form . "conclude") (:end . 21)\n (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n (:id . 45))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 32) (:start . 27)\n (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n (:id . 47))\n ((:tag . "NN") (:stem . "neur") (:form . "neur") (:end . 41) (:start . 37)\n (:id . 48))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 46) (:start . 42)\n (:id . 49))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 55)\n (:start . 47) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n (:id . 51))\n ((:tag . "JJ") (:stem . "complementary") (:form . "complementary")\n (:end . 73) (:start . 60) (:id . 52))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 83)\n (:start . 74) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 97)\n (:start . 87) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s5.134) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101544@unknown@formal@none@1@S@D-mib Co-Localizes with Dl and Ser at the Apical Cortex@(((:tag . "JJ") (:stem . "d-mib") (:form . "D-mib") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Co-Localiz") (:form . "Co-Localizes") (:end . 18)\n (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 23) (:start . 19)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 26) (:start . 24)\n (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 37) (:start . 35)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n (:id . 49))\n ((:tag . "NNP") (:stem . "Apical") (:form . "Apical") (:end . 48)\n (:start . 42) (:id . 50))\n ((:tag . "NNP") (:stem . "Cortex") (:form . "Cortex") (:end . 55)\n (:start . 49) (:id . 51)))@@@1@10@((:identifiers (:sid . :s5.135) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101545@unknown@formal@none@1@S@We next studied the subcellular localization of D-mib (Figure 3).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "next") (:form . "next") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "study") (:form . "studied") (:end . 15)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "JJ") (:stem . "subcellular") (:form . "subcellular") (:end . 31)\n (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "localization") (:form . "localization") (:end . 44)\n (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n (:id . 48))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 53) (:start . 48)\n (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 61)\n (:start . 55) (:id . 51))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 63) (:start . 62)\n (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 64) (:start . 63)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s5.136) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101546@unknown@formal@none@1@S@Anti-D-mib antibodies were generated that specifically detected D-mib on Western blots (see Figure 1C) and on fixed tissues (Figure 3F–F?).@(((:tag . "JJ") (:stem . "anti-d-mib") (:form . "Anti-D-mib") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 21)\n (:start . 11) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 26) (:start . 22)\n (:id . 44))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 36)\n (:start . 27) (:id . 45))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 41) (:start . 37)\n (:id . 46))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 54)\n (:start . 42) (:id . 47))\n ((:tag . "VBD") (:stem . "detect") (:form . "detected") (:end . 63)\n (:start . 55) (:id . 48))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 69) (:start . 64)\n (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 72) (:start . 70)\n (:id . 50))\n ((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 80)\n (:start . 73) (:id . 51))\n ((:tag . "NNS") (:stem . "blot") (:form . "blots") (:end . 86) (:start . 81)\n (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 88) (:start . 87)\n (:id . 53))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 91) (:start . 88)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 98)\n (:start . 92) (:id . 55))\n ((:tag . "NN") (:stem . "1c") (:form . "1C") (:end . 101) (:start . 99)\n (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 109) (:start . 107)\n (:id . 59))\n ((:tag . "VBN") (:stem . "fix") (:form . "fixed") (:end . 115) (:start . 110)\n (:id . 60))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 123)\n (:start . 116) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 131)\n (:start . 125) (:id . 63))\n ((:tag . "NNP") (:stem . "3F–F") (:form . "3F–F") (:end . 136) (:start . 132)\n (:id . 64))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 137) (:start . 136)\n (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s5.137) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101547@unknown@formal@none@1@S@Using these antibodies, we found that D-mib was detected in all imaginal disc cells (Figure 3A and 3B).@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 22)\n (:start . 12) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 32) (:start . 27)\n (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 37) (:start . 33)\n (:id . 48))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 43) (:start . 38)\n (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 47) (:start . 44)\n (:id . 50))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 56)\n (:start . 48) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n (:id . 52))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 63) (:start . 60)\n (:id . 53))\n ((:tag . "JJ") (:stem . "imaginal") (:form . "imaginal") (:end . 72)\n (:start . 64) (:id . 54))\n ((:tag . "NN") (:stem . "disc") (:form . "disc") (:end . 77) (:start . 73)\n (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 83) (:start . 78)\n (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n (:id . 57))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 91)\n (:start . 85) (:id . 58))\n ((:tag . "NN") (:stem . "3a") (:form . "3A") (:end . 94) (:start . 92)\n (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n (:id . 60))\n ((:tag . "NN") (:stem . "3b") (:form . "3B") (:end . 101) (:start . 99)\n (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s5.138) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101548@unknown@formal@none@1@S@We then examined D-mib subcellular distribution in epithelial cells located along the edge of the wing discs because cross-sectional imaging affords better resolution along the apical-basal axis.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "examine") (:form . 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(:end . 173) (:start . 172)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x5.142.1) (:span 112 120)))\n (:hscopes ((:id . :x5.142.1) (:span 112 155)))\n (:identifiers (:sid . :s5.142) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101552@unknown@formal@none@1@S@The reduced cytoplasmic staining seen in D-mib mutant cells (Figure 3F–3F??)'' suggests that D-mib is also present in the cytoplasm.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "cytoplasmic") (:end . 23)\n (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 32)\n (:start . 24) (:id . 45))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 37) (:start . 33)\n (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . 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(:end . 114) (:start . 113)\n (:id . 62)))@@@1@21@((:hcues ((:id . :x5.145.1) (:span 43 46)) ((:id . :x5.145.2) (:span 24 31)))\n (:hscopes ((:id . :x5.145.1) (:span 43 113))\n ((:id . :x5.145.2) (:span 24 113)))\n (:identifiers (:sid . :s5.145) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101555@unknown@formal@none@1@S@D-mib Co-Localizes with Dl and Ser at the Apical Cell Cortex@(((:tag . "JJ") (:stem . "d-mib") (:form . "D-mib") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Co-Localiz") (:form . "Co-Localizes") (:end . 18)\n (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 23) (:start . 19)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 26) (:start . 24)\n (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Ser") (:form . 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(:end . 82) (:start . 81)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s5.159) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101570@unknown@formal@none@1@S@D-mib Regulates the Cell-Surface Level of Ser@(((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "regulate") (:form . "Regulates") (:end . 15)\n (:start . 6) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Cell-Surface") (:form . "Cell-Surface") (:end . 32)\n (:start . 20) (:id . 45))\n ((:tag . "NNP") (:stem . "Level") (:form . "Level") (:end . 38) (:start . 33)\n (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 45) (:start . 42)\n (:id . 48)))@@@1@7@((:identifiers (:sid . :s5.161) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101571@unknown@formal@none@1@S@We next examined the potential role of D-mib in regulating Dl and Ser distribution in wing imaginal discs.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "next") (:form . "next") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "examine") (:form . "examined") (:end . 16)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 30)\n (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 35) (:start . 31)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . 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(:end . 150) (:start . 149)\n (:id . 74)))@@@1@33@((:ncues ((:id . :x5.165.1) (:span 63 66)))\n (:nscopes ((:id . :x5.165.1) (:span 63 119)))\n (:identifiers (:sid . :s5.165) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101575@unknown@formal@none@1@S@In contrast, the accumulation of Ser at the apical cortex was strongly increased (Figure 4E) and Ser accumulation in Dl-positive vesicles was dramatically reduced (Figure 4E?) in D-mib1 mutant discs.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "NN") (:stem . "accumulation") (:form . "accumulation") (:end . 29)\n (:start . 17) (:id . 46))\n ((:tag . 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(:end . 118) (:start . 117)\n (:id . 66)))@@@1@25@((:ncues ((:id . :x5.168.1) (:span 47 50)))\n (:nscopes ((:id . :x5.168.1) (:span 47 104)))\n (:identifiers (:sid . :s5.168) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101578@unknown@formal@none@1@S@Thus, trafficking of Ser towards this intracellular compartment is, at least in part, D-mib-independent.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "trafficking") (:form . "trafficking") (:end . 17)\n (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 24) (:start . 21)\n (:id . 46))\n ((:tag . "IN") (:stem . "towards") (:form . "towards") (:end . 32)\n (:start . 25) (:id . 47))\n ((:tag . "DT") (:stem . 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(:end . 110) (:start . 108)\n (:id . 65))\n ((:tag . "NNP") (:stem . "Qin") (:form . "Qin") (:end . 114) (:start . 111)\n (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n (:id . 67))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 118) (:start . 116)\n (:id . 68))\n ((:tag . "NNP") (:stem . "Le") (:form . "Le") (:end . 121) (:start . 119)\n (:id . 69))\n ((:tag . "NNP") (:stem . "Borgne") (:form . "Borgne") (:end . 128)\n (:start . 122) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n (:id . 71))\n ((:tag . "NNP") (:stem . "F.") (:form . "F.") (:end . 132) (:start . 130)\n (:id . 72))\n ((:tag . "NNP") (:stem . "Schweisguth") (:form . "Schweisguth") (:end . 144)\n (:start . 133) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n (:id . 74))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 148) (:start . 146)\n (:id . 75))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 152) (:start . 149)\n (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n (:id . 77))\n ((:tag . "JJ") (:stem . "unpublished") (:form . "unpublished") (:end . 165)\n (:start . 154) (:id . 78))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 170)\n (:start . 166) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 171) (:start . 170)\n (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n (:id . 81)))@@@1@40@((:identifiers (:sid . :s5.185) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101595@unknown@formal@none@1@S@Moreover, a mutation in the C-terminal catalytic RING domain of D-mib abolished its ability to internalize Ser in transfected S2 cells (R. L. B. and F. S., unpublished data) implying that the E3 ubiquitin ligase activity of D-mib is required for Ser internalization.@(((:tag . "RB") (:stem . 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"an") (:end . 209) (:start . 207)\n (:id . 78))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 218)\n (:start . 210) (:id . 79))\n ((:tag . "NN") (:stem . "uptake") (:form . "uptake") (:end . 225)\n (:start . 219) (:id . 80))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 231)\n (:start . 226) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n (:id . 82)))@@@1@41@((:hcues ((:id . :x5.188.1) (:span 8 15)))\n (:hscopes ((:id . :x5.188.1) (:span 8 139)))\n (:identifiers (:sid . :s5.188) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101598@unknown@formal@none@1@S@Briefly, dissected wing discs were cultured for 15 min in the presence of antibodies that recognize the extracellular part of Ser or Dl, then washed, cultured for another 45 min in medium without antibodies, and then fixed.@(((:tag . "NNP") (:stem . "Briefly") (:form . 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(:end . 223) (:start . 222)\n (:id . 83)))@@@1@42@((:ncues ((:id . :x5.189.1) (:span 188 195)))\n (:nscopes ((:id . :x5.189.1) (:span 188 206)))\n (:identifiers (:sid . :s5.189) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101600@unknown@formal@none@1@S@The results are shown in Figure 5.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 21) (:start . 16)\n (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 31)\n (:start . 25) (:id . 47))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 33) (:start . 32)\n (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 34) (:start . 33)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s5.191) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101601@unknown@formal@none@1@S@Using this assay, we found that anti-Ser-and anti-Dl antibodies were internalized in wild-type epithelial cells (Figure 5A–5C??).@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 16) (:start . 11)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 20) (:start . 18)\n (:id . 46))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 26) (:start . 21)\n (:id . 47))\n ((:tag . 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"(") (:form . "(") (:end . 113) (:start . 112)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 119)\n (:start . 113) (:id . 59))\n ((:tag . "NNP") (:stem . "5A–5C") (:form . "5A–5C") (:end . 125)\n (:start . 120) (:id . 60))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 126) (:start . 125)\n (:id . 61))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 127) (:start . 126)\n (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 128) (:start . 127)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") 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(:end . 107) (:start . 106)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s5.194) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101604@unknown@formal@none@1@S@Moreover, high levels of anti-Ser antibodies were seen at the apical surface (Figure 5D? and 5F?), confirming that D-mib mutant cells accumulate high levels of Ser at their surface.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 21)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n (:id . 46))\n ((:tag . "JJ") (:stem . "anti-ser") (:form . "anti-Ser") (:end . 33)\n (:start . 25) (:id . 47))\n ((:tag . "NNS") (:stem . 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(:end . 181) (:start . 180)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s5.195) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101605@unknown@formal@none@1@S@We therefore conclude that D-mib is specifically required for the endocytosis of Ser in wing discs.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . "VBP") (:stem . "conclude") (:form . "conclude") (:end . 21)\n (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n (:id . 45))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 32) (:start . 27)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 35) (:start . 33)\n (:id . 47))\n ((:tag . "RB") (:stem . "specifically") (:form . 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(:end . 99) (:start . 98)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s5.196) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101606@unknown@formal@none@1@S@D-mib Is Required for Ser Endocytosis@(((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "Is") (:end . 8) (:start . 6)\n (:id . 43))\n ((:tag . "VBN") (:stem . "require") (:form . "Required") (:end . 17)\n (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 21) (:start . 18)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 25) (:start . 22)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Endocytosis") (:form . 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(:end . 75) (:start . 74)\n (:id . 53)))@@@1@12@((:hcues ((:id . :x5.244.1) (:span 31 34)))\n (:hscopes ((:id . :x5.244.1) (:span 31 74)))\n (:identifiers (:sid . :s5.244) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101654@unknown@formal@none@1@S@Consistent with the latter hypothesis, the neur gene is not expressed in wing pouch and wing margin cells, where it is not required, and appears to be expressed only in sensory cells [52], where it is required.@(((:tag . "JJ") (:stem . "consistent") (:form . "Consistent") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 15) (:start . 11)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 44))\n ((:tag . "JJ") (:stem . "latter") (:form . "latter") (:end . 26)\n (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "hypothesis") (:form . 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(:end . 210) (:start . 209)\n (:id . 85)))@@@1@44@((:hcues ((:id . :x5.245.1) (:span 137 144)))\n (:ncues ((:id . :x5.245.2) (:span 119 122))\n ((:id . :x5.245.3) (:span 56 59)))\n (:hscopes ((:id . :x5.245.1) (:span 137 209)))\n (:nscopes ((:id . :x5.245.2) (:span 113 131))\n ((:id . :x5.245.3) (:span 39 131)))\n (:identifiers (:sid . :s5.245) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101655@unknown@formal@none@1@S@By contrast, D-mib appears to be uniformly expressed in imaginal discs.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "appear") (:form . 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(:end . 71) (:start . 70)\n (:id . 54)))@@@1@13@((:hcues ((:id . :x5.246.1) (:span 19 26)))\n (:hscopes ((:id . :x5.246.1) (:span 13 70)))\n (:identifiers (:sid . :s5.246) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101656@unknown@formal@none@1@S@To test this hypothesis, we examined whether the forced ubiquitous expression of the neur gene can suppress the D-mib loss-of-function phenotype.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 23)\n (:start . 13) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . 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(:end . 145) (:start . 144)\n (:id . 64)))@@@1@23@((:hcues ((:id . :x5.247.1) (:span 37 44)))\n (:hscopes ((:id . :x5.247.1) (:span 37 144)))\n (:identifiers (:sid . :s5.247) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101657@unknown@formal@none@1@S@Expression of Neur, using actin-GAL4, restored growth of the wing pouch and formation of the wing margin (data not shown).@(((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 25) (:start . 20)\n (:id . 46))\n ((:tag . "NN") (:stem . "actin-gal4") (:form . 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(:end . 122) (:start . 121)\n (:id . 66)))@@@1@25@((:ncues ((:id . :x5.248.1) (:span 111 114)))\n (:nscopes ((:id . :x5.248.1) (:span 105 121)))\n (:identifiers (:sid . :s5.248) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101658@unknown@formal@none@1@S@Moreover, expression of Neur in dorsal cells, using Ser-GAL4, was sufficient to rescue growth of the wing pouch as well as the expression of Cut in margin cells in D-mib mutant discs (Figure 8D).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 20)\n (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 28) (:start . 24)\n (:id . 46))\n ((:tag . 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"of") (:end . 146) (:start . 144)\n (:id . 66))\n ((:tag . "NN") (:stem . "neurpgal4/neur1f65") (:form . "neurPGAL4/neur1F65")\n (:end . 165) (:start . 147) (:id . 67))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 173)\n (:start . 166) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n (:id . 69)))@@@1@28@((:ncues ((:id . :x5.251.1) (:span 98 101)))\n (:nscopes ((:id . :x5.251.1) (:span 98 173)))\n (:identifiers (:sid . :s5.251) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101661@unknown@formal@none@1@S@Three UAS-D-mib transgenic lines were tested, and none showed detectable rescue whereas the two UAS-neur lines used as positive controls either fully or partially rescued the cuticular neurogenic phenotype of neurPGAL4/neur1F65 embryos (data not shown; UAS-D-mib+/+, neurPGAL4+/+ embryos developed normally).@(((:tag . "CD") (:stem . "three") (:form . 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"neurPGAL4/neur1F65")\n (:end . 227) (:start . 209) (:id . 73))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 235)\n (:start . 228) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 237) (:start . 236)\n (:id . 75))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 241)\n (:start . 237) (:id . 76))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 245) (:start . 242)\n (:id . 77))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 251)\n (:start . 246) (:id . 78))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 252) (:start . 251)\n (:id . 79))\n ((:tag . "JJ") (:stem . "uas-d-mib+/+") (:form . "UAS-D-mib+/+") (:end . 265)\n (:start . 253) (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 266) (:start . 265)\n (:id . 81))\n ((:tag . "JJ") (:stem . "neurpgal4+/+") (:form . "neurPGAL4+/+") (:end . 279)\n (:start . 267) (:id . 82))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 287)\n (:start . 280) (:id . 83))\n ((:tag . "VBD") (:stem . "develop") (:form . "developed") (:end . 297)\n (:start . 288) (:id . 84))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 306)\n (:start . 298) (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 307) (:start . 306)\n (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 308) (:start . 307)\n (:id . 87)))@@@1@46@((:hcues ((:id . :x5.252.2) (:span 137 143 150 152)))\n (:ncues ((:id . :x5.252.1) (:span 242 245))\n ((:id . :x5.252.4) (:span 50 54)))\n (:hscopes ((:id . :x5.252.2) (:span 137 162)))\n (:nscopes ((:id . :x5.252.1) (:span 236 251))\n ((:id . :x5.252.4) (:span 50 79)))\n (:identifiers (:sid . :s5.252) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101662@unknown@formal@none@1@S@This indicates that a key function of Neur in the embryo cannot be provided by D-mib.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 14)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 21) (:start . 20)\n (:id . 45))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 25) (:start . 22)\n (:id . 46))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 34)\n (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 42) (:start . 38)\n (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n (:id . 51))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 56)\n (:start . 50) (:id . 52))\n ((:tag . "NN") (:stem . "cannot") (:form . "cannot") (:end . 63)\n (:start . 57) (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 66) (:start . 64)\n (:id . 54))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 75)\n (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 78) (:start . 76)\n (:id . 56))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 84) (:start . 79)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n (:id . 58)))@@@1@17@((:hcues ((:id . :x5.253.2) (:span 5 19)))\n (:ncues ((:id . :x5.253.1) (:span 57 63)))\n (:hscopes ((:id . :x5.253.2) (:span 5 84)))\n (:nscopes ((:id . :x5.253.1) (:span 20 84)))\n (:identifiers (:sid . :s5.253) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101663@unknown@formal@none@1@S@We therefore suggest that Neur and D-mib functions overlap but are not strictly identical.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 20)\n (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 30) (:start . 26)\n (:id . 46))\n ((:tag . "CC") (:stem . 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(:end . 90) (:start . 89)\n (:id . 56)))@@@1@15@((:hcues ((:id . :x5.254.1) (:span 13 20)))\n (:hscopes ((:id . :x5.254.1) (:span 13 89)))\n (:identifiers (:sid . :s5.254) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101664@unknown@formal@none@1@S@Discussion@(((:tag . "NN") (:stem . "discussion") (:form . "Discussion") (:end . 10)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s5.255) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101665@unknown@formal@none@1@S@Many recent studies have revealed that endocytosis plays multiple roles in the regulation of N signaling (reviewed in [2]; see also [53,54]).@(((:tag . "JJ") (:stem . "many") (:form . "Many") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 19)\n (:start . 12) (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 24) (:start . 20)\n (:id . 45))\n ((:tag . "VBN") (:stem . "reveal") (:form . "revealed") (:end . 33)\n (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 38) (:start . 34)\n (:id . 47))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 50)\n (:start . 39) (:id . 48))\n ((:tag . "VBZ") (:stem . "play") (:form . "plays") (:end . 56) (:start . 51)\n (:id . 49))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 65)\n (:start . 57) (:id . 50))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 71) (:start . 66)\n (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n (:id . 53))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 89)\n (:start . 79) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n (:id . 55))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 94) (:start . 93)\n (:id . 56))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 104)\n (:start . 95) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n (:id . 58))\n ((:tag . "VBN") (:stem . "review") (:form . "reviewed") (:end . 114)\n (:start . 106) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 117) (:start . 115)\n (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 119) (:start . 118)\n (:id . 61))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 120) (:start . 119)\n (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 121) (:start . 120)\n (:id . 63))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 122) (:start . 121)\n (:id . 64))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 126) (:start . 123)\n (:id . 65))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 131) (:start . 127)\n (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 133) (:start . 132)\n (:id . 67))\n ((:tag . "CD") (:stem . "53,54") (:form . "53,54") (:end . 138)\n (:start . 133) (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 139) (:start . 138)\n (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 140) (:start . 139)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s5.256) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101666@unknown@formal@none@1@S@Here, we show that the conserved E3 ubiquitin ligases Neur and D-mib have similar molecular activities in the regulation of Dl and Ser endocytosis but distinct developmental functions in Drosophila.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n (:id . 44))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 13) (:start . 9)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 47))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 32)\n (:start . 23) (:id . 48))\n ((:tag . "NN") (:stem . "e3") (:form . "E3") (:end . 35) (:start . 33)\n (:id . 49))\n ((:tag . "NN") (:stem . "ubiquitin") (:form . "ubiquitin") (:end . 45)\n (:start . 36) (:id . 50))\n ((:tag . "NNS") (:stem . "ligas") (:form . "ligases") (:end . 53)\n (:start . 46) (:id . 51))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 58) (:start . 54)\n (:id . 52))\n ((:tag . 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"Dl") (:end . 126) (:start . 124)\n (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n (:id . 64))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 134) (:start . 131)\n (:id . 65))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 146)\n (:start . 135) (:id . 66))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 150) (:start . 147)\n (:id . 67))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 159)\n (:start . 151) (:id . 68))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n (:end . 173) (:start . 160) (:id . 69))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 183)\n (:start . 174) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 186) (:start . 184)\n (:id . 71))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 197)\n (:start . 187) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s5.257) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101667@unknown@formal@none@1@S@Our analysis first establishes that D-mib regulates Ser signaling during wing development.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "establish") (:form . "establishes") (:end . 30)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 35) (:start . 31)\n (:id . 46))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 41) (:start . 36)\n (:id . 47))\n ((:tag . "VBZ") (:stem . "regulate") (:form . "regulates") (:end . 51)\n (:start . 42) (:id . 48))\n ((:tag . "NN") (:stem . "ser") (:form . "Ser") (:end . 55) (:start . 52)\n (:id . 49))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 65)\n (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 72)\n (:start . 66) (:id . 51))\n ((:tag . "VBG") (:stem . "wing") (:form . "wing") (:end . 77) (:start . 73)\n (:id . 52))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 89)\n (:start . 78) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s5.258) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101668@unknown@formal@none@1@S@First, clonal analysis revealed that the activity of the D-mib gene is specifically required in dorsal cells for the expression of Cut at the wing margin.@(((:tag . "RB") (:stem . "first") (:form . "First") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . 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(:end . 152) (:start . 151)\n (:id . 71)))@@@1@30@((:hcues ((:id . :x5.261.2) (:span 53 67)))\n (:ncues ((:id . :x5.261.1) (:span 96 99)))\n (:hscopes ((:id . :x5.261.2) (:span 53 151)))\n (:nscopes ((:id . :x5.261.1) (:span 96 106)))\n (:identifiers (:sid . :s5.261) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101671@unknown@formal@none@1@S@This inhibition correlated with the strong accumulation of Ser (but not Dl) at the apical cortex of D-mib mutant cells.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 15)\n (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "correlate") (:form . "correlated") (:end . 26)\n (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 31) (:start . 27)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . 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(:end . 119) (:start . 118)\n (:id . 64)))@@@1@23@((:ncues ((:id . :x5.262.1) (:span 68 71)))\n (:nscopes ((:id . :x5.262.1) (:span 68 75)))\n (:identifiers (:sid . :s5.262) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101672@unknown@formal@none@1@S@Thus, an essential function of D-mib in the wing is to regulate the endocytosis of Ser in dorsal cells to non-autonomously promote the activation of N along the D-V boundary.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 8) (:start . 6)\n (:id . 44))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 18)\n (:start . 9) (:id . 45))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 27)\n (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . 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(:end . 151) (:start . 150)\n (:id . 72)))@@@1@31@((:hcues ((:id . :x5.264.2) (:span 51 54)))\n (:ncues ((:id . :x5.264.1) (:span 81 85)))\n (:hscopes ((:id . :x5.264.2) (:span 51 145)))\n (:nscopes ((:id . :x5.264.1) (:span 81 145)))\n (:identifiers (:sid . :s5.264) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101674@unknown@formal@none@1@S@Because D-mib co-localizes with Ser at the apical cortex of wing disc cells, acts in a RING-finger-dependent manner to regulate Ser endocytosis in S2 cells (R. L. B. and F. S., unpublished results), and physically associates with Ser in co-immunoprecipitation experiments (E. C. Lai, F. Roegiers, X. Qin, R. Le Borgne, F. Schweisguth, et al., unpublished data), D-mib may ubiquitinate Ser and directly regulate its endocytosis.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D-mib") (:form . 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"Ser") (:end . 388) (:start . 385)\n (:id . 116))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 392) (:start . 389)\n (:id . 117))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 401)\n (:start . 393) (:id . 118))\n ((:tag . "VB") (:stem . "regulate") (:form . "regulate") (:end . 410)\n (:start . 402) (:id . 119))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 414) (:start . 411)\n (:id . 120))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 426)\n (:start . 415) (:id . 121))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 427) (:start . 426)\n (:id . 122)))@@@1@81@((:hcues ((:id . :x5.265.1) (:span 368 371)))\n (:hscopes ((:id . :x5.265.1) (:span 368 426)))\n (:identifiers (:sid . :s5.265) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101675@unknown@formal@none@1@S@Our analysis further suggests that endocytosis of Ser is required for Ser signaling.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "RB") (:stem . "further") (:form . "further") (:end . 20)\n (:start . 13) (:id . 44))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 29)\n (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n (:id . 46))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 46)\n (:start . 35) (:id . 47))\n ((:tag . 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(:end . 84) (:start . 83)\n (:id . 55)))@@@1@14@((:hcues ((:id . :x5.266.1) (:span 21 29)))\n (:hscopes ((:id . :x5.266.1) (:span 21 83)))\n (:identifiers (:sid . :s5.266) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101676@unknown@formal@none@1@S@This conclusion is consistent with observations made earlier showing that secreted versions of Ser cannot activate N but instead antagonize Ser signaling [56,57].@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "conclusion") (:form . "conclusion") (:end . 15)\n (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n (:id . 44))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 29)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 34) (:start . 30)\n (:id . 46))\n ((:tag . "NNS") (:stem . 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(:end . 162) (:start . 161)\n (:id . 67)))@@@1@26@((:ncues ((:id . :x5.267.1) (:span 99 105)))\n (:nscopes ((:id . :x5.267.1) (:span 99 116)))\n (:identifiers (:sid . :s5.267) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101677@unknown@formal@none@1@S@Thus, endocytosis of both N ligands appears to be strictly required for N activation in Drosophila.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 17)\n (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 45))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 25) (:start . 21)\n (:id . 46))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 27) (:start . 26)\n (:id . 47))\n ((:tag . "NNS") (:stem . 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(:end . 188) (:start . 187)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s5.269) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101680@unknown@formal@none@1@S@Noticeably, there is no C. elegans Mib homolog, and the function of C. elegans neur (F10D7.5) is not known.@(((:tag . "RB") (:stem . "noticeably") (:form . "Noticeably") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 43))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 17) (:start . 12)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 20) (:start . 18)\n (:id . 45))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 23) (:start . 21)\n (:id . 46))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 26) (:start . 24)\n (:id . 47))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 34)\n (:start . 27) (:id . 48))\n ((:tag . 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(:end . 107) (:start . 106)\n (:id . 65)))@@@1@24@((:hcues ((:id . :x5.271.1) (:span 97 106)))\n (:ncues ((:id . :x5.271.2) (:span 21 23)))\n (:hscopes ((:id . :x5.271.1) (:span 52 106)))\n (:nscopes ((:id . :x5.271.2) (:span 21 46)))\n (:identifiers (:sid . :s5.271) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101681@unknown@formal@none@1@S@We speculate that endocytosis of the ligands may have evolved as a means to ensure tight spatial regulation of the activation of N.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "speculate") (:form . "speculate") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 17) (:start . 13)\n (:id . 44))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 29)\n (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . 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(:end . 228) (:start . 227)\n (:id . 81)))@@@1@40@((:hcues ((:id . :x5.283.1) (:span 183 193))\n ((:id . :x5.283.2) (:span 145 160)))\n (:ncues ((:id . :x5.283.3) (:span 89 95)))\n (:hscopes ((:id . :x5.283.1) (:span 183 227))\n ((:id . :x5.283.2) (:span 145 181)))\n (:nscopes ((:id . :x5.283.3) (:span 89 136)))\n (:identifiers (:sid . :s5.283) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101693@unknown@formal@none@1@S@Consistent with this interpretation, overexpression studies indicate that D-mib up-regulates the signaling activity of Dl, whereas a dominant-negative form of D-mib inhibits it (E. C. Lai, F. Roegiers, X. Qin, R. Le Borgne, F. Schweisguth, et al., unpublished data).@(((:tag . "JJ") (:stem . "consistent") (:form . "Consistent") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 15) (:start . 11)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . 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(:form . "X.") (:end . 204) (:start . 202)\n (:id . 75))\n ((:tag . "NNP") (:stem . "Qin") (:form . "Qin") (:end . 208) (:start . 205)\n (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 209) (:start . 208)\n (:id . 77))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 212) (:start . 210)\n (:id . 78))\n ((:tag . "NNP") (:stem . "Le") (:form . "Le") (:end . 215) (:start . 213)\n (:id . 79))\n ((:tag . "NNP") (:stem . "Borgne") (:form . "Borgne") (:end . 222)\n (:start . 216) (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 223) (:start . 222)\n (:id . 81))\n ((:tag . "NNP") (:stem . "F.") (:form . "F.") (:end . 226) (:start . 224)\n (:id . 82))\n ((:tag . "NNP") (:stem . "Schweisguth") (:form . "Schweisguth") (:end . 238)\n (:start . 227) (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 239) (:start . 238)\n (:id . 84))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 242) (:start . 240)\n (:id . 85))\n ((:tag . "FW") (:stem . 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(:end . 126) (:start . 125)\n (:id . 63)))@@@1@22@((:ncues ((:id . :x5.285.1) (:span 23 25)))\n (:nscopes ((:id . :x5.285.1) (:span 23 125)))\n (:identifiers (:sid . :s5.285) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101695@unknown@formal@none@1@S@It is conceivable that the contribution of D-mib to the endocytosis of Dl is masked by the activity of D-mib-independent processes that may, or may not, be linked to Dl signaling.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "conceivable") (:form . "conceivable") (:end . 17)\n (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "NN") (:stem . 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(:end . 179) (:start . 178)\n (:id . 75)))@@@1@34@((:hcues ((:id . :x5.286.1) (:span 136 151)) ((:id . :x5.286.2) (:span 6 17)))\n (:hscopes ((:id . :x5.286.1) (:span 136 178))\n ((:id . :x5.286.2) (:span 6 178)))\n (:identifiers (:sid . :s5.286) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101696@unknown@formal@none@1@S@We have also shown that, reciprocally, Neur and D-mib may similarly regulate Ser.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . 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(:end . 81) (:start . 80)\n (:id . 57)))@@@1@16@((:hcues ((:id . :x5.287.1) (:span 54 57)))\n (:hscopes ((:id . :x5.287.1) (:span 54 80)))\n (:identifiers (:sid . :s5.287) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101697@unknown@formal@none@1@S@Neur and D-mib were shown to similarly promote down-regulation of Ser from the cell surface when overexpressed (E. C. Lai, F. Roegiers, X. Qin, R. Le Borgne, F. Schweisguth, et al., unpublished data).@(((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 19) (:start . 15)\n (:id . 45))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 25) (:start . 20)\n (:id . 46))\n ((:tag . "TO") (:stem . 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"NN") (:stem . "study") (:form . "study") (:end . 154)\n (:start . 149) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 155) (:start . 154)\n (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n (:id . 79)))@@@1@38@((:identifiers (:sid . :s5.289) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101700@unknown@formal@none@1@S@However, the ability of Neur to rescue the D-mib mutant wing phenotype when expressed in dorsal cells strongly indicates that Neur can promote Ser signaling.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 20)\n (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . 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(:end . 84) (:start . 83)\n (:id . 55)))@@@1@14@((:hcues ((:id . :x5.292.1) (:span 21 34)))\n (:hscopes ((:id . :x5.292.1) (:span 21 83)))\n (:identifiers (:sid . :s5.292) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101702@unknown@formal@none@1@S@D-mib and Neur may have identical molecular activities but distinct expression patterns, hence distinct functions at the level of the organism.@(((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "JJ") (:stem . "identical") (:form . 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(:end . 143) (:start . 142)\n (:id . 64)))@@@1@23@((:hcues ((:id . :x5.293.1) (:span 15 18)))\n (:hscopes ((:id . :x5.293.1) (:span 15 142)))\n (:identifiers (:sid . :s5.293) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101703@unknown@formal@none@1@S@Consistent with this possibility, D-mib is uniformly distributed in imaginal discs, whereas Neur is specifically detected in sensory cells [52].@(((:tag . "JJ") (:stem . "consistent") (:form . "Consistent") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 15) (:start . 11)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 20) (:start . 16)\n (:id . 44))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 32)\n (:start . 21) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n (:id . 46))\n ((:tag . "NNP") (:stem . "D-mib") (:form . 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(:end . 144) (:start . 143)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s5.294) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101704@unknown@formal@none@1@S@Importantly, the rescue of the D-mib mutant phenotype by ectopic expression of Neur strongly supports this interpretation.@(((:tag . "RB") (:stem . "importantly") (:form . "Importantly") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 23)\n (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n (:id . 47))\n ((:tag . "NNP") (:stem . "D-mib") (:form . 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"this") (:end . 106) (:start . 102)\n (:id . 58))\n ((:tag . "NN") (:stem . "interpretation") (:form . "interpretation")\n (:end . 121) (:start . 107) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n (:id . 60)))@@@1@19@((:hcues ((:id . :x5.295.1) (:span 93 101)))\n (:hscopes ((:id . :x5.295.1) (:span 93 121)))\n (:identifiers (:sid . :s5.295) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101705@unknown@formal@none@1@S@This result further suggests that Neur can regulate Ser signaling.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "RB") (:stem . "further") (:form . "further") (:end . 19)\n (:start . 12) (:id . 44))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 28)\n (:start . 20) (:id . 45))\n ((:tag . 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(:end . 66) (:start . 65)\n (:id . 52)))@@@1@11@((:hcues ((:id . :x5.296.1) (:span 39 42)) ((:id . :x5.296.2) (:span 20 28)))\n (:hscopes ((:id . :x5.296.1) (:span 39 65))\n ((:id . :x5.296.2) (:span 20 65)))\n (:identifiers (:sid . :s5.296) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101706@unknown@formal@none@1@S@Consistent with this idea, overexpression of Neur in imaginal discs resulted in a strong reduction of Ser accumulation at the apical cortex (data not shown).@(((:tag . "JJ") (:stem . "consistent") (:form . "Consistent") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 15) (:start . 11)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 20) (:start . 16)\n (:id . 44))\n ((:tag . "NN") (:stem . "idea") (:form . "idea") (:end . 25) (:start . 21)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . 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(:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n (:id . 65)))@@@1@24@((:hcues ((:id . :x5.298.1) (:span 67 73)))\n (:hscopes ((:id . :x5.298.1) (:span 52 131)))\n (:identifiers (:sid . :s5.298) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101708@unknown@formal@none@1@S@Nevertheless, our observation that D-mib could not compensate for the loss of neur activity in the embryo indicates that D-mib and Neur have overlapping rather than identical molecular activities.@(((:tag . "RB") (:stem . "nevertheless") (:form . "Nevertheless") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 29)\n (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . 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"rather") (:end . 159)\n (:start . 153) (:id . 67))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 164) (:start . 160)\n (:id . 68))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 174)\n (:start . 165) (:id . 69))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 184)\n (:start . 175) (:id . 70))\n ((:tag . "NNS") (:stem . "activity") (:form . "activities") (:end . 195)\n (:start . 185) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n (:id . 72)))@@@1@31@((:hcues ((:id . :x5.299.2) (:span 106 120)))\n (:ncues ((:id . :x5.299.1) (:span 153 164))\n ((:id . :x5.299.3) (:span 41 50)))\n (:hscopes ((:id . :x5.299.2) (:span 106 195)))\n (:nscopes ((:id . :x5.299.1) (:span 153 195))\n ((:id . :x5.299.3) (:span 41 105)))\n (:identifiers (:sid . :s5.299) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101710@unknown@formal@none@1@S@The conservation from Drosophila to mammals of these two structurally distinct but functionally similar E3 ubiquitin ligases is likely to reflect a combination of evolutionary advantages associated with: (i) specialized expression pattern, as evidenced by the cell-specific expression of the neur gene in sensory organ precursor cells [52]; (ii) specialized function, as suggested by the role of murine MIB in TNF?? signaling [32]; (iii) regulation of protein stability, localization, and/or activity.@(((:tag . 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(:end . 501) (:start . 500)\n (:id . 132)))@@@1@91@((:hcues ((:id . :x5.301.1) (:span 371 380))\n ((:id . :x5.301.2) (:span 128 134)))\n (:hscopes ((:id . :x5.301.1) (:span 371 425))\n ((:id . :x5.301.2) (:span 0 500)))\n (:identifiers (:sid . :s5.301) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101711@unknown@formal@none@1@S@For instance, Neur, but not D-mib, localizes asymmetrically during asymmetric sensory organ precursor cell divisions [22].@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 18) (:start . 14)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n (:id . 46))\n ((:tag . "CC") (:stem . 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"precursor") (:end . 101)\n (:start . 92) (:id . 57))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 106) (:start . 102)\n (:id . 58))\n ((:tag . "NNS") (:stem . "division") (:form . "divisions") (:end . 116)\n (:start . 107) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 118) (:start . 117)\n (:id . 60))\n ((:tag . "CD") (:stem . "22") (:form . "22") (:end . 120) (:start . 118)\n (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 121) (:start . 120)\n (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n (:id . 63)))@@@1@22@((:ncues ((:id . :x5.302.1) (:span 24 27)))\n (:nscopes ((:id . :x5.302.1) (:span 24 33)))\n (:identifiers (:sid . :s5.302) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101712@unknown@formal@none@1@S@Materials and Methods@(((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 13) (:start . 10)\n (:id . 43))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 21)\n (:start . 14) (:id . 44)))@@@1@3@((:identifiers (:sid . :s5.303) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101713@unknown@formal@none@1@S@Flies.@(((:tag . "NNS") (:stem . "fly") (:form . "Flies") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 6) (:start . 5) (:id . 43)))@@@1@2@((:identifiers (:sid . :s5.304) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101714@unknown@formal@none@1@S@The D-mib1 mutation corresponds to the EY97600 P-element insertion generated by the Gene Disruption Project (http://flypush.imgen.bcm.tmc.edu/pscreen/).@(((:tag . "DT") (:stem . "the") (:form . 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(:end . 152) (:start . 151)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s5.305) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101715@unknown@formal@none@1@S@The D-mib2 allele was selected as w- D-mib mutant derivative by imprecise excision of the EY97600 P-element.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "d-mib2") (:form . "D-mib2") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 17)\n (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 21) (:start . 18)\n (:id . 45))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 30)\n (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 33) (:start . 31)\n (:id . 47))\n ((:tag . "JJ") (:stem . "w-") (:form . "w-") (:end . 36) (:start . 34)\n (:id . 48))\n ((:tag . 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(:end . 108) (:start . 107)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s5.306) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101716@unknown@formal@none@1@S@The precise breakpoints of the D-mib2 deletion were determined by sequencing a PCR fragment amplified from genomic DNA prepared from D-mib2 homozygous larvae.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "precise") (:form . "precise") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "breakpoint") (:form . "breakpoints") (:end . 23)\n (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "NN") (:stem . "d-mib2") (:form . "D-mib2") (:end . 37)\n (:start . 31) (:id . 47))\n ((:tag . "NN") (:stem . "deletion") (:form . 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(:end . 158) (:start . 157)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s5.307) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101717@unknown@formal@none@1@S@The l(3)72CdaJ12 and l(3)72CdaI5 alleles originally isolated by [35] failed to complement the D-mib1 and D-mib2 mutations and were renamed D-mib3 and D-mib4.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "l(3)72CdaJ12") (:form . "l(3)72CdaJ12") (:end . 16)\n (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n (:id . 44))\n ((:tag . "CD") (:stem . "l(3)72CdaI5") (:form . "l(3)72CdaI5") (:end . 32)\n (:start . 21) (:id . 45))\n ((:tag . "NNS") (:stem . "allele") (:form . "alleles") (:end . 40)\n (:start . 33) (:id . 46))\n ((:tag . "RB") (:stem . "originally") (:form . "originally") (:end . 51)\n (:start . 41) (:id . 47))\n ((:tag . "VBN") (:stem . 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(:end . 157) (:start . 156)\n (:id . 67)))@@@1@26@((:ncues ((:id . :x5.308.1) (:span 69 75)))\n (:nscopes ((:id . :x5.308.1) (:span 69 121)))\n (:identifiers (:sid . :s5.308) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101718@unknown@formal@none@1@S@The D-mib1, D-mib2, and D-mib3 alleles appear to be genetically null alleles since the phenotypes of D-mib1/D-mib1 and D-mib1/D-mib3 mutant pupae are indistinguishable from the ones seen in D-mib1/D-mib2 and D-mib2/D-mib3 pupae.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "d-mib1") (:form . "D-mib1") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 44))\n ((:tag . "NNP") (:stem . "D-mib2") (:form . "D-mib2") (:end . 18)\n (:start . 12) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . 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"which") (:form . "which") (:end . 103)\n (:start . 98) (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 107) (:start . 104)\n (:id . 59))\n ((:tag . "VBN") (:stem . "believe") (:form . "believed") (:end . 116)\n (:start . 108) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 119) (:start . 117)\n (:id . 61))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 124) (:start . 120)\n (:id . 62))\n ((:tag . "VBN") (:stem . "emerge") (:form . "emerged") (:end . 132)\n (:start . 125) (:id . 63))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 146) (:start . 133) (:id . 64))\n ((:tag . "CD") (:stem . "500") (:form . "500") (:end . 150) (:start . 147)\n (:id . 65))\n ((:tag . "CD") (:stem . "million") (:form . "million") (:end . 158)\n (:start . 151) (:id . 66))\n ((:tag . "NNS") (:stem . "year") (:form . "years") (:end . 164)\n (:start . 159) (:id . 67))\n ((:tag . "RB") (:stem . "ago") (:form . "ago") (:end . 168) (:start . 165)\n (:id . 68))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 173) (:start . 169)\n (:id . 69))\n ((:tag . "JJ") (:stem . "transposon-encoded") (:form . "transposon-encoded")\n (:end . 192) (:start . 174) (:id . 70))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 201)\n (:start . 193) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n (:id . 72)))@@@1@31@((:hcues ((:id . :x6.3.1) (:span 108 116)))\n (:hscopes ((:id . :x6.3.1) (:span 98 201)))\n (:identifiers (:sid . :s6.3) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101743@unknown@formal@none@1@S@Yet no transposase sequence similar to RAG1 or RAG2 has been found.@(((:tag . "RB") (:stem . "yet") (:form . "Yet") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 6) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "transposase") (:form . "transposase") (:end . 18)\n (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 27)\n (:start . 19) (:id . 45))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 35)\n (:start . 28) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n (:id . 47))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 43) (:start . 39)\n (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 46) (:start . 44)\n (:id . 49))\n ((:tag . "NNP") (:stem . "RAG2") (:form . "RAG2") (:end . 51) (:start . 47)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 55) (:start . 52)\n (:id . 51))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 60) (:start . 56)\n (:id . 52))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 66) (:start . 61)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n (:id . 54)))@@@1@13@((:ncues ((:id . :x6.4.1) (:span 4 6)))\n (:nscopes ((:id . :x6.4.1) (:span 4 66)))\n (:identifiers (:sid . :s6.4) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101744@unknown@formal@none@1@S@Here we show that the approximately 600-amino acid “core” region of RAG1 required for its catalytic activity is significantly similar to the transposase encoded by DNA transposons that belong to the Transib superfamily.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 17) (:start . 13)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 35) (:start . 22) (:id . 47))\n ((:tag . "JJ") (:stem . "600-amino") (:form . "600-amino") (:end . 45)\n (:start . 36) (:id . 48))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 50) (:start . 46)\n (:id . 49))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 52) (:start . 51)\n (:id . 50))\n ((:tag . "JJ") (:stem . "core") (:form . "core") (:end . 56) (:start . 52)\n (:id . 51))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 57) (:start . 56)\n (:id . 52))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 64)\n (:start . 58) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n (:id . 54))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 72) (:start . 68)\n (:id . 55))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 81)\n (:start . 73) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 85) (:start . 82)\n (:id . 57))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 89) (:start . 86)\n (:id . 58))\n ((:tag . "JJ") (:stem . "catalytic") (:form . "catalytic") (:end . 99)\n (:start . 90) (:id . 59))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 108)\n (:start . 100) (:id . 60))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 111) (:start . 109)\n (:id . 61))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 125) (:start . 112) (:id . 62))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 133)\n (:start . 126) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 136) (:start . 134)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n (:id . 65))\n ((:tag . "NN") (:stem . "transposase") (:form . "transposase") (:end . 152)\n (:start . 141) (:id . 66))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 160)\n (:start . 153) (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 163) (:start . 161)\n (:id . 68))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 167) (:start . 164)\n (:id . 69))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 179)\n (:start . 168) (:id . 70))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 184) (:start . 180)\n (:id . 71))\n ((:tag . "VBP") (:stem . "belong") (:form . "belong") (:end . 191)\n (:start . 185) (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 194) (:start . 192)\n (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 198) (:start . 195)\n (:id . 74))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 206)\n (:start . 199) (:id . 75))\n ((:tag . "NN") (:stem . "superfamily") (:form . "superfamily") (:end . 218)\n (:start . 207) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s6.5) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101745@unknown@formal@none@1@S@This superfamily was discovered recently based on computational analysis of the fruit fly and African malaria mosquito genomes.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "superfamily") (:form . "superfamily") (:end . 16)\n (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 20) (:start . 17)\n (:id . 44))\n ((:tag . "VBN") (:stem . "discover") (:form . "discovered") (:end . 31)\n (:start . 21) (:id . 45))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 40)\n (:start . 32) (:id . 46))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 46) (:start . 41)\n (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 49) (:start . 47)\n (:id . 48))\n ((:tag . "JJ") (:stem . "computational") (:form . "computational")\n (:end . 63) (:start . 50) (:id . 49))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 72)\n (:start . 64) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n (:id . 52))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 85) (:start . 80)\n (:id . 53))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 89) (:start . 86)\n (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n (:id . 55))\n ((:tag . "JJ") (:stem . "african") (:form . "African") (:end . 101)\n (:start . 94) (:id . 56))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 109)\n (:start . 102) (:id . 57))\n ((:tag . "NN") (:stem . "mosquito") (:form . "mosquito") (:end . 118)\n (:start . 110) (:id . 58))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 126)\n (:start . 119) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.6) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101746@unknown@formal@none@1@S@Transib transposons also are present in the genomes of sea urchin, yellow fever mosquito, silkworm, dog hookworm, hydra, and soybean rust.@(((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 19)\n (:start . 8) (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 24) (:start . 20)\n (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 28) (:start . 25)\n (:id . 45))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 36)\n (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n (:id . 48))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 51)\n (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n (:id . 50))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 58) (:start . 55)\n (:id . 51))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 65)\n (:start . 59) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n (:id . 53))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 73)\n (:start . 67) (:id . 54))\n ((:tag . "NN") (:stem . "fever") (:form . "fever") (:end . 79) (:start . 74)\n (:id . 55))\n ((:tag . "NN") (:stem . "mosquito") (:form . "mosquito") (:end . 88)\n (:start . 80) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n (:id . 57))\n ((:tag . "NN") (:stem . "silkworm") (:form . "silkworm") (:end . 98)\n (:start . 90) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n (:id . 59))\n ((:tag . "NN") (:stem . "dog") (:form . "dog") (:end . 103) (:start . 100)\n (:id . 60))\n ((:tag . "NN") (:stem . "hookworm") (:form . "hookworm") (:end . 112)\n (:start . 104) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n (:id . 62))\n ((:tag . "NN") (:stem . "hydra") (:form . "hydra") (:end . 119)\n (:start . 114) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n (:id . 65))\n ((:tag . "NN") (:stem . "soybean") (:form . "soybean") (:end . 132)\n (:start . 125) (:id . 66))\n ((:tag . "NN") (:stem . "rust") (:form . "rust") (:end . 137) (:start . 133)\n (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s6.7) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101747@unknown@formal@none@1@S@We demonstrate that recombination signal sequences (RSSs) were derived from terminal inverted repeats of an ancient Transib transposon.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 14)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 33) (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 40)\n (:start . 34) (:id . 46))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 50)\n (:start . 41) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n (:id . 48))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSSs") (:end . 56) (:start . 52)\n (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 57) (:start . 56)\n (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 62) (:start . 58)\n (:id . 51))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 70)\n (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 75) (:start . 71)\n (:id . 53))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 84)\n (:start . 76) (:id . 54))\n ((:tag . "JJ") (:stem . "inverted") (:form . "inverted") (:end . 93)\n (:start . 85) (:id . 55))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 101)\n (:start . 94) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n (:id . 57))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 107) (:start . 105)\n (:id . 58))\n ((:tag . "JJ") (:stem . "ancient") (:form . "ancient") (:end . 115)\n (:start . 108) (:id . 59))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 123)\n (:start . 116) (:id . 60))\n ((:tag . "NN") (:stem . "transposon") (:form . "transposon") (:end . 134)\n (:start . 124) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.8) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101748@unknown@formal@none@1@S@Furthermore, the critical DDE catalytic triad of RAG1 is shared with the Transib transposase as part of conserved motifs.@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "critical") (:form . "critical") (:end . 25)\n (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "dde") (:form . "DDE") (:end . 29) (:start . 26)\n (:id . 46))\n ((:tag . "JJ") (:stem . "catalytic") (:form . "catalytic") (:end . 39)\n (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "triad") (:form . "triad") (:end . 45) (:start . 40)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n (:id . 49))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 53) (:start . 49)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 56) (:start . 54)\n (:id . 51))\n ((:tag . "VBN") (:stem . "share") (:form . "shared") (:end . 63)\n (:start . 57) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 68) (:start . 64)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 80)\n (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "transposase") (:form . "transposase") (:end . 92)\n (:start . 81) (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 95) (:start . 93)\n (:id . 57))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 100) (:start . 96)\n (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n (:id . 59))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 113)\n (:start . 104) (:id . 60))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 120)\n (:start . 114) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.9) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101750@unknown@formal@none@1@S@Our results provide the first direct evidence linking RAG1 and RSSs to a specific superfamily of DNA transposons and indicate that the V(D)J machinery evolved from transposons.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 19)\n (:start . 12) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 29) (:start . 24)\n (:id . 46))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 36)\n (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 45)\n (:start . 37) (:id . 48))\n ((:tag . "VBG") (:stem . "link") (:form . "linking") (:end . 53)\n (:start . 46) (:id . 49))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 58) (:start . 54)\n (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n (:id . 51))\n ((:tag . "NNS") (:stem . "rss") (:form . "RSSs") (:end . 67) (:start . 63)\n (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 70) (:start . 68)\n (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 72) (:start . 71)\n (:id . 54))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 81)\n (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "superfamily") (:form . "superfamily") (:end . 93)\n (:start . 82) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n (:id . 57))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 100) (:start . 97)\n (:id . 58))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 112)\n (:start . 101) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n (:id . 60))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 125)\n (:start . 117) (:id . 61))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 130) (:start . 126)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n (:id . 63))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 140)\n (:start . 135) (:id . 64))\n ((:tag . "NN") (:stem . "machinery") (:form . "machinery") (:end . 150)\n (:start . 141) (:id . 65))\n ((:tag . "VBN") (:stem . "evolve") (:form . "evolved") (:end . 158)\n (:start . 151) (:id . 66))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 163) (:start . 159)\n (:id . 67))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 175)\n (:start . 164) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n (:id . 69)))@@@1@28@((:hcues ((:id . :x6.11.1) (:span 117 130)))\n (:hscopes ((:id . :x6.11.1) (:span 117 175)))\n (:identifiers (:sid . :s6.11) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101751@unknown@formal@none@1@S@We propose that only the RAG1 core was derived from the Transib transposase, whereas the N-terminal domain was assembled from separate proteins of unknown function that may still be active in sea urchin, lancelet, hydra, and starlet sea anemone.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "propose") (:form . "propose") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "RB") (:stem . "only") (:form . 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"1") (:end . 151) (:start . 150)\n (:id . 65))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 152) (:start . 151)\n (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n (:id . 67)))@@@1@26@((:ncues ((:id . :x6.17.1) (:span 45 51)))\n (:nscopes ((:id . :x6.17.1) (:span 8 74)))\n (:identifiers (:sid . :s6.17) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101757@unknown@formal@none@1@S@The variable portions of the BCR and TCR genes are composed of separate V (variable), D (diversity), and J (joining) segments, which are represented by fewer than a few hundred copies each.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "variable") (:form . "variable") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 21)\n (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . 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"(") (:form . "(") (:end . 75) (:start . 74)\n (:id . 56))\n ((:tag . "JJ") (:stem . "variable") (:form . "variable") (:end . 83)\n (:start . 75) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 84) (:start . 83)\n (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n (:id . 59))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 87) (:start . 86)\n (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n (:id . 61))\n ((:tag . "NN") (:stem . "diversity") (:form . "diversity") (:end . 98)\n (:start . 89) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 104) (:start . 101)\n (:id . 65))\n ((:tag . "NNP") (:stem . "J") (:form . "J") (:end . 106) (:start . 105)\n (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n (:id . 67))\n ((:tag . "NN") (:stem . "joining") (:form . "joining") (:end . 115)\n (:start . 108) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n (:id . 69))\n ((:tag . "NNS") (:stem . "segment") (:form . "segments") (:end . 125)\n (:start . 117) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n (:id . 71))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 132)\n (:start . 127) (:id . 72))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 136) (:start . 133)\n (:id . 73))\n ((:tag . "VBN") (:stem . "represent") (:form . "represented") (:end . 148)\n (:start . 137) (:id . 74))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 151) (:start . 149)\n (:id . 75))\n ((:tag . "JJR") (:stem . "few") (:form . "fewer") (:end . 157) (:start . 152)\n (:id . 76))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 162) (:start . 158)\n (:id . 77))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 164) (:start . 163)\n (:id . 78))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 168) (:start . 165)\n (:id . 79))\n ((:tag . "CD") (:stem . "hundred") (:form . "hundred") (:end . 176)\n (:start . 169) (:id . 80))\n ((:tag . "NNS") (:stem . "copy") (:form . "copies") (:end . 183)\n (:start . 177) (:id . 81))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 188) (:start . 184)\n (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n (:id . 83)))@@@1@42@((:identifiers (:sid . :s6.18) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101758@unknown@formal@none@1@S@In a B and T cell site-specific recombination reaction, commonly known as V(D)J recombination, one V, one D, and one J segment are joined together into a single exon encoding the variable antigen-binding region of the receptor.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n (:id . 43))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 6) (:start . 5)\n (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 10) (:start . 7)\n (:id . 45))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 12) (:start . 11)\n (:id . 46))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 17) (:start . 13)\n (:id . 47))\n ((:tag . "JJ") (:stem . "site-specific") (:form . "site-specific")\n (:end . 31) (:start . 18) (:id . 48))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 45) (:start . 32) (:id . 49))\n ((:tag . "NN") (:stem . "reaction") (:form . "reaction") (:end . 54)\n (:start . 46) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n (:id . 51))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 64)\n (:start . 56) (:id . 52))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 70) (:start . 65)\n (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 73) (:start . 71)\n (:id . 54))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 79) (:start . 74)\n (:id . 55))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 93) (:start . 80) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n (:id . 57))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 98) (:start . 95)\n (:id . 58))\n ((:tag . "NNP") (:stem . "V") (:form . "V") (:end . 100) (:start . 99)\n (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n (:id . 60))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 105) (:start . 102)\n (:id . 61))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 107) (:start . 106)\n (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n (:id . 64))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 116) (:start . 113)\n (:id . 65))\n ((:tag . "NNP") (:stem . "J") (:form . "J") (:end . 118) (:start . 117)\n (:id . 66))\n ((:tag . "NN") (:stem . "segment") (:form . "segment") (:end . 126)\n (:start . 119) (:id . 67))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 130) (:start . 127)\n (:id . 68))\n ((:tag . "VBN") (:stem . "join") (:form . "joined") (:end . 137)\n (:start . 131) (:id . 69))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 146)\n (:start . 138) (:id . 70))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 151) (:start . 147)\n (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 153) (:start . 152)\n (:id . 72))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 160)\n (:start . 154) (:id . 73))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 165) (:start . 161)\n (:id . 74))\n ((:tag . "VBG") (:stem . "encode") (:form . "encoding") (:end . 174)\n (:start . 166) (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 178) (:start . 175)\n (:id . 76))\n ((:tag . "JJ") (:stem . "variable") (:form . "variable") (:end . 187)\n (:start . 179) (:id . 77))\n ((:tag . "JJ") (:stem . "antigen-binding") (:form . "antigen-binding")\n (:end . 203) (:start . 188) (:id . 78))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 210)\n (:start . 204) (:id . 79))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 213) (:start . 211)\n (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 217) (:start . 214)\n (:id . 81))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 226)\n (:start . 218) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n (:id . 83)))@@@1@42@((:identifiers (:sid . :s6.19) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101760@unknown@formal@none@1@S@In V(D)J recombination, DNA cleavage is catalyzed by two proteins encoded by the recombination-activating genes, approximately 1040-amino acid (aa) RAG1 and approximately 530-aa RAG2 [2,3].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 22) (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n (:id . 45))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 27) (:start . 24)\n (:id . 46))\n ((:tag . "NN") (:stem . "cleavage") (:form . "cleavage") (:end . 36)\n (:start . 28) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 39) (:start . 37)\n (:id . 48))\n ((:tag . "VBN") (:stem . "catalyze") (:form . "catalyzed") (:end . 49)\n (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 52) (:start . 50)\n (:id . 50))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 56) (:start . 53)\n (:id . 51))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 65)\n (:start . 57) (:id . 52))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 73)\n (:start . 66) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 76) (:start . 74)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n (:id . 55))\n ((:tag . "JJ") (:stem . "recombination-activating")\n (:form . "recombination-activating") (:end . 105) (:start . 81) (:id . 56))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 111)\n (:start . 106) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n (:id . 58))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 126) (:start . 113) (:id . 59))\n ((:tag . "JJ") (:stem . "1040-amino") (:form . "1040-amino") (:end . 137)\n (:start . 127) (:id . 60))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 142) (:start . 138)\n (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 144) (:start . 143)\n (:id . 62))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 146) (:start . 144)\n (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n (:id . 64))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 152) (:start . 148)\n (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n (:id . 66))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 170) (:start . 157) (:id . 67))\n ((:tag . "JJ") (:stem . "530-aa") (:form . "530-aa") (:end . 177)\n (:start . 171) (:id . 68))\n ((:tag . "NN") (:stem . "rag2") (:form . "RAG2") (:end . 182) (:start . 178)\n (:id . 69))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 184) (:start . 183)\n (:id . 70))\n ((:tag . "CD") (:stem . "2,3") (:form . "2,3") (:end . 187) (:start . 184)\n (:id . 71))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 188) (:start . 187)\n (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s6.21) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101761@unknown@formal@none@1@S@The site specificity of the recombination is defined by the binding of RAG1/2 to RSSs flanking the V, D, and J segments [4].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 20)\n (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n (:id . 46))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 41) (:start . 28) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 44) (:start . 42)\n (:id . 48))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 52)\n (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 55) (:start . 53)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n (:id . 51))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 67)\n (:start . 60) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n (:id . 53))\n ((:tag . "NNP") (:stem . "RAG1/2") (:form . "RAG1/2") (:end . 77)\n (:start . 71) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 80) (:start . 78)\n (:id . 55))\n ((:tag . "NNS") (:stem . "rss") (:form . "RSSs") (:end . 85) (:start . 81)\n (:id . 56))\n ((:tag . "VBG") (:stem . "flank") (:form . "flanking") (:end . 94)\n (:start . 86) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n (:id . 58))\n ((:tag . "NNP") (:stem . "V") (:form . "V") (:end . 100) (:start . 99)\n (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n (:id . 60))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 103) (:start . 102)\n (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n (:id . 63))\n ((:tag . "NNP") (:stem . "J") (:form . "J") (:end . 110) (:start . 109)\n (:id . 64))\n ((:tag . "NNS") (:stem . "segment") (:form . "segments") (:end . 119)\n (:start . 111) (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 121) (:start . 120)\n (:id . 66))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 122) (:start . 121)\n (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 123) (:start . 122)\n (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s6.22) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101762@unknown@formal@none@1@S@All RSSs can be divided into two groups, referred to as RSS12 and RSS23, and consist of conserved heptamer and nonamer sequences separated by a variable spacer either 12 ± 1 (RSS12) or 23 ± 1 (RSS23) bp long [4–7].@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNPS") (:stem . "RSS") (:form . "RSSs") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "VBN") (:stem . "divide") (:form . "divided") (:end . 23)\n (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 28) (:start . 24)\n (:id . 47))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 32) (:start . 29)\n (:id . 48))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 39)\n (:start . 33) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n (:id . 50))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 49)\n (:start . 41) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 55) (:start . 53)\n (:id . 53))\n ((:tag . "NN") (:stem . "rss12") (:form . "RSS12") (:end . 61) (:start . 56)\n (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n (:id . 55))\n ((:tag . "NNP") (:stem . "RSS23") (:form . "RSS23") (:end . 71) (:start . 66)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n (:id . 58))\n ((:tag . "VBP") (:stem . "consist") (:form . "consist") (:end . 84)\n (:start . 77) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n (:id . 60))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 97)\n (:start . 88) (:id . 61))\n ((:tag . "NN") (:stem . "heptamer") (:form . "heptamer") (:end . 106)\n (:start . 98) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n (:id . 63))\n ((:tag . "NN") (:stem . "nonamer") (:form . "nonamer") (:end . 118)\n (:start . 111) (:id . 64))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 128)\n (:start . 119) (:id . 65))\n ((:tag . "VBN") (:stem . "separate") (:form . "separated") (:end . 138)\n (:start . 129) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 141) (:start . 139)\n (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 143) (:start . 142)\n (:id . 68))\n ((:tag . "JJ") (:stem . "variable") (:form . "variable") (:end . 152)\n (:start . 144) (:id . 69))\n ((:tag . "NN") (:stem . "spacer") (:form . "spacer") (:end . 159)\n (:start . 153) (:id . 70))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 166)\n (:start . 160) (:id . 71))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 169) (:start . 167)\n (:id . 72))\n ((:tag . "NN") (:stem . "±") (:form . "±") (:end . 171) (:start . 170)\n (:id . 73))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 173) (:start . 172)\n (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 175) (:start . 174)\n (:id . 75))\n ((:tag . "NN") (:stem . "rss12") (:form . "RSS12") (:end . 180)\n (:start . 175) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 181) (:start . 180)\n (:id . 77))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 184) (:start . 182)\n (:id . 78))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 187) (:start . 185)\n (:id . 79))\n ((:tag . "NN") (:stem . "±") (:form . "±") (:end . 189) (:start . 188)\n (:id . 80))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 191) (:start . 190)\n (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 193) (:start . 192)\n (:id . 82))\n ((:tag . "NN") (:stem . "rss23") (:form . "RSS23") (:end . 198)\n (:start . 193) (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 199) (:start . 198)\n (:id . 84))\n ((:tag . "NN") (:stem . "bp") (:form . "bp") (:end . 202) (:start . 200)\n (:id . 85))\n ((:tag . "RB") (:stem . "long") (:form . "long") (:end . 207) (:start . 203)\n (:id . 86))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 209) (:start . 208)\n (:id . 87))\n ((:tag . "CD") (:stem . "4–7") (:form . "4–7") (:end . 212) (:start . 209)\n (:id . 88))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 213) (:start . 212)\n (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n (:id . 90)))@@@1@49@((:identifiers (:sid . :s6.23) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101763@unknown@formal@none@1@S@During V(D)J recombination, RAG1/2 complex binds one RSS12 and one RSS23, bringing them into juxtaposition, and cuts the chromosome between the RSS heptamers and the corresponding V and D, D and J, or V and J coding segments [3,8].@(((:tag . "IN") (:stem . "during") (:form . "During") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 12) (:start . 7)\n (:id . 43))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 26) (:start . 13) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n (:id . 45))\n ((:tag . "NNP") (:stem . "RAG1/2") (:form . "RAG1/2") (:end . 34)\n (:start . 28) (:id . 46))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 42)\n (:start . 35) (:id . 47))\n ((:tag . "VBZ") (:stem . "bind") (:form . "binds") (:end . 48) (:start . 43)\n (:id . 48))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 52) (:start . 49)\n (:id . 49))\n ((:tag . "NN") (:stem . "rss12") (:form . "RSS12") (:end . 58) (:start . 53)\n (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n (:id . 51))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 66) (:start . 63)\n (:id . 52))\n ((:tag . "NN") (:stem . "rss23") (:form . "RSS23") (:end . 72) (:start . 67)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n (:id . 54))\n ((:tag . "VBG") (:stem . 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"the") (:end . 143) (:start . 140)\n (:id . 65))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSS") (:end . 147) (:start . 144)\n (:id . 66))\n ((:tag . "NNS") (:stem . "heptamer") (:form . "heptamers") (:end . 157)\n (:start . 148) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 161) (:start . 158)\n (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n (:id . 69))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 179)\n (:start . 166) (:id . 70))\n ((:tag . "NNP") (:stem . "V") (:form . "V") (:end . 181) (:start . 180)\n (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 185) (:start . 182)\n (:id . 72))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 187) (:start . 186)\n (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 188) (:start . 187)\n (:id . 74))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 190) (:start . 189)\n (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 194) (:start . 191)\n (:id . 76))\n ((:tag . "NNP") (:stem . "J") (:form . "J") (:end . 196) (:start . 195)\n (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n (:id . 78))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 200) (:start . 198)\n (:id . 79))\n ((:tag . "NNP") (:stem . "V") (:form . "V") (:end . 202) (:start . 201)\n (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 206) (:start . 203)\n (:id . 81))\n ((:tag . "NNP") (:stem . "J") (:form . "J") (:end . 208) (:start . 207)\n (:id . 82))\n ((:tag . "NN") (:stem . "coding") (:form . "coding") (:end . 215)\n (:start . 209) (:id . 83))\n ((:tag . "NNS") (:stem . "segment") (:form . "segments") (:end . 224)\n (:start . 216) (:id . 84))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 226) (:start . 225)\n (:id . 85))\n ((:tag . "CD") (:stem . "3,8") (:form . "3,8") (:end . 229) (:start . 226)\n (:id . 86))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 230) (:start . 229)\n (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 231) (:start . 230)\n (:id . 88)))@@@1@47@((:identifiers (:sid . :s6.24) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101764@unknown@formal@none@1@S@A rule requiring that efficient V(D)J recombination occur between RSS12 and RSS23 is known as the “12/23” rule [1].@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "rule") (:form . "rule") (:end . 6) (:start . 2)\n (:id . 43))\n ((:tag . "VBG") (:stem . "require") (:form . "requiring") (:end . 16)\n (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n (:id . 45))\n ((:tag . "JJ") (:stem . "efficient") (:form . "efficient") (:end . 31)\n (:start . 22) (:id . 46))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 37) (:start . 32)\n (:id . 47))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 51) (:start . 38) (:id . 48))\n ((:tag . "VBP") (:stem . "occur") (:form . "occur") (:end . 57) (:start . 52)\n (:id . 49))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 65)\n (:start . 58) (:id . 50))\n ((:tag . "NN") (:stem . "rss12") (:form . "RSS12") (:end . 71) (:start . 66)\n (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n (:id . 52))\n ((:tag . "NNP") (:stem . "RSS23") (:form . "RSS23") (:end . 81) (:start . 76)\n (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 84) (:start . 82)\n (:id . 54))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 90) (:start . 85)\n (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 93) (:start . 91)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n (:id . 57))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 99) (:start . 98)\n (:id . 58))\n ((:tag . "JJ") (:stem . "12/23") (:form . "12/23") (:end . 104) (:start . 99)\n (:id . 59))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 105) (:start . 104)\n (:id . 60))\n ((:tag . "NN") (:stem . "rule") (:form . "rule") (:end . 110) (:start . 106)\n (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 112) (:start . 111)\n (:id . 62))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 113) (:start . 112)\n (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 114) (:start . 113)\n (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s6.25) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101765@unknown@formal@none@1@S@Even prior to the discovery of RAG1 and RAG2, it had been suggested that the first two RSSs were originally terminal inverted repeats (TIRs) of an ancient transposon whose accidental insertion into a gene ancestral to BCR and TCR, followed by gene duplications, triggered the emergence of the V(D)J machinery [4].@(((:tag . "RB") (:stem . "even") (:form . "Even") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 45))\n ((:tag . "NN") (:stem . "discovery") (:form . "discovery") (:end . 27)\n (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 47))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 35) (:start . 31)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n (:id . 49))\n ((:tag . "NNP") (:stem . "RAG2") (:form . "RAG2") (:end . 44) (:start . 40)\n (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n (:id . 51))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 48) (:start . 46)\n (:id . 52))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 52) (:start . 49)\n (:id . 53))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 57) (:start . 53)\n (:id . 54))\n ((:tag . "VBN") (:stem . "suggest") (:form . "suggested") (:end . 67)\n (:start . 58) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 72) (:start . 68)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n (:id . 57))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 82) (:start . 77)\n (:id . 58))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 86) (:start . 83)\n (:id . 59))\n ((:tag . "NNS") (:stem . "rss") (:form . "RSSs") (:end . 91) (:start . 87)\n (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 96) (:start . 92)\n (:id . 61))\n ((:tag . "RB") (:stem . "originally") (:form . "originally") (:end . 107)\n (:start . 97) (:id . 62))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 116)\n (:start . 108) (:id . 63))\n ((:tag . "JJ") (:stem . "inverted") (:form . "inverted") (:end . 125)\n (:start . 117) (:id . 64))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 133)\n (:start . 126) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n (:id . 66))\n ((:tag . "NNP") (:stem . "TIR") (:form . "TIRs") (:end . 139) (:start . 135)\n (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 140) (:start . 139)\n (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 143) (:start . 141)\n (:id . 69))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 146) (:start . 144)\n (:id . 70))\n ((:tag . "JJ") (:stem . "ancient") (:form . "ancient") (:end . 154)\n (:start . 147) (:id . 71))\n ((:tag . "NN") (:stem . "transposon") (:form . "transposon") (:end . 165)\n (:start . 155) (:id . 72))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 171)\n (:start . 166) (:id . 73))\n ((:tag . "JJ") (:stem . "accidental") (:form . "accidental") (:end . 182)\n (:start . 172) (:id . 74))\n ((:tag . "NN") (:stem . "insertion") (:form . "insertion") (:end . 192)\n (:start . 183) (:id . 75))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 197) (:start . 193)\n (:id . 76))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 199) (:start . 198)\n (:id . 77))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 204) (:start . 200)\n (:id . 78))\n ((:tag . "JJ") (:stem . "ancestral") (:form . "ancestral") (:end . 214)\n (:start . 205) (:id . 79))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 217) (:start . 215)\n (:id . 80))\n ((:tag . "NNP") (:stem . "BCR") (:form . "BCR") (:end . 221) (:start . 218)\n (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 225) (:start . 222)\n (:id . 82))\n ((:tag . "NNP") (:stem . "TCR") (:form . "TCR") (:end . 229) (:start . 226)\n (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 230) (:start . 229)\n (:id . 84))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 239)\n (:start . 231) (:id . 85))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 242) (:start . 240)\n (:id . 86))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 247) (:start . 243)\n (:id . 87))\n ((:tag . "NNS") (:stem . "duplication") (:form . "duplications") (:end . 260)\n (:start . 248) (:id . 88))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 261) (:start . 260)\n (:id . 89))\n ((:tag . "VBD") (:stem . "trigger") (:form . "triggered") (:end . 271)\n (:start . 262) (:id . 90))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 275) (:start . 272)\n (:id . 91))\n ((:tag . "NN") (:stem . "emergence") (:form . "emergence") (:end . 285)\n (:start . 276) (:id . 92))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 288) (:start . 286)\n (:id . 93))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 292) (:start . 289)\n (:id . 94))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 298)\n (:start . 293) (:id . 95))\n ((:tag . "NN") (:stem . "machinery") (:form . "machinery") (:end . 308)\n (:start . 299) (:id . 96))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 310) (:start . 309)\n (:id . 97))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 311) (:start . 310)\n (:id . 98))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 312) (:start . 311)\n (:id . 99))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 313) (:start . 312)\n (:id . 100)))@@@1@59@((:hcues ((:id . :x6.26.1) (:span 58 67)))\n (:hscopes ((:id . :x6.26.1) (:span 58 308)))\n (:identifiers (:sid . :s6.26) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101766@unknown@formal@none@1@S@Later, this model was expanded by the suggestion that both RAG1 and RAG2 might have evolved from a transposase (TPase) that catalyzed transpositions of ancient transposons flanked by TIRs that were precursors of RSSs [9].@(((:tag . "RB") (:stem . "later") (:form . "Later") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 17) (:start . 12)\n (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "VBN") (:stem . "expand") (:form . "expanded") (:end . 30)\n (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 33) (:start . 31)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n (:id . 49))\n ((:tag . "NN") (:stem . "suggestion") (:form . "suggestion") (:end . 48)\n (:start . 38) (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 53) (:start . 49)\n (:id . 51))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 58) (:start . 54)\n (:id . 52))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 63) (:start . 59)\n (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n (:id . 54))\n ((:tag . "NN") (:stem . "rag2") (:form . "RAG2") (:end . 72) (:start . 68)\n (:id . 55))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 78) (:start . 73)\n (:id . 56))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 83) (:start . 79)\n (:id . 57))\n ((:tag . "VBN") (:stem . "evolve") (:form . "evolved") (:end . 91)\n (:start . 84) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 96) (:start . 92)\n (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 98) (:start . 97)\n (:id . 60))\n ((:tag . "NN") (:stem . "transposase") (:form . "transposase") (:end . 110)\n (:start . 99) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n (:id . 62))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 117)\n (:start . 112) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n (:id . 64))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 123) (:start . 119)\n (:id . 65))\n ((:tag . "VBD") (:stem . "catalyze") (:form . "catalyzed") (:end . 133)\n (:start . 124) (:id . 66))\n ((:tag . "NNS") (:stem . "transposition") (:form . "transpositions")\n (:end . 148) (:start . 134) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n (:id . 68))\n ((:tag . "JJ") (:stem . "ancient") (:form . "ancient") (:end . 159)\n (:start . 152) (:id . 69))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 171)\n (:start . 160) (:id . 70))\n ((:tag . "VBN") (:stem . "flank") (:form . "flanked") (:end . 179)\n (:start . 172) (:id . 71))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 182) (:start . 180)\n (:id . 72))\n ((:tag . "NNP") (:stem . "TIR") (:form . "TIRs") (:end . 187) (:start . 183)\n (:id . 73))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 192) (:start . 188)\n (:id . 74))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 197) (:start . 193)\n (:id . 75))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 208)\n (:start . 198) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 211) (:start . 209)\n (:id . 77))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSSs") (:end . 216) (:start . 212)\n (:id . 78))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 218) (:start . 217)\n (:id . 79))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 219) (:start . 218)\n (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 220) (:start . 219)\n (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 221) (:start . 220)\n (:id . 82)))@@@1@41@((:hcues ((:id . :x6.27.1) (:span 73 78)) ((:id . :x6.27.2) (:span 38 48)))\n (:hscopes ((:id . :x6.27.1) (:span 73 216))\n ((:id . :x6.27.2) (:span 38 216)))\n (:identifiers (:sid . :s6.27) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101767@unknown@formal@none@1@S@This model has received additional support through observations of similar biochemical reactions in transposition and V(D)J recombination [10,11].@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "VBN") (:stem . "receive") (:form . "received") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 34)\n (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 42)\n (:start . 35) (:id . 47))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 50)\n (:start . 43) (:id . 48))\n ((:tag . "NNS") (:stem . "observation") (:form . "observations") (:end . 63)\n (:start . 51) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n (:id . 50))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 74)\n (:start . 67) (:id . 51))\n ((:tag . "JJ") (:stem . "biochemical") (:form . "biochemical") (:end . 86)\n (:start . 75) (:id . 52))\n ((:tag . "NNS") (:stem . "reaction") (:form . "reactions") (:end . 96)\n (:start . 87) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n (:id . 54))\n ((:tag . "NN") (:stem . "transposition") (:form . "transposition")\n (:end . 113) (:start . 100) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n (:id . 56))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 123)\n (:start . 118) (:id . 57))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 137) (:start . 124) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 139) (:start . 138)\n (:id . 59))\n ((:tag . "CD") (:stem . "10,11") (:form . "10,11") (:end . 144)\n (:start . 139) (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 145) (:start . 144)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.28) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101768@unknown@formal@none@1@S@Finally, it was demonstrated that RAG1/2 catalyzed transpositions of a DNA segment flanked by RSS12 and RSS23 in vitro [12,13] and in vivo in yeast [14].@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 15) (:start . 12)\n (:id . 45))\n ((:tag . "VBN") (:stem . "demonstrate") (:form . "demonstrated") (:end . 28)\n (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "NNP") (:stem . "RAG1/2") (:form . "RAG1/2") (:end . 40)\n (:start . 34) (:id . 48))\n ((:tag . "VBD") (:stem . "catalyze") (:form . "catalyzed") (:end . 50)\n (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "transposition") (:form . "transpositions")\n (:end . 65) (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 70) (:start . 69)\n (:id . 52))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 74) (:start . 71)\n (:id . 53))\n ((:tag . "NN") (:stem . "segment") (:form . "segment") (:end . 82)\n (:start . 75) (:id . 54))\n ((:tag . "VBN") (:stem . "flank") (:form . "flanked") (:end . 90)\n (:start . 83) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 93) (:start . 91)\n (:id . 56))\n ((:tag . "NN") (:stem . "rss12") (:form . "RSS12") (:end . 99) (:start . 94)\n (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n (:id . 58))\n ((:tag . "NN") (:stem . "rss23") (:form . "RSS23") (:end . 109)\n (:start . 104) (:id . 59))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 112) (:start . 110)\n (:id . 60))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 118)\n (:start . 113) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 120) (:start . 119)\n (:id . 62))\n ((:tag . "CD") (:stem . "12,13") (:form . "12,13") (:end . 125)\n (:start . 120) (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 126) (:start . 125)\n (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n (:id . 65))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 133) (:start . 131)\n (:id . 66))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 138) (:start . 134)\n (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 141) (:start . 139)\n (:id . 68))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 147)\n (:start . 142) (:id . 69))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 149) (:start . 148)\n (:id . 70))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 151) (:start . 149)\n (:id . 71))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 152) (:start . 151)\n (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s6.29) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101770@unknown@formal@none@1@S@So far, only one putative instance of such a transposition has been reported [15].@(((:tag . "RB") (:stem . "so") (:form . "So") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "far") (:form . "far") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 44))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 12) (:start . 8)\n (:id . 45))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 16) (:start . 13)\n (:id . 46))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 25)\n (:start . 17) (:id . 47))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 34)\n (:start . 26) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n (:id . 49))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 42) (:start . 38)\n (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n (:id . 51))\n ((:tag . "NN") (:stem . "transposition") (:form . "transposition")\n (:end . 58) (:start . 45) (:id . 52))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 62) (:start . 59)\n (:id . 53))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 67) (:start . 63)\n (:id . 54))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 76)\n (:start . 68) (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 78) (:start . 77)\n (:id . 56))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 80) (:start . 78)\n (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 81) (:start . 80)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s6.31) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101771@unknown@formal@none@1@S@However, given the lack of significant structural similarities between RAGs and known TPases, the “RAG transposon” model [9,12,13,16] remained unproven.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "lack") (:form . "lack") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 47))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 38)\n (:start . 27) (:id . 48))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 49)\n (:start . 39) (:id . 49))\n ((:tag . "NNS") (:stem . "similarity") (:form . "similarities") (:end . 62)\n (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 70)\n (:start . 63) (:id . 51))\n ((:tag . "NNS") (:stem . "rag") (:form . "RAGs") (:end . 75) (:start . 71)\n (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 79) (:start . 76)\n (:id . 53))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 85) (:start . 80)\n (:id . 54))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 92) (:start . 86)\n (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n (:id . 57))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 99) (:start . 98)\n (:id . 58))\n ((:tag . "NN") (:stem . "RAG") (:form . "RAG") (:end . 102) (:start . 99)\n (:id . 59))\n ((:tag . "NN") (:stem . "transposon") (:form . "transposon") (:end . 113)\n (:start . 103) (:id . 60))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 114) (:start . 113)\n (:id . 61))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 120)\n (:start . 115) (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 122) (:start . 121)\n (:id . 63))\n ((:tag . "CD") (:stem . "9,12,13,16") (:form . "9,12,13,16") (:end . 132)\n (:start . 122) (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 133) (:start . 132)\n (:id . 65))\n ((:tag . "VBD") (:stem . "remain") (:form . "remained") (:end . 142)\n (:start . 134) (:id . 66))\n ((:tag . "JJ") (:stem . "unproven") (:form . "unproven") (:end . 151)\n (:start . 143) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n (:id . 68)))@@@1@27@((:hcues ((:id . :x6.32.1) (:span 143 151)))\n (:ncues ((:id . :x6.32.2) (:span 19 23)))\n (:hscopes ((:id . :x6.32.1) (:span 94 151)))\n (:nscopes ((:id . :x6.32.2) (:span 19 92)))\n (:identifiers (:sid . :s6.32) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101772@unknown@formal@none@1@S@Here we demonstrate that the RAG1 core and RSSs were derived from a TPase and TIRs encoded by ancient DNA transposons from the Transib superfamily [17].@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 19)\n (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 38) (:start . 34)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n (:id . 49))\n ((:tag . "NNS") (:stem . "rss") (:form . "RSSs") (:end . 47) (:start . 43)\n (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 52) (:start . 48)\n (:id . 51))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 60)\n (:start . 53) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 65) (:start . 61)\n (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 67) (:start . 66)\n (:id . 54))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 73) (:start . 68)\n (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n (:id . 56))\n ((:tag . "NNP") (:stem . "TIR") (:form . "TIRs") (:end . 82) (:start . 78)\n (:id . 57))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 90)\n (:start . 83) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 93) (:start . 91)\n (:id . 59))\n ((:tag . "JJ") (:stem . "ancient") (:form . "ancient") (:end . 101)\n (:start . 94) (:id . 60))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 105) (:start . 102)\n (:id . 61))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 117)\n (:start . 106) (:id . 62))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 122) (:start . 118)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n (:id . 64))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 134)\n (:start . 127) (:id . 65))\n ((:tag . "NN") (:stem . "superfamily") (:form . "superfamily") (:end . 146)\n (:start . 135) (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 148) (:start . 147)\n (:id . 67))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 150) (:start . 148)\n (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 151) (:start . 150)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s6.33) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101773@unknown@formal@none@1@S@The Transib superfamily is one of ten superfamilies of DNA transposons detected so far in eukaryotes [17].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "superfamily") (:form . "superfamily") (:end . 23)\n (:start . 12) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n (:id . 45))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n (:id . 47))\n ((:tag . "CD") (:stem . "ten") (:form . "ten") (:end . 37) (:start . 34)\n (:id . 48))\n ((:tag . "NNS") (:stem . "superfamily") (:form . "superfamilies") (:end . 51)\n (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n (:id . 50))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 58) (:start . 55)\n (:id . 51))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 70)\n (:start . 59) (:id . 52))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 79)\n (:start . 71) (:id . 53))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 82) (:start . 80)\n (:id . 54))\n ((:tag . "RB") (:stem . "far") (:form . "far") (:end . 86) (:start . 83)\n (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n (:id . 56))\n ((:tag . "NNS") (:stem . "eukaryote") (:form . "eukaryotes") (:end . 100)\n (:start . 90) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 102) (:start . 101)\n (:id . 58))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 104) (:start . 102)\n (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 105) (:start . 104)\n (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.34) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101774@unknown@formal@none@1@S@Like other DNA transposons, Transib transposons exist as autonomous and nonautonomous elements.@(((:tag . "IN") (:stem . "like") (:form . "Like") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 26)\n (:start . 15) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 35)\n (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 47)\n (:start . 36) (:id . 48))\n ((:tag . "VBP") (:stem . "exist") (:form . "exist") (:end . 53) (:start . 48)\n (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 56) (:start . 54)\n (:id . 50))\n ((:tag . "JJ") (:stem . "autonomous") (:form . "autonomous") (:end . 67)\n (:start . 57) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n (:id . 52))\n ((:tag . "JJ") (:stem . "nonautonomous") (:form . "nonautonomous")\n (:end . 85) (:start . 72) (:id . 53))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 94)\n (:start . 86) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s6.35) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101775@unknown@formal@none@1@S@The autonomous Transib transposons are 3–4 kb long and code for an approximately 700-aa TPase that is not similar to TPases from any other transposon superfamilies.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "autonomous") (:form . "autonomous") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 22)\n (:start . 15) (:id . 44))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 34)\n (:start . 23) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 38) (:start . 35)\n (:id . 46))\n ((:tag . "CD") (:stem . "3–4") (:form . "3–4") (:end . 42) (:start . 39)\n (:id . 47))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 45) (:start . 43)\n (:id . 48))\n ((:tag . "JJ") (:stem . "long") (:form . "long") (:end . 50) (:start . 46)\n (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n (:id . 50))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 59) (:start . 55)\n (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 63) (:start . 60)\n (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 66) (:start . 64)\n (:id . 53))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 80) (:start . 67) (:id . 54))\n ((:tag . "JJ") (:stem . "700-aa") (:form . "700-aa") (:end . 87)\n (:start . 81) (:id . 55))\n ((:tag . "NN") (:stem . "tpase") (:form . "TPase") (:end . 93) (:start . 88)\n (:id . 56))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 98) (:start . 94)\n (:id . 57))\n ((:tag . 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(:end . 164) (:start . 163)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s6.36) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101776@unknown@formal@none@1@S@Computational analysis of Transib elements, including their numerous insertions into copies of other transposons, demonstrated that Transib transposons are flanked by 5-bp target site duplications (TSDs), which also distinguishes this superfamily from all the others [17].@(((:tag . "JJ") (:stem . "computational") (:form . "Computational")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 22)\n (:start . 14) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 33)\n (:start . 26) (:id . 45))\n ((:tag . "NNS") (:stem . "element") (:form . 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(:end . 272) (:start . 271)\n (:id . 85)))@@@1@44@((:identifiers (:sid . :s6.37) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101777@unknown@formal@none@1@S@Transib transpositions are expected to be catalyzed by the binding of the TPase to TIRs of autonomous and nonautonomous transposons [17].@(((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "transposition") (:form . "transpositions")\n (:end . 22) (:start . 8) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 26) (:start . 23)\n (:id . 44))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 35)\n (:start . 27) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 41) (:start . 39)\n (:id . 47))\n ((:tag . "VBN") (:stem . "catalyze") (:form . 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"and") (:form . "and") (:end . 105) (:start . 102)\n (:id . 59))\n ((:tag . "JJ") (:stem . "nonautonomous") (:form . "nonautonomous")\n (:end . 119) (:start . 106) (:id . 60))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 131)\n (:start . 120) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 133) (:start . 132)\n (:id . 62))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 135) (:start . 133)\n (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 136) (:start . 135)\n (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n (:id . 65)))@@@1@24@((:hcues ((:id . :x6.38.1) (:span 27 35)))\n (:hscopes ((:id . :x6.38.1) (:span 27 131)))\n (:identifiers (:sid . :s6.38) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101778@unknown@formal@none@1@S@As discussed in this paper, in addition to the fruit fly (Drosophila melanogaster) and African malaria mosquito (Anopheles gambiae) genomes, in which Transib transposons were originally discovered, these genes are also present in diverse animals (Table S1), including other species of fruit fly (e.g., Drosophila pseudoobscura, Drosophila willistoni), yellow fever mosquito (Anopheles aegypti), silkworm (Bombyx mori), red flour beetle (Tribolium castaneum), dog hookworm (Ancylostoma caninum), freshwater flatworm (Schmidtea mediterranea), hydra (Hydra magnipapillata), sea urchin (Strongylocentrotus purpuratus), and soybean rust (Phakopsora pachyrhizi).@(((:tag . 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(:end . 656) (:start . 655)\n (:id . 161)))@@@1@120@((:identifiers (:sid . :s6.39) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101780@unknown@formal@none@1@S@Schematic Presentation of Transib transposons, RAG1, RAG2, and RAG1-Like Proteins in Eukaryotes@(((:tag . "JJ") (:stem . "schematic") (:form . "Schematic") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Presentation") (:form . "Presentation") (:end . 22)\n (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 33)\n (:start . 26) (:id . 45))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 45)\n (:start . 34) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n (:id . 47))\n ((:tag . "NNP") (:stem . "RAG1") (:form . 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(:end . 86) (:start . 85)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s6.42) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101782@unknown@formal@none@1@S@Red circles mark species in which Transib TPases were found.@(((:tag . "JJ") (:stem . "red") (:form . "Red") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "circle") (:form . "circles") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "mark") (:form . "mark") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 24)\n (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 33) (:start . 28)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 41)\n (:start . 34) (:id . 48))\n ((:tag . "NNP") (:stem . "TPas") (:form . 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(:end . 76) (:start . 75)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s6.46) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101786@unknown@formal@none@1@S@A lack of any labels means that the Transib TPase and RAG1/2 are not present in the sequenced portions of the corresponding genomes.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "lack") (:form . "lack") (:end . 6) (:start . 2)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 9) (:start . 7)\n (:id . 44))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 13) (:start . 10)\n (:id . 45))\n ((:tag . "NNS") (:stem . "label") (:form . "labels") (:end . 20)\n (:start . 14) (:id . 46))\n ((:tag . "VBZ") (:stem . "mean") (:form . "means") (:end . 26) (:start . 21)\n (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 31) (:start . 27)\n (:id . 48))\n ((:tag . 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"sequenced") (:end . 93)\n (:start . 84) (:id . 59))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 102)\n (:start . 94) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n (:id . 62))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 123)\n (:start . 110) (:id . 63))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 131)\n (:start . 124) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n (:id . 65)))@@@1@24@((:ncues ((:id . :x6.47.1) (:span 65 68)) ((:id . :x6.47.2) (:span 2 6)))\n (:nscopes ((:id . :x6.47.1) (:span 65 131)) ((:id . :x6.47.2) (:span 2 20)))\n (:identifiers (:sid . :s6.47) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101787@unknown@formal@none@1@S@Among branches lacking Transib TPases, only lamprey and crocodile genomes are not extensively sequenced to date.@(((:tag . "IN") (:stem . "among") (:form . "Among") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "branch") (:form . "branches") (:end . 14)\n (:start . 6) (:id . 43))\n ((:tag . "VBG") (:stem . "lack") (:form . "lacking") (:end . 22)\n (:start . 15) (:id . 44))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 30)\n (:start . 23) (:id . 45))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 37) (:start . 31)\n (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n (:id . 47))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 43) (:start . 39)\n (:id . 48))\n ((:tag . "NN") (:stem . "lamprey") (:form . "lamprey") (:end . 51)\n (:start . 44) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n (:id . 50))\n ((:tag . "NN") (:stem . "crocodile") (:form . "crocodile") (:end . 65)\n (:start . 56) (:id . 51))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 73)\n (:start . 66) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 77) (:start . 74)\n (:id . 53))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 81) (:start . 78)\n (:id . 54))\n ((:tag . "RB") (:stem . "extensively") (:form . "extensively") (:end . 93)\n (:start . 82) (:id . 55))\n ((:tag . "VBN") (:stem . "sequence") (:form . "sequenced") (:end . 103)\n (:start . 94) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 106) (:start . 104)\n (:id . 57))\n ((:tag . "NN") (:stem . "date") (:form . "date") (:end . 111) (:start . 107)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n (:id . 59)))@@@1@18@((:ncues ((:id . :x6.48.1) (:span 78 81)) ((:id . :x6.48.2) (:span 15 22)))\n (:nscopes ((:id . :x6.48.1) (:span 44 111)) ((:id . :x6.48.2) (:span 15 37)))\n (:identifiers (:sid . :s6.48) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101788@unknown@formal@none@1@S@In sea anemone, the RAG1 core–like protein is capped by the ring finger motif, which also forms the C-terminus in the RAG1 N-terminal domain.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "anemone") (:form . "anemone") (:end . 14)\n (:start . 7) (:id . 44))\n ((:tag . 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"finger") (:end . 71)\n (:start . 65) (:id . 55))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 77) (:start . 72)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n (:id . 57))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 84) (:start . 79)\n (:id . 58))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 89) (:start . 85)\n (:id . 59))\n ((:tag . "VBZ") (:stem . "form") (:form . "forms") (:end . 95) (:start . 90)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n (:id . 61))\n ((:tag . "NNP") (:stem . "C-terminus") (:form . "C-terminus") (:end . 110)\n (:start . 100) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 113) (:start . 111)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n (:id . 64))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 122) (:start . 118)\n (:id . 65))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 133)\n (:start . 123) (:id . 66))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 140)\n (:start . 134) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s6.49) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101790@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s6.51) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101791@unknown@formal@none@1@S@Detection of Similarity between Transib TPases and RAG1@(((:tag . "NNP") (:stem . "Detection") (:form . "Detection") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Similarity") (:form . "Similarity") (:end . 23)\n (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 31)\n (:start . 24) (:id . 45))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 39)\n (:start . 32) (:id . 46))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 46) (:start . 40)\n (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n (:id . 48))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 55) (:start . 51)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s6.52) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101792@unknown@formal@none@1@S@Using protein sequences of seven known Transib TPases (Transib1 through Transib4 and Transib1_AG through Transib3_AG from D. melanogaster and A. gambiae, respectively) [17] as queries in a standard BLASTP search against all GenBank proteins, we found that the approximately 60-aa C-terminal portion of the Transib2_AG TPase was 35%-38% identical to the C-terminal portion of the RAG1 core (Figure S1).@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 13)\n (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 23)\n (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . 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"Transib1_AG") (:end . 96)\n (:start . 85) (:id . 55))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 104)\n (:start . 97) (:id . 56))\n ((:tag . "NNP") (:stem . "Transib3_AG") (:form . "Transib3_AG") (:end . 116)\n (:start . 105) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 121) (:start . 117)\n (:id . 58))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 124) (:start . 122)\n (:id . 59))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 137)\n (:start . 125) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 141) (:start . 138)\n (:id . 61))\n ((:tag . "NN") (:stem . "a.") (:form . "A.") (:end . 144) (:start . 142)\n (:id . 62))\n ((:tag . "NN") (:stem . "gambiae") (:form . "gambiae") (:end . 152)\n (:start . 145) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n (:id . 64))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 166)\n (:start . 154) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 169) (:start . 168)\n (:id . 67))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 171) (:start . 169)\n (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 172) (:start . 171)\n (:id . 69))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 175) (:start . 173)\n (:id . 70))\n ((:tag . "NNS") (:stem . "query") (:form . "queries") (:end . 183)\n (:start . 176) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 186) (:start . 184)\n (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 188) (:start . 187)\n (:id . 73))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 197)\n (:start . 189) (:id . 74))\n ((:tag . "NNP") (:stem . "BLASTP") (:form . "BLASTP") (:end . 204)\n (:start . 198) (:id . 75))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 211)\n (:start . 205) (:id . 76))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 219)\n (:start . 212) (:id . 77))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 223) (:start . 220)\n (:id . 78))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 231)\n (:start . 224) (:id . 79))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 240)\n (:start . 232) (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 241) (:start . 240)\n (:id . 81))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 244) (:start . 242)\n (:id . 82))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 250)\n (:start . 245) (:id . 83))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 255) (:start . 251)\n (:id . 84))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 259) (:start . 256)\n (:id . 85))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 273) (:start . 260) (:id . 86))\n ((:tag . "JJ") (:stem . "60-aa") (:form . "60-aa") (:end . 279)\n (:start . 274) (:id . 87))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 290)\n (:start . 280) (:id . 88))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 298)\n (:start . 291) (:id . 89))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 301) (:start . 299)\n (:id . 90))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 305) (:start . 302)\n (:id . 91))\n ((:tag . "NNP") (:stem . "Transib2_AG") (:form . "Transib2_AG") (:end . 317)\n (:start . 306) (:id . 92))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 323)\n (:start . 318) (:id . 93))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 327) (:start . 324)\n (:id . 94))\n ((:tag . "CD") (:stem . "35%-38") (:form . "35%-38") (:end . 334)\n (:start . 328) (:id . 95))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 335) (:start . 334)\n (:id . 96))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 345)\n (:start . 336) (:id . 97))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 348) (:start . 346)\n (:id . 98))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 352) (:start . 349)\n (:id . 99))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 363)\n (:start . 353) (:id . 100))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 371)\n (:start . 364) (:id . 101))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 374) (:start . 372)\n (:id . 102))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 378) (:start . 375)\n (:id . 103))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 383) (:start . 379)\n (:id . 104))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 388) (:start . 384)\n (:id . 105))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 390) (:start . 389)\n (:id . 106))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 396)\n (:start . 390) (:id . 107))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 399) (:start . 397)\n (:id . 108))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 400) (:start . 399)\n (:id . 109))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 401) (:start . 400)\n (:id . 110)))@@@1@69@((:identifiers (:sid . :s6.53) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101793@unknown@formal@none@1@S@However, this similarity was only marginally significant (E = 0.07 where the E-value is an expected number of sequences matching by chance; Table 1).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 24)\n (:start . 14) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "RB") (:stem . "marginally") (:form . "marginally") (:end . 44)\n (:start . 34) (:id . 48))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 56)\n (:start . 45) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n (:id . 50))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 59) (:start . 58)\n (:id . 51))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 61) (:start . 60)\n (:id . 52))\n ((:tag . "CD") (:stem . "0.07") (:form . "0.07") (:end . 66) (:start . 62)\n (:id . 53))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 72) (:start . 67)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n (:id . 55))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-value") (:end . 84)\n (:start . 77) (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 87) (:start . 85)\n (:id . 57))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 90) (:start . 88)\n (:id . 58))\n ((:tag . "JJ") (:stem . "expected") (:form . "expected") (:end . 99)\n (:start . 91) (:id . 59))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 106)\n (:start . 100) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 109) (:start . 107)\n (:id . 61))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 119)\n (:start . 110) (:id . 62))\n ((:tag . "VBG") (:stem . "match") (:form . "matching") (:end . 128)\n (:start . 120) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 131) (:start . 129)\n (:id . 64))\n ((:tag . "NN") (:stem . "chance") (:form . "chance") (:end . 138)\n (:start . 132) (:id . 65))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 139) (:start . 138)\n (:id . 66))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 145)\n (:start . 140) (:id . 67))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 147) (:start . 146)\n (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s6.54) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101794@unknown@formal@none@1@S@In another search against GenBank, using PSI-BLAST [18] (see Materials and Methods) with the Transib2_AG TPase as a query, we found that two unclassified proteins (GenBank gi 30923617 and 30923765; annotated as hypothetical proteins) and RAG1s constituted the only group of any GenBank proteins similar to the Transib2_AG TPase (Table 1).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 17)\n (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 25)\n (:start . 18) (:id . 45))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 33)\n (:start . 26) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 40) (:start . 35)\n (:id . 48))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 50)\n (:start . 41) (:id . 49))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 52) (:start . 51)\n (:id . 50))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 54) (:start . 52)\n (:id . 51))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 55) (:start . 54)\n (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n (:id . 53))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 60) (:start . 57)\n (:id . 54))\n ((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 70)\n (:start . 61) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n (:id . 56))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 82)\n (:start . 75) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 88) (:start . 84)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n (:id . 60))\n ((:tag . "NNP") (:stem . "Transib2_AG") (:form . "Transib2_AG") (:end . 104)\n (:start . 93) (:id . 61))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 110)\n (:start . 105) (:id . 62))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 113) (:start . 111)\n (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 115) (:start . 114)\n (:id . 64))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 121)\n (:start . 116) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n (:id . 66))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 125) (:start . 123)\n (:id . 67))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 131)\n (:start . 126) (:id . 68))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 136) (:start . 132)\n (:id . 69))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 140) (:start . 137)\n (:id . 70))\n ((:tag . "JJ") (:stem . "unclassified") (:form . "unclassified") (:end . 153)\n (:start . 141) (:id . 71))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 162)\n (:start . 154) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 164) (:start . 163)\n (:id . 73))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 171)\n (:start . 164) (:id . 74))\n ((:tag . "NNP") (:stem . "gi") (:form . "gi") (:end . 174) (:start . 172)\n (:id . 75))\n ((:tag . "CD") (:stem . "30923617") (:form . "30923617") (:end . 183)\n (:start . 175) (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 187) (:start . 184)\n (:id . 77))\n ((:tag . "CD") (:stem . "30923765") (:form . 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(:end . 139) (:start . 138)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s6.59) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101800@unknown@formal@none@1@S@As a result, Ei-values for matches of RAG1s to a new PSSM based on alignment of nine Transib TPases (the two GenBank TPase-like proteins plus seven added TPases) noticeably dropped in comparison with the Ei-values obtained for the PSSM constructed in the previous step based on alignment of the three TPases (Table 1).@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 11) (:start . 5)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 45))\n ((:tag . "NNS") (:stem . "ei-value") (:form . "Ei-values") (:end . 22)\n (:start . 13) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 26) (:start . 23)\n (:id . 47))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 34)\n (:start . 27) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n (:id . 49))\n ((:tag . "NNS") (:stem . "rag1") (:form . "RAG1s") (:end . 43) (:start . 38)\n (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 46) (:start . 44)\n (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n (:id . 52))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 52) (:start . 49)\n (:id . 53))\n ((:tag . "NN") (:stem . "pssm") (:form . "PSSM") (:end . 57) (:start . 53)\n (:id . 54))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 63) (:start . 58)\n (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 66) (:start . 64)\n (:id . 56))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 76)\n (:start . 67) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n (:id . 58))\n ((:tag . "CD") (:stem . "nine") (:form . "nine") (:end . 84) (:start . 80)\n (:id . 59))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 92)\n (:start . 85) (:id . 60))\n ((:tag . "NNPS") (:stem . "TPas") (:form . "TPases") (:end . 99)\n (:start . 93) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 101) (:start . 100)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n (:id . 63))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 108) (:start . 105)\n (:id . 64))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 116)\n (:start . 109) (:id . 65))\n ((:tag . "JJ") (:stem . "tpase-like") (:form . "TPase-like") (:end . 127)\n (:start . 117) (:id . 66))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 136)\n (:start . 128) (:id . 67))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 141) (:start . 137)\n (:id . 68))\n ((:tag . "CD") (:stem . "seven") (:form . "seven") (:end . 147)\n (:start . 142) (:id . 69))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 153) (:start . 148)\n (:id . 70))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 160)\n (:start . 154) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 161) (:start . 160)\n (:id . 72))\n ((:tag . "RB") (:stem . "noticeably") (:form . "noticeably") (:end . 172)\n (:start . 162) (:id . 73))\n ((:tag . "VBD") (:stem . "drop") (:form . "dropped") (:end . 180)\n (:start . 173) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 183) (:start . 181)\n (:id . 75))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 194)\n (:start . 184) (:id . 76))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 199) (:start . 195)\n (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 203) (:start . 200)\n (:id . 78))\n ((:tag . "NNS") (:stem . "ei-value") (:form . "Ei-values") (:end . 213)\n (:start . 204) (:id . 79))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 222)\n (:start . 214) (:id . 80))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 226) (:start . 223)\n (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 230) (:start . 227)\n (:id . 82))\n ((:tag . "NN") (:stem . "pssm") (:form . "PSSM") (:end . 235) (:start . 231)\n (:id . 83))\n ((:tag . "VBN") (:stem . "construct") (:form . "constructed") (:end . 247)\n (:start . 236) (:id . 84))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 250) (:start . 248)\n (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 254) (:start . 251)\n (:id . 86))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 263)\n (:start . 255) (:id . 87))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 268) (:start . 264)\n (:id . 88))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 274)\n (:start . 269) (:id . 89))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 277) (:start . 275)\n (:id . 90))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 287)\n (:start . 278) (:id . 91))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 290) (:start . 288)\n (:id . 92))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 294) (:start . 291)\n (:id . 93))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 300)\n (:start . 295) (:id . 94))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 307)\n (:start . 301) (:id . 95))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 309) (:start . 308)\n (:id . 96))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 314)\n (:start . 309) (:id . 97))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 316) (:start . 315)\n (:id . 98))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 317) (:start . 316)\n (:id . 99))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 318) (:start . 317)\n (:id . 100)))@@@1@59@((:identifiers (:sid . :s6.61) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101801@unknown@formal@none@1@S@To support the observation that Ei-values of matches between RAG1s and the Transib TPase PSSM decrease as the number of TPase sequences used for construction of the PSSM increases, we identified six new Transib TPases (Transib5, Transib3_DP, Transib4_DP, Transib1_AA, Transib2_AA, Transib3_AA; Figure S2).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "support") (:form . "support") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 26)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 31) (:start . 27)\n (:id . 46))\n ((:tag . "NNS") (:stem . "ei-value") (:form . "Ei-values") (:end . 41)\n (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n (:id . 48))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 52)\n (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 60)\n (:start . 53) (:id . 50))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1s") (:end . 66) (:start . 61)\n (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 82)\n (:start . 75) (:id . 54))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 88) (:start . 83)\n (:id . 55))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 93) (:start . 89)\n (:id . 56))\n ((:tag . "NN") (:stem . "decrease") (:form . "decrease") (:end . 102)\n (:start . 94) (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 105) (:start . 103)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n (:id . 59))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 116)\n (:start . 110) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n (:id . 61))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 125)\n (:start . 120) (:id . 62))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 135)\n (:start . 126) (:id . 63))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 140) (:start . 136)\n (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 144) (:start . 141)\n (:id . 65))\n ((:tag . "NN") (:stem . "construction") (:form . "construction") (:end . 157)\n (:start . 145) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 160) (:start . 158)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 164) (:start . 161)\n (:id . 68))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 169) (:start . 165)\n (:id . 69))\n ((:tag . "VBZ") (:stem . "increase") (:form . "increases") (:end . 179)\n (:start . 170) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 180) (:start . 179)\n (:id . 71))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 183) (:start . 181)\n (:id . 72))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 194)\n (:start . 184) (:id . 73))\n ((:tag . "CD") (:stem . "six") (:form . "six") (:end . 198) (:start . 195)\n (:id . 74))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 202) (:start . 199)\n (:id . 75))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 210)\n (:start . 203) (:id . 76))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 217)\n (:start . 211) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 219) (:start . 218)\n (:id . 78))\n ((:tag . "NNP") (:stem . "Transib5") (:form . "Transib5") (:end . 227)\n (:start . 219) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 228) (:start . 227)\n (:id . 80))\n ((:tag . "NNP") (:stem . "Transib3_DP") (:form . "Transib3_DP") (:end . 240)\n (:start . 229) (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 241) (:start . 240)\n (:id . 82))\n ((:tag . "NNP") (:stem . "Transib4_DP") (:form . "Transib4_DP") (:end . 253)\n (:start . 242) (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 254) (:start . 253)\n (:id . 84))\n ((:tag . "NNP") (:stem . "Transib1_AA") (:form . "Transib1_AA") (:end . 266)\n (:start . 255) (:id . 85))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 267) (:start . 266)\n (:id . 86))\n ((:tag . "NNP") (:stem . "Transib2_AA") (:form . "Transib2_AA") (:end . 279)\n (:start . 268) (:id . 87))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 280) (:start . 279)\n (:id . 88))\n ((:tag . "NNP") (:stem . "Transib3_AA") (:form . "Transib3_AA") (:end . 292)\n (:start . 281) (:id . 89))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 293) (:start . 292)\n (:id . 90))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 300)\n (:start . 294) (:id . 91))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 303) (:start . 301)\n (:id . 92))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 304) (:start . 303)\n (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 305) (:start . 304)\n (:id . 94)))@@@1@53@((:identifiers (:sid . :s6.62) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101802@unknown@formal@none@1@S@During the next step of the PSI-BLAST analysis, the original GenBank set was combined with 13 Transib TPases.@(((:tag . "IN") (:stem . "during") (:form . "During") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n (:id . 43))\n ((:tag . "JJ") (:stem . "next") (:form . "next") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 37)\n (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 46)\n (:start . 38) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n (:id . 51))\n ((:tag . "JJ") (:stem . "original") (:form . "original") (:end . 60)\n (:start . 52) (:id . 52))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 68)\n (:start . 61) (:id . 53))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 72) (:start . 69)\n (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 76) (:start . 73)\n (:id . 55))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 85)\n (:start . 77) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 90) (:start . 86)\n (:id . 57))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 93) (:start . 91)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 101)\n (:start . 94) (:id . 59))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 108)\n (:start . 102) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.63) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101803@unknown@formal@none@1@S@Again, Ei-values of matches between RAG1s and the new PSSM derived from multiple alignment of 15 Transib TPases (the two GenBank proteins plus all our TPases) were much smaller (approximately 10-6–10-3; Table 1) than those obtained based on the PSSM constructed from the nine TPases at the preceding step (approximately 10-3–10-2).@(((:tag . "RB") (:stem . "again") (:form . "Again") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "NNS") (:stem . "ei-value") (:form . "Ei-values") (:end . 16)\n (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 27)\n (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 35)\n (:start . 28) (:id . 47))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1s") (:end . 41) (:start . 36)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n (:id . 50))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 53) (:start . 50)\n (:id . 51))\n ((:tag . "NN") (:stem . "pssm") (:form . "PSSM") (:end . 58) (:start . 54)\n (:id . 52))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 66)\n (:start . 59) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 71) (:start . 67)\n (:id . 54))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 80)\n (:start . 72) (:id . 55))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 90)\n (:start . 81) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n (:id . 57))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 96) (:start . 94)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 104)\n (:start . 97) (:id . 59))\n ((:tag . "NNPS") (:stem . "TPas") (:form . "TPases") (:end . 111)\n (:start . 105) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 113) (:start . 112)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n (:id . 62))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 120) (:start . 117)\n (:id . 63))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 128)\n (:start . 121) (:id . 64))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 137)\n (:start . 129) (:id . 65))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 142) (:start . 138)\n (:id . 66))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 146) (:start . 143)\n (:id . 67))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 150) (:start . 147)\n (:id . 68))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 157)\n (:start . 151) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n (:id . 70))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 163) (:start . 159)\n (:id . 71))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 168) (:start . 164)\n (:id . 72))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 176)\n (:start . 169) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 178) (:start . 177)\n (:id . 74))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 191) (:start . 178) (:id . 75))\n ((:tag . "CD") (:stem . "10-6–10-3") (:form . "10-6–10-3") (:end . 201)\n (:start . 192) (:id . 76))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 202) (:start . 201)\n (:id . 77))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 208)\n (:start . 203) (:id . 78))\n ((:tag . "LS") (:stem . "1") (:form . "1") (:end . 210) (:start . 209)\n (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 211) (:start . 210)\n (:id . 80))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 216) (:start . 212)\n (:id . 81))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 222)\n (:start . 217) (:id . 82))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 231)\n (:start . 223) (:id . 83))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 237)\n (:start . 232) (:id . 84))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 240) (:start . 238)\n (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 244) (:start . 241)\n (:id . 86))\n ((:tag . "NN") (:stem . "pssm") (:form . "PSSM") (:end . 249) (:start . 245)\n (:id . 87))\n ((:tag . "VBN") (:stem . "construct") (:form . "constructed") (:end . 261)\n (:start . 250) (:id . 88))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 266) (:start . 262)\n (:id . 89))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 270) (:start . 267)\n (:id . 90))\n ((:tag . "CD") (:stem . "nine") (:form . "nine") (:end . 275) (:start . 271)\n (:id . 91))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 282)\n (:start . 276) (:id . 92))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 285) (:start . 283)\n (:id . 93))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 289) (:start . 286)\n (:id . 94))\n ((:tag . "VBG") (:stem . "precede") (:form . "preceding") (:end . 299)\n (:start . 290) (:id . 95))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 304) (:start . 300)\n (:id . 96))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 306) (:start . 305)\n (:id . 97))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 319) (:start . 306) (:id . 98))\n ((:tag . "CD") (:stem . "10-3–10-2") (:form . "10-3–10-2") (:end . 329)\n (:start . 320) (:id . 99))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 330) (:start . 329)\n (:id . 100))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 331) (:start . 330)\n (:id . 101)))@@@1@60@((:identifiers (:sid . :s6.64) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101804@unknown@formal@none@1@S@In the final step, we identified one more set of five new Transib TPases (Transib1_DP, Transib2_DP, Transib4_AA, Transib5_AA, and Transib1_SP).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 12) (:start . 7)\n (:id . 44))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 17) (:start . 13)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 21) (:start . 19)\n (:id . 47))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 32)\n (:start . 22) (:id . 48))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 36) (:start . 33)\n (:id . 49))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 41) (:start . 37)\n (:id . 50))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 45) (:start . 42)\n (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n (:id . 52))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 53) (:start . 49)\n (:id . 53))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 57) (:start . 54)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 65)\n (:start . 58) (:id . 55))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 72) (:start . 66)\n (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 74) (:start . 73)\n (:id . 57))\n ((:tag . "NNP") (:stem . "Transib1_DP") (:form . "Transib1_DP") (:end . 85)\n (:start . 74) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n (:id . 59))\n ((:tag . "NNP") (:stem . "Transib2_DP") (:form . "Transib2_DP") (:end . 98)\n (:start . 87) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n (:id . 61))\n ((:tag . "NNP") (:stem . "Transib4_AA") (:form . "Transib4_AA") (:end . 111)\n (:start . 100) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n (:id . 63))\n ((:tag . "NNP") (:stem . "Transib5_AA") (:form . "Transib5_AA") (:end . 124)\n (:start . 113) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n (:id . 66))\n ((:tag . "NNP") (:stem . "Transib1_SP") (:form . "Transib1_SP") (:end . 141)\n (:start . 130) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s6.65) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101805@unknown@formal@none@1@S@When all 18 TPases were combined with the original GenBank set, the Ei values of matches between RAG1s and the Transib PSSM dropped significantly further (10-9–10-4; Table 1).@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 18) (:start . 12)\n (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 32)\n (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 37) (:start . 33)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n (:id . 49))\n ((:tag . "JJ") (:stem . "original") (:form . "original") (:end . 50)\n (:start . 42) (:id . 50))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 58)\n (:start . 51) (:id . 51))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 62) (:start . 59)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Ei") (:form . "Ei") (:end . 70) (:start . 68)\n (:id . 55))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 77)\n (:start . 71) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n (:id . 57))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 88)\n (:start . 81) (:id . 58))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 96)\n (:start . 89) (:id . 59))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1s") (:end . 102) (:start . 97)\n (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n (:id . 62))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 118)\n (:start . 111) (:id . 63))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 123) (:start . 119)\n (:id . 64))\n ((:tag . "VBD") (:stem . "drop") (:form . "dropped") (:end . 131)\n (:start . 124) (:id . 65))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 145) (:start . 132) (:id . 66))\n ((:tag . "RB") (:stem . "further") (:form . "further") (:end . 153)\n (:start . 146) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 155) (:start . 154)\n (:id . 68))\n ((:tag . "CD") (:stem . "10-9–10-4") (:form . "10-9–10-4") (:end . 164)\n (:start . 155) (:id . 69))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 165) (:start . 164)\n (:id . 70))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 171)\n (:start . 166) (:id . 71))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 173) (:start . 172)\n (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 174) (:start . 173)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s6.66) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101806@unknown@formal@none@1@S@During the final revision of this manuscript, we identified an intermediate RAG1-like sequence in Hydra magnipapillata, called RAG1L_HM, which is significantly similar to both RAG1 and Transib TPase, as shown later.@(((:tag . "IN") (:stem . "during") (:form . "During") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n (:id . 43))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 16) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "revision") (:form . "revision") (:end . 25)\n (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "NN") (:stem . "manuscript") (:form . "manuscript") (:end . 44)\n (:start . 34) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n (:id . 49))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 48) (:start . 46)\n (:id . 50))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 59)\n (:start . 49) (:id . 51))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 62) (:start . 60)\n (:id . 52))\n ((:tag . "JJ") (:stem . "intermediate") (:form . "intermediate") (:end . 75)\n (:start . 63) (:id . 53))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 85)\n (:start . 76) (:id . 54))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 94)\n (:start . 86) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 97) (:start . 95)\n (:id . 56))\n ((:tag . "NNP") (:stem . "Hydra") (:form . "Hydra") (:end . 103)\n (:start . 98) (:id . 57))\n ((:tag . "NNS") (:stem . "magnipapillata") (:form . "magnipapillata")\n (:end . 118) (:start . 104) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n (:id . 59))\n ((:tag . "VBN") (:stem . "call") (:form . "called") (:end . 126)\n (:start . 120) (:id . 60))\n ((:tag . "NNP") (:stem . "RAG1L_HM") (:form . "RAG1L_HM") (:end . 135)\n (:start . 127) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n (:id . 62))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 142)\n (:start . 137) (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 145) (:start . 143)\n (:id . 64))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 159) (:start . 146) (:id . 65))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 167)\n (:start . 160) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 170) (:start . 168)\n (:id . 67))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 175) (:start . 171)\n (:id . 68))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 180) (:start . 176)\n (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 184) (:start . 181)\n (:id . 70))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 192)\n (:start . 185) (:id . 71))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 198)\n (:start . 193) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 199) (:start . 198)\n (:id . 73))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 202) (:start . 200)\n (:id . 74))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 208)\n (:start . 203) (:id . 75))\n ((:tag . "RB") (:stem . "later") (:form . "later") (:end . 214)\n (:start . 209) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s6.67) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101807@unknown@formal@none@1@S@This direct result represents an independent validation of our analysis.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 18)\n (:start . 12) (:id . 44))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 29)\n (:start . 19) (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 32) (:start . 30)\n (:id . 46))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 44)\n (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "validation") (:form . "validation") (:end . 55)\n (:start . 45) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n (:id . 49))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 62) (:start . 59)\n (:id . 50))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 71)\n (:start . 63) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s6.68) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101808@unknown@formal@none@1@S@The PSI-BLAST PSSM of Transib TPases approximates conservation/variability of the Transib TPase consensus sequence.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "pssm") (:form . "PSSM") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 29)\n (:start . 22) (:id . 46))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 36) (:start . 30)\n (:id . 47))\n ((:tag . "VBZ") (:stem . "approximate") (:form . "approximates") (:end . 49)\n (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "conservation/variability")\n (:form . "conservation/variability") (:end . 74) (:start . 50) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n (:id . 51))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 89)\n (:start . 82) (:id . 52))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 95) (:start . 90)\n (:id . 53))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 105)\n (:start . 96) (:id . 54))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 114)\n (:start . 106) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s6.69) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101810@unknown@formal@none@1@S@The RAG1 Ei values decreased as the number of Transib TPases used for the PSSM construction increased due to the fact that RAG1 evolved from a Transib TPase.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Ei") (:form . "Ei") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 18)\n (:start . 12) (:id . 45))\n ((:tag . "VBD") (:stem . "decrease") (:form . "decreased") (:end . 28)\n (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 31) (:start . 29)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n (:id . 48))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 42)\n (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 53)\n (:start . 46) (:id . 51))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 60) (:start . 54)\n (:id . 52))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 65) (:start . 61)\n (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 69) (:start . 66)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n (:id . 55))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 78) (:start . 74)\n (:id . 56))\n ((:tag . "NN") (:stem . "construction") (:form . "construction") (:end . 91)\n (:start . 79) (:id . 57))\n ((:tag . "VBD") (:stem . "increase") (:form . "increased") (:end . 101)\n (:start . 92) (:id . 58))\n ((:tag . "IN") (:stem . "due") (:form . "due") (:end . 105) (:start . 102)\n (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 108) (:start . 106)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n (:id . 61))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 117) (:start . 113)\n (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 122) (:start . 118)\n (:id . 63))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 127) (:start . 123)\n (:id . 64))\n ((:tag . "VBN") (:stem . "evolve") (:form . "evolved") (:end . 135)\n (:start . 128) (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 140) (:start . 136)\n (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 142) (:start . 141)\n (:id . 67))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 150)\n (:start . 143) (:id . 68))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 156)\n (:start . 151) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s6.71) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101811@unknown@formal@none@1@S@In all cases, the E values obtained after several rounds of iterations were less than 10-20 at the point of convergence.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 12) (:start . 7)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 46))\n ((:tag . "NN") (:stem . "e") (:form . "E") (:end . 19) (:start . 18)\n (:id . 47))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 26)\n (:start . 20) (:id . 48))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 35)\n (:start . 27) (:id . 49))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 41) (:start . 36)\n (:id . 50))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 49)\n (:start . 42) (:id . 51))\n ((:tag . "NNS") (:stem . "round") (:form . "rounds") (:end . 56)\n (:start . 50) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n (:id . 53))\n ((:tag . "NNS") (:stem . "iteration") (:form . "iterations") (:end . 70)\n (:start . 60) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 75) (:start . 71)\n (:id . 55))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 80) (:start . 76)\n (:id . 56))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 85) (:start . 81)\n (:id . 57))\n ((:tag . "CD") (:stem . "10-20") (:form . "10-20") (:end . 91) (:start . 86)\n (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 94) (:start . 92)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n (:id . 60))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 104) (:start . 99)\n (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n (:id . 62))\n ((:tag . "NN") (:stem . "convergence") (:form . "convergence") (:end . 119)\n (:start . 108) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s6.72) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101812@unknown@formal@none@1@S@Nearly the entire sequences of several Transib TPases, excluding their 100–140-aa N-terminal domains, converged with an approximately 600-aa portion of RAG1 defined by positions approximately 360–1010 (Figure S3).@(((:tag . "RB") (:stem . "nearly") (:form . "Nearly") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n (:id . 43))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 17)\n (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 27)\n (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 38)\n (:start . 31) (:id . 47))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 46)\n (:start . 39) (:id . 48))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 53) (:start . 47)\n (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n (:id . 50))\n ((:tag . "VBG") (:stem . "exclude") (:form . "excluding") (:end . 64)\n (:start . 55) (:id . 51))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 70)\n (:start . 65) (:id . 52))\n ((:tag . "JJ") (:stem . "100–140-aa") (:form . "100–140-aa") (:end . 81)\n (:start . 71) (:id . 53))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 92)\n (:start . 82) (:id . 54))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 100)\n (:start . 93) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n (:id . 56))\n ((:tag . "VBD") (:stem . "converge") (:form . "converged") (:end . 111)\n (:start . 102) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 116) (:start . 112)\n (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 119) (:start . 117)\n (:id . 59))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 133) (:start . 120) (:id . 60))\n ((:tag . "JJ") (:stem . "600-aa") (:form . "600-aa") (:end . 140)\n (:start . 134) (:id . 61))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 148)\n (:start . 141) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n (:id . 63))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 156) (:start . 152)\n (:id . 64))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 164)\n (:start . 157) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 167) (:start . 165)\n (:id . 66))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 177)\n (:start . 168) (:id . 67))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 191) (:start . 178) (:id . 68))\n ((:tag . "CD") (:stem . "360–1010") (:form . "360–1010") (:end . 200)\n (:start . 192) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 202) (:start . 201)\n (:id . 70))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 208)\n (:start . 202) (:id . 71))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 211) (:start . 209)\n (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 212) (:start . 211)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 213) (:start . 212)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s6.73) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101813@unknown@formal@none@1@S@This portion of RAG1 corresponds to the “RAG1 core,” hereafter numbered relative to human RAG1 (residues 387–1011), which along with RAG2 is known to be sufficient to perform V(D)J cleavage even after deletions of the 383-aa N-terminal and 32-aa C-terminal portions of RAG1 [19,20].@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "correspond") (:form . "corresponds") (:end . 32)\n (:start . 21) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 41) (:start . 40)\n (:id . 49))\n ((:tag . "JJ") (:stem . "RAG1") (:form . "RAG1") (:end . 45) (:start . 41)\n (:id . 50))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 50) (:start . 46)\n (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n (:id . 52))\n ((:tag . "VBP") (:stem . "”") (:form . "”") (:end . 52) (:start . 51)\n (:id . 53))\n ((:tag . "RB") (:stem . "hereafter") (:form . "hereafter") (:end . 62)\n (:start . 53) (:id . 54))\n ((:tag . "VBN") (:stem . "number") (:form . "numbered") (:end . 71)\n (:start . 63) (:id . 55))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 80)\n (:start . 72) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 83) (:start . 81)\n (:id . 57))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 89) (:start . 84)\n (:id . 58))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 94) (:start . 90)\n (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n (:id . 60))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 104)\n (:start . 96) (:id . 61))\n ((:tag . "CD") (:stem . "387–1011") (:form . "387–1011") (:end . 113)\n (:start . 105) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 121)\n (:start . 116) (:id . 65))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 127)\n (:start . 122) (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 132) (:start . 128)\n (:id . 67))\n ((:tag . "NN") (:stem . "rag2") (:form . "RAG2") (:end . 137) (:start . 133)\n (:id . 68))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 140) (:start . 138)\n (:id . 69))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 146)\n (:start . 141) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 149) (:start . 147)\n (:id . 71))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 152) (:start . 150)\n (:id . 72))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 163)\n (:start . 153) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 166) (:start . 164)\n (:id . 74))\n ((:tag . "VB") (:stem . "perform") (:form . "perform") (:end . 174)\n (:start . 167) (:id . 75))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 180)\n (:start . 175) (:id . 76))\n ((:tag . "NN") (:stem . "cleavage") (:form . "cleavage") (:end . 189)\n (:start . 181) (:id . 77))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 194) (:start . 190)\n (:id . 78))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 200)\n (:start . 195) (:id . 79))\n ((:tag . "NNS") (:stem . "deletion") (:form . "deletions") (:end . 210)\n (:start . 201) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 213) (:start . 211)\n (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 217) (:start . 214)\n (:id . 82))\n ((:tag . "JJ") (:stem . "383-aa") (:form . "383-aa") (:end . 224)\n (:start . 218) (:id . 83))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 235)\n (:start . 225) (:id . 84))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 239) (:start . 236)\n (:id . 85))\n ((:tag . "JJ") (:stem . "32-aa") (:form . "32-aa") (:end . 245)\n (:start . 240) (:id . 86))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 256)\n (:start . 246) (:id . 87))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 265)\n (:start . 257) (:id . 88))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 268) (:start . 266)\n (:id . 89))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 273) (:start . 269)\n (:id . 90))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 275) (:start . 274)\n (:id . 91))\n ((:tag . "CD") (:stem . "19,20") (:form . "19,20") (:end . 280)\n (:start . 275) (:id . 92))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 281) (:start . 280)\n (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 282) (:start . 281)\n (:id . 94)))@@@1@53@((:identifiers (:sid . :s6.74) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101814@unknown@formal@none@1@S@During studies reported here, we identified 11 additional new families of Transib transposons and TPases (see Figure S2) that are well preserved in the genomes of fruit flies (Transib5 in D. melanogaster; and Transib1_DP, Transib2_DP, Transib3_DP, and Transib4_DP in D. pseudoobscura), mosquitoes (Transib1_AA, Transib2_AA, Transib3_AA, Transib4_AA, and Transib5_AA from A. aegypti) and sea urchin (Transib1_SP).@(((:tag . "IN") (:stem . "during") (:form . "During") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 14)\n (:start . 7) (:id . 43))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 23)\n (:start . 15) (:id . 44))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 28) (:start . 24)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 32) (:start . 30)\n (:id . 47))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 43)\n (:start . 33) (:id . 48))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 46) (:start . 44)\n (:id . 49))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 57)\n (:start . 47) (:id . 50))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 61) (:start . 58)\n (:id . 51))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 70)\n (:start . 62) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 81)\n (:start . 74) (:id . 54))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 93)\n (:start . 82) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n (:id . 56))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 104)\n (:start . 98) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n (:id . 58))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 109) (:start . 106)\n (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 116)\n (:start . 110) (:id . 60))\n ((:tag . "NN") (:stem . "s2") (:form . "S2") (:end . 119) (:start . 117)\n (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 120) (:start . 119)\n (:id . 62))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 125) (:start . 121)\n (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 129) (:start . 126)\n (:id . 64))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 134) (:start . 130)\n (:id . 65))\n ((:tag . "VBN") (:stem . "preserve") (:form . "preserved") (:end . 144)\n (:start . 135) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 147) (:start . 145)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n (:id . 68))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 159)\n (:start . 152) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 162) (:start . 160)\n (:id . 70))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 168)\n (:start . 163) (:id . 71))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 174) (:start . 169)\n (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 176) (:start . 175)\n (:id . 73))\n ((:tag . "NNP") (:stem . "Transib5") (:form . "Transib5") (:end . 184)\n (:start . 176) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 187) (:start . 185)\n (:id . 75))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 190) (:start . 188)\n (:id . 76))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n (:end . 203) (:start . 191) (:id . 77))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 204) (:start . 203)\n (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 208) (:start . 205)\n (:id . 79))\n ((:tag . "NNP") (:stem . "Transib1_DP") (:form . "Transib1_DP") (:end . 220)\n (:start . 209) (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 221) (:start . 220)\n (:id . 81))\n ((:tag . "NNP") (:stem . "Transib2_DP") (:form . "Transib2_DP") (:end . 233)\n (:start . 222) (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 234) (:start . 233)\n (:id . 83))\n ((:tag . "NNP") (:stem . "Transib3_DP") (:form . "Transib3_DP") (:end . 246)\n (:start . 235) (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 247) (:start . 246)\n (:id . 85))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 251) (:start . 248)\n (:id . 86))\n ((:tag . "NNP") (:stem . "Transib4_DP") (:form . "Transib4_DP") (:end . 263)\n (:start . 252) (:id . 87))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 266) (:start . 264)\n (:id . 88))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 269) (:start . 267)\n (:id . 89))\n ((:tag . "NN") (:stem . "pseudoobscura") (:form . "pseudoobscura")\n (:end . 283) (:start . 270) (:id . 90))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 284) (:start . 283)\n (:id . 91))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 285) (:start . 284)\n (:id . 92))\n ((:tag . "NNS") (:stem . "mosquito") (:form . "mosquitoes") (:end . 296)\n (:start . 286) (:id . 93))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 298) (:start . 297)\n (:id . 94))\n ((:tag . "NNP") (:stem . "Transib1_AA") (:form . "Transib1_AA") (:end . 309)\n (:start . 298) (:id . 95))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 310) (:start . 309)\n (:id . 96))\n ((:tag . "NNP") (:stem . "Transib2_AA") (:form . "Transib2_AA") (:end . 322)\n (:start . 311) (:id . 97))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 323) (:start . 322)\n (:id . 98))\n ((:tag . "NNP") (:stem . "Transib3_AA") (:form . "Transib3_AA") (:end . 335)\n (:start . 324) (:id . 99))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 336) (:start . 335)\n (:id . 100))\n ((:tag . "NNP") (:stem . "Transib4_AA") (:form . "Transib4_AA") (:end . 348)\n (:start . 337) (:id . 101))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 349) (:start . 348)\n (:id . 102))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 353) (:start . 350)\n (:id . 103))\n ((:tag . "NNP") (:stem . "Transib5_AA") (:form . "Transib5_AA") (:end . 365)\n (:start . 354) (:id . 104))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 370) (:start . 366)\n (:id . 105))\n ((:tag . "NNP") (:stem . "A.") (:form . "A.") (:end . 373) (:start . 371)\n (:id . 106))\n ((:tag . "NN") (:stem . "aegypti") (:form . "aegypti") (:end . 381)\n (:start . 374) (:id . 107))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 382) (:start . 381)\n (:id . 108))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 386) (:start . 383)\n (:id . 109))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 390) (:start . 387)\n (:id . 110))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 397)\n (:start . 391) (:id . 111))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 399) (:start . 398)\n (:id . 112))\n ((:tag . "NNP") (:stem . "Transib1_SP") (:form . "Transib1_SP") (:end . 410)\n (:start . 399) (:id . 113))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 411) (:start . 410)\n (:id . 114))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 412) (:start . 411)\n (:id . 115)))@@@1@74@((:identifiers (:sid . :s6.75) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101815@unknown@formal@none@1@S@Transib1_SP is the first Transib transposon identified outside of insect genomes.@(((:tag . "NNP") (:stem . "Transib1_SP") (:form . "Transib1_SP") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 44))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 24) (:start . 19)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 32)\n (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "transposon") (:form . "transposon") (:end . 43)\n (:start . 33) (:id . 47))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 54)\n (:start . 44) (:id . 48))\n ((:tag . "JJ") (:stem . "outside") (:form . "outside") (:end . 62)\n (:start . 55) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n (:id . 50))\n ((:tag . "NN") (:stem . "insect") (:form . "insect") (:end . 72)\n (:start . 66) (:id . 51))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 80)\n (:start . 73) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s6.76) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101816@unknown@formal@none@1@S@A well-preserved 4132-bp Transib1_SP element (contig 7839, positions 376–4506) is flanked by a 5-bp CGGCG TSD, and it encodes a 676-aa TPase (two exons) that is most similar to the Transib2 TPase (34% identity).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "well-preserved") (:form . "well-preserved")\n (:end . 16) (:start . 2) (:id . 43))\n ((:tag . "JJ") (:stem . "4132-bp") (:form . "4132-bp") (:end . 24)\n (:start . 17) (:id . 44))\n ((:tag . "NNP") (:stem . "Transib1_SP") (:form . "Transib1_SP") (:end . 36)\n (:start . 25) (:id . 45))\n ((:tag . "NN") (:stem . "element") (:form . "element") (:end . 44)\n (:start . 37) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 46) (:start . 45)\n (:id . 47))\n ((:tag . "NN") (:stem . "contig") (:form . "contig") (:end . 52)\n (:start . 46) (:id . 48))\n ((:tag . "CD") (:stem . "7839") (:form . "7839") (:end . 57) (:start . 53)\n (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n (:id . 50))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 68)\n (:start . 59) (:id . 51))\n ((:tag . "CD") (:stem . "376–4506") (:form . "376–4506") (:end . 77)\n (:start . 69) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 78) (:start . 77)\n (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 81) (:start . 79)\n (:id . 54))\n ((:tag . "VBN") (:stem . "flank") (:form . "flanked") (:end . 89)\n (:start . 82) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 92) (:start . 90)\n (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 94) (:start . 93)\n (:id . 57))\n ((:tag . "JJ") (:stem . "5-bp") (:form . "5-bp") (:end . 99) (:start . 95)\n (:id . 58))\n ((:tag . "NNP") (:stem . "CGGCG") (:form . "CGGCG") (:end . 105)\n (:start . 100) (:id . 59))\n ((:tag . "NNP") (:stem . "TSD") (:form . "TSD") (:end . 109) (:start . 106)\n (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n (:id . 62))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 117) (:start . 115)\n (:id . 63))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 125)\n (:start . 118) (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 127) (:start . 126)\n (:id . 65))\n ((:tag . "JJ") (:stem . "676-aa") (:form . "676-aa") (:end . 134)\n (:start . 128) (:id . 66))\n ((:tag . "NN") (:stem . "tpase") (:form . "TPase") (:end . 140)\n (:start . 135) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n (:id . 68))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 145) (:start . 142)\n (:id . 69))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 151)\n (:start . 146) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n (:id . 71))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 157) (:start . 153)\n (:id . 72))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 160) (:start . 158)\n (:id . 73))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 165) (:start . 161)\n (:id . 74))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 173)\n (:start . 166) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 176) (:start . 174)\n (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 180) (:start . 177)\n (:id . 77))\n ((:tag . "NNP") (:stem . "Transib2") (:form . "Transib2") (:end . 189)\n (:start . 181) (:id . 78))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 195)\n (:start . 190) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 197) (:start . 196)\n (:id . 80))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 199) (:start . 197)\n (:id . 81))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 200) (:start . 199)\n (:id . 82))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 209)\n (:start . 201) (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 210) (:start . 209)\n (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n (:id . 85)))@@@1@44@((:identifiers (:sid . :s6.77) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101817@unknown@formal@none@1@S@Based on the currently available sequence data, we also reconstructed portions of TPases that were missed in previous studies [17] (Materials and Methods; see Figure S2).@(((:tag . "VBN") (:stem . "base") (:form . "Based") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 8) (:start . 6)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 22)\n (:start . 13) (:id . 45))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 32)\n (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 41)\n (:start . 33) (:id . 47))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 46) (:start . 42)\n (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n (:id . 49))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 50) (:start . 48)\n (:id . 50))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 55) (:start . 51)\n (:id . 51))\n ((:tag . "VBD") (:stem . "reconstruct") (:form . "reconstructed") (:end . 69)\n (:start . 56) (:id . 52))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 78)\n (:start . 70) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n (:id . 54))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 88) (:start . 82)\n (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 93) (:start . 89)\n (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 98) (:start . 94)\n (:id . 57))\n ((:tag . "VBN") (:stem . "miss") (:form . "missed") (:end . 105)\n (:start . 99) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n (:id . 59))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 117)\n (:start . 109) (:id . 60))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 125)\n (:start . 118) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 127) (:start . 126)\n (:id . 62))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 129) (:start . 127)\n (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 130) (:start . 129)\n (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 132) (:start . 131)\n (:id . 65))\n ((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 141)\n (:start . 132) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 145) (:start . 142)\n (:id . 67))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 153)\n (:start . 146) (:id . 68))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 154) (:start . 153)\n (:id . 69))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 158) (:start . 155)\n (:id . 70))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 165)\n (:start . 159) (:id . 71))\n ((:tag . "NN") (:stem . "s2") (:form . "S2") (:end . 168) (:start . 166)\n (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s6.78) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101818@unknown@formal@none@1@S@Using the Transib1_SP TPase as a query in TBLASTN searches against all GenBank sections (NR, HTGs, WGS, dbGSS, dbEST, dbSTS, and Trace Archives) we also found diverse Transib TPases in silkworm, red flour beetle, dog hookworm, freshwater flatworm, soybean rust, and hydra (Table S1).@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Transib1_SP") (:form . "Transib1_SP") (:end . 21)\n (:start . 10) (:id . 44))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 27) (:start . 22)\n (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n (:id . 47))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 38) (:start . 33)\n (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n (:id . 49))\n ((:tag . "NNP") (:stem . "TBLASTN") (:form . "TBLASTN") (:end . 49)\n (:start . 42) (:id . 50))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 58)\n (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 66)\n (:start . 59) (:id . 52))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 70) (:start . 67)\n (:id . 53))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 78)\n (:start . 71) (:id . 54))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 87)\n (:start . 79) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n (:id . 56))\n ((:tag . "NNP") (:stem . "NR") (:form . "NR") (:end . 91) (:start . 89)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n (:id . 58))\n ((:tag . "NNP") (:stem . "HTGs") (:form . "HTGs") (:end . 97) (:start . 93)\n (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n (:id . 60))\n ((:tag . "NNP") (:stem . "WGS") (:form . "WGS") (:end . 102) (:start . 99)\n (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n (:id . 62))\n ((:tag . "NN") (:stem . "dbgss") (:form . "dbGSS") (:end . 109)\n (:start . 104) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n (:id . 64))\n ((:tag . "NN") (:stem . "dbest") (:form . "dbEST") (:end . 116)\n (:start . 111) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n (:id . 66))\n ((:tag . "NN") (:stem . "dbsts") (:form . "dbSTS") (:end . 123)\n (:start . 118) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n (:id . 69))\n ((:tag . "NNP") (:stem . "Trace") (:form . "Trace") (:end . 134)\n (:start . 129) (:id . 70))\n ((:tag . "NNPS") (:stem . "Archives") (:form . "Archives") (:end . 143)\n (:start . 135) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 144) (:start . 143)\n (:id . 72))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 147) (:start . 145)\n (:id . 73))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 152) (:start . 148)\n (:id . 74))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 158)\n (:start . 153) (:id . 75))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 166)\n (:start . 159) (:id . 76))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 174)\n (:start . 167) (:id . 77))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 181)\n (:start . 175) (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 184) (:start . 182)\n (:id . 79))\n ((:tag . "NN") (:stem . "silkworm") (:form . "silkworm") (:end . 193)\n (:start . 185) (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 194) (:start . 193)\n (:id . 81))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 198) (:start . 195)\n (:id . 82))\n ((:tag . "NN") (:stem . "flour") (:form . "flour") (:end . 204)\n (:start . 199) (:id . 83))\n ((:tag . "NN") (:stem . "beetle") (:form . "beetle") (:end . 211)\n (:start . 205) (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 212) (:start . 211)\n (:id . 85))\n ((:tag . "NN") (:stem . "dog") (:form . "dog") (:end . 216) (:start . 213)\n (:id . 86))\n ((:tag . "NN") (:stem . "hookworm") (:form . "hookworm") (:end . 225)\n (:start . 217) (:id . 87))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 226) (:start . 225)\n (:id . 88))\n ((:tag . "NN") (:stem . "freshwater") (:form . "freshwater") (:end . 237)\n (:start . 227) (:id . 89))\n ((:tag . "NN") (:stem . "flatworm") (:form . "flatworm") (:end . 246)\n (:start . 238) (:id . 90))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 247) (:start . 246)\n (:id . 91))\n ((:tag . "NN") (:stem . "soybean") (:form . "soybean") (:end . 255)\n (:start . 248) (:id . 92))\n ((:tag . "NN") (:stem . "rust") (:form . "rust") (:end . 260) (:start . 256)\n (:id . 93))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 261) (:start . 260)\n (:id . 94))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 265) (:start . 262)\n (:id . 95))\n ((:tag . "NN") (:stem . "hydra") (:form . "hydra") (:end . 271)\n (:start . 266) (:id . 96))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 273) (:start . 272)\n (:id . 97))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 278)\n (:start . 273) (:id . 98))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 281) (:start . 279)\n (:id . 99))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 282) (:start . 281)\n (:id . 100))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 283) (:start . 282)\n (:id . 101)))@@@1@60@((:identifiers (:sid . :s6.79) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101820@unknown@formal@none@1@S@The observed patchy distribution could be caused by horizontal transfers and extinctions of Transib transposons in eukaryotic species.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "patchy") (:form . "patchy") (:end . 19)\n (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 32)\n (:start . 20) (:id . 45))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 38) (:start . 33)\n (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 41) (:start . 39)\n (:id . 47))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 48)\n (:start . 42) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 51) (:start . 49)\n (:id . 49))\n ((:tag . "JJ") (:stem . "horizontal") (:form . "horizontal") (:end . 62)\n (:start . 52) (:id . 50))\n ((:tag . "NNS") (:stem . "transfer") (:form . "transfers") (:end . 72)\n (:start . 63) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n (:id . 52))\n ((:tag . "NNS") (:stem . "extinction") (:form . "extinctions") (:end . 88)\n (:start . 77) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 99)\n (:start . 92) (:id . 55))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 111)\n (:start . 100) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n (:id . 57))\n ((:tag . "JJ") (:stem . "eukaryotic") (:form . "eukaryotic") (:end . 125)\n (:start . 115) (:id . 58))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 133)\n (:start . 126) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n (:id . 60)))@@@1@19@((:hcues ((:id . :x6.81.1) (:span 33 38)))\n (:hscopes ((:id . :x6.81.1) (:span 0 133)))\n (:identifiers (:sid . :s6.81) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101821@unknown@formal@none@1@S@Significance of Similarities between the Transib TPases and RAG1 Core@(((:tag . "NN") (:stem . "significance") (:form . "Significance") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 43))\n ((:tag . "NNS") (:stem . "similarity") (:form . "Similarities") (:end . 28)\n (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 36)\n (:start . 29) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 48)\n (:start . 41) (:id . 47))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 55) (:start . 49)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n (:id . 49))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 64) (:start . 60)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Core") (:form . "Core") (:end . 69) (:start . 65)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s6.82) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011 5101822@unknown@formal@none@1@S@The first column lists all 18 Transib TPases used as queries in our analysis, and the shaded areas indicate those added to the original set of all GenBank proteins in subsequent PSI-BLAST searches.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "column") (:form . "column") (:end . 16)\n (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "list") (:form . "lists") (:end . 22) (:start . 17)\n (:id . 45))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 29) (:start . 27)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 37)\n (:start . 30) (:id . 48))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 44) (:start . 38)\n (:id . 49))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 49) (:start . 45)\n (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 52) (:start . 50)\n (:id . 51))\n ((:tag . "NNS") (:stem . "query") (:form . "queries") (:end . 60)\n (:start . 53) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n (:id . 53))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 67) (:start . 64)\n (:id . 54))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 76)\n (:start . 68) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n (:id . 58))\n ((:tag . "JJ") (:stem . "shaded") (:form . "shaded") (:end . 92)\n (:start . 86) (:id . 59))\n ((:tag . "NNS") (:stem . "area") (:form . "areas") (:end . 98) (:start . 93)\n (:id . 60))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 107)\n (:start . 99) (:id . 61))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 113)\n (:start . 108) (:id . 62))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 119) (:start . 114)\n (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 122) (:start . 120)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n (:id . 65))\n ((:tag . "JJ") (:stem . "original") (:form . "original") (:end . 135)\n (:start . 127) (:id . 66))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 139) (:start . 136)\n (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n (:id . 68))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 146) (:start . 143)\n (:id . 69))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 154)\n (:start . 147) (:id . 70))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 163)\n (:start . 155) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 166) (:start . 164)\n (:id . 72))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 177)\n (:start . 167) (:id . 73))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 187)\n (:start . 178) (:id . 74))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 196)\n (:start . 188) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s6.83) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101823@unknown@formal@none@1@S@The original GenBank set included two incomplete Transib TPase-like proteins.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "original") (:form . "original") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 20)\n (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 24) (:start . 21)\n (:id . 45))\n ((:tag . "VBD") (:stem . "include") (:form . "included") (:end . 33)\n (:start . 25) (:id . 46))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 37) (:start . 34)\n (:id . 47))\n ((:tag . "JJ") (:stem . "incomplete") (:form . "incomplete") (:end . 48)\n (:start . 38) (:id . 48))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 56)\n (:start . 49) (:id . 49))\n ((:tag . "JJ") (:stem . "tpase-like") (:form . "TPase-like") (:end . 67)\n (:start . 57) (:id . 50))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 76)\n (:start . 68) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s6.84) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101824@unknown@formal@none@1@S@Column 2 lists E-values of best matches between RAG1s and Transib TPases detected in BLASTP searches against the original GenBank set.@(((:tag . "NN") (:stem . "column") (:form . "Column") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 8) (:start . 7)\n (:id . 43))\n ((:tag . "NNS") (:stem . "list") (:form . "lists") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "NNS") (:stem . "e-value") (:form . "E-values") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 31) (:start . 27)\n (:id . 47))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 39)\n (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 47)\n (:start . 40) (:id . 49))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1s") (:end . 53) (:start . 48)\n (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n (:id . 51))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 65)\n (:start . 58) (:id . 52))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 72) (:start . 66)\n (:id . 53))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 81)\n (:start . 73) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n (:id . 55))\n ((:tag . "NNP") (:stem . "BLASTP") (:form . "BLASTP") (:end . 91)\n (:start . 85) (:id . 56))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 100)\n (:start . 92) (:id . 57))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 108)\n (:start . 101) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n (:id . 59))\n ((:tag . "JJ") (:stem . "original") (:form . "original") (:end . 121)\n (:start . 113) (:id . 60))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 129)\n (:start . 122) (:id . 61))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 133) (:start . 130)\n (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.85) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101825@unknown@formal@none@1@S@Column 3 reports Ei-values of best matches between RAG1s and a PSSM derived from the chosen query sequence and the two GenBank TPase-like proteins in PSI-BLAST searches against the original set of all GenBank proteins (see Materials and Methods).@(((:tag . "NN") (:stem . "column") (:form . "Column") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 8) (:start . 7)\n (:id . 43))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 16)\n (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "ei-value") (:form . "Ei-values") (:end . 26)\n (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 34) (:start . 30)\n (:id . 47))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 42)\n (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 50)\n (:start . 43) (:id . 49))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1s") (:end . 56) (:start . 51)\n (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 62) (:start . 61)\n (:id . 52))\n ((:tag . "NN") (:stem . "pssm") (:form . "PSSM") (:end . 67) (:start . 63)\n (:id . 53))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 75)\n (:start . 68) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 80) (:start . 76)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n (:id . 56))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 91)\n (:start . 85) (:id . 57))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 97) (:start . 92)\n (:id . 58))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 106)\n (:start . 98) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n (:id . 61))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 118) (:start . 115)\n (:id . 62))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 126)\n (:start . 119) (:id . 63))\n ((:tag . "JJ") (:stem . "tpase-like") (:form . "TPase-like") (:end . 137)\n (:start . 127) (:id . 64))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 146)\n (:start . 138) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n (:id . 66))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 159)\n (:start . 150) (:id . 67))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 168)\n (:start . 160) (:id . 68))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 176)\n (:start . 169) (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 180) (:start . 177)\n (:id . 70))\n ((:tag . "JJ") (:stem . "original") (:form . "original") (:end . 189)\n (:start . 181) (:id . 71))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 193) (:start . 190)\n (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 196) (:start . 194)\n (:id . 73))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 200) (:start . 197)\n (:id . 74))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 208)\n (:start . 201) (:id . 75))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 217)\n (:start . 209) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 219) (:start . 218)\n (:id . 77))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 222) (:start . 219)\n (:id . 78))\n ((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 232)\n (:start . 223) (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 236) (:start . 233)\n (:id . 80))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 244)\n (:start . 237) (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 245) (:start . 244)\n (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 246) (:start . 245)\n (:id . 83)))@@@1@42@((:identifiers (:sid . :s6.86) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101826@unknown@formal@none@1@S@Columns 4–6 report the Ei-values for best matches between RAG1s and a Transib-derived PSSM after adding 7, 13, and 18 Transib TPases to the GenBank set, respectively.@(((:tag . "NNS") (:stem . "column") (:form . "Columns") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "CD") (:stem . "4–6") (:form . "4–6") (:end . 11) (:start . 8)\n (:id . 43))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 18)\n (:start . 12) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "NNS") (:stem . "ei-value") (:form . "Ei-values") (:end . 32)\n (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 36) (:start . 33)\n (:id . 47))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 41) (:start . 37)\n (:id . 48))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 49)\n (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 57)\n (:start . 50) (:id . 50))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1s") (:end . 63) (:start . 58)\n (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 69) (:start . 68)\n (:id . 53))\n ((:tag . "JJ") (:stem . "transib-derived") (:form . "Transib-derived")\n (:end . 85) (:start . 70) (:id . 54))\n ((:tag . "NN") (:stem . "pssm") (:form . "PSSM") (:end . 90) (:start . 86)\n (:id . 55))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 96) (:start . 91)\n (:id . 56))\n ((:tag . "VBG") (:stem . "add") (:form . "adding") (:end . 103) (:start . 97)\n (:id . 57))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 105) (:start . 104)\n (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n (:id . 59))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 109) (:start . 107)\n (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n (:id . 62))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 117) (:start . 115)\n (:id . 63))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 125)\n (:start . 118) (:id . 64))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 132)\n (:start . 126) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 135) (:start . 133)\n (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n (:id . 67))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 147)\n (:start . 140) (:id . 68))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 151) (:start . 148)\n (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n (:id . 70))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 165)\n (:start . 153) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n (:id . 72)))@@@1@31@((:identifiers (:sid . :s6.87) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101827@unknown@formal@none@1@S@The numbers of the PSI-BLAST iterations after which the entire RAG1 core significantly aligned with the TPases are indicated in parentheses.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 28)\n (:start . 19) (:id . 46))\n ((:tag . "NNS") (:stem . "iteration") (:form . "iterations") (:end . 39)\n (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 45) (:start . 40)\n (:id . 48))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 51) (:start . 46)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n (:id . 50))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 62)\n (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 67) (:start . 63)\n (:id . 52))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 72) (:start . 68)\n (:id . 53))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 86) (:start . 73) (:id . 54))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 94)\n (:start . 87) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 99) (:start . 95)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n (:id . 57))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 110)\n (:start . 104) (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 114) (:start . 111)\n (:id . 59))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 124)\n (:start . 115) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 127) (:start . 125)\n (:id . 61))\n ((:tag . "NNS") (:stem . "parenthesis") (:form . "parentheses") (:end . 139)\n (:start . 128) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.88) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101828@unknown@formal@none@1@S@Ei-values greater than 1 are indicated by dashes.@(((:tag . "NNS") (:stem . "ei-value") (:form . "Ei-values") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 17)\n (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 22) (:start . 18)\n (:id . 44))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 24) (:start . 23)\n (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 38)\n (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 41) (:start . 39)\n (:id . 48))\n ((:tag . "NNS") (:stem . "dash") (:form . "dashes") (:end . 48) (:start . 42)\n (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s6.89) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101830@unknown@formal@none@1@S@Diversity of the Transib TPases and RAG1 Core–Like Proteins in Animals@(((:tag . "NN") (:stem . "diversity") (:form . "Diversity") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 24)\n (:start . 17) (:id . 45))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 31) (:start . 25)\n (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n (:id . 47))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 40) (:start . 36)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Core–Like") (:form . "Core–Like") (:end . 50)\n (:start . 41) (:id . 49))\n ((:tag . "NNPS") (:stem . "Protein") (:form . "Proteins") (:end . 59)\n (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n (:id . 51))\n ((:tag . "NNPS") (:stem . "Animal") (:form . "Animals") (:end . 70)\n (:start . 63) (:id . 52)))@@@1@11@((:identifiers (:sid . :s6.91) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5101831@unknown@formal@none@1@S@The phylogenetic tree was obtained by using the neighbor-joining algorithm implemented in MEGA [44].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 16)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "tree") (:form . "tree") (:end . 21) (:start . 17)\n (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 34)\n (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 37) (:start . 35)\n (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 43) (:start . 38)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n (:id . 49))\n ((:tag . "JJ") (:stem . "neighbor-joining") (:form . "neighbor-joining")\n (:end . 64) (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 74)\n (:start . 65) (:id . 51))\n ((:tag . "VBN") (:stem . "implement") (:form . "implemented") (:end . 86)\n (:start . 75) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n (:id . 53))\n ((:tag . "NNP") (:stem . "MEGA") (:form . "MEGA") (:end . 94) (:start . 90)\n (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 96) (:start . 95)\n (:id . 55))\n ((:tag . "CD") (:stem . "44") (:form . "44") (:end . 98) (:start . 96)\n (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 99) (:start . 98)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s6.92) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101832@unknown@formal@none@1@S@Evolutionary distance for each pair of protein sequences was measured as the proportion of aa sites at which the two sequences were different.@(((:tag . "JJ") (:stem . "evolutionary") (:form . "Evolutionary") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 21)\n (:start . 13) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 25) (:start . 22)\n (:id . 44))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 30) (:start . 26)\n (:id . 45))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 35) (:start . 31)\n (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 46)\n (:start . 39) (:id . 48))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 56)\n (:start . 47) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 60) (:start . 57)\n (:id . 50))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 69)\n (:start . 61) (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 72) (:start . 70)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n (:id . 53))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 87)\n (:start . 77) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n (:id . 55))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 93) (:start . 91)\n (:id . 56))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 99) (:start . 94)\n (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 102) (:start . 100)\n (:id . 58))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 108)\n (:start . 103) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n (:id . 60))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 116) (:start . 113)\n (:id . 61))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 126)\n (:start . 117) (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 131) (:start . 127)\n (:id . 63))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 141)\n (:start . 132) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s6.93) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101833@unknown@formal@none@1@S@Its scale is shown by the horizontal bar.@(((:tag . "PRP$") (:stem . "its") (:form . "Its") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n (:id . 44))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 21) (:start . 19)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 47))\n ((:tag . "JJ") (:stem . "horizontal") (:form . "horizontal") (:end . 36)\n (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 40) (:start . 37)\n (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 41) (:start . 40)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s6.94) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101834@unknown@formal@none@1@S@Bootstrap values higher than 60% are reported at the corresponding nodes.@(((:tag . "NNP") (:stem . "Bootstrap") (:form . "Bootstrap") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 16)\n (:start . 10) (:id . 43))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 23) (:start . 17)\n (:id . 44))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 28) (:start . 24)\n (:id . 45))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 31) (:start . 29)\n (:id . 46))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 32) (:start . 31)\n (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 36) (:start . 33)\n (:id . 48))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 45)\n (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 48) (:start . 46)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n (:id . 51))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 66)\n (:start . 53) (:id . 52))\n ((:tag . "NNS") (:stem . "node") (:form . "nodes") (:end . 72) (:start . 67)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.95) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101835@unknown@formal@none@1@S@Species abbreviations are as follows: AA, yellow fever mosquito; AG, African malaria mosquito; BF, lancelet; CL, bull shark; DP, D. pseudoobscura fruit fly; FR, fugu fish; HM, hydra; HS, human; NV, starlet sea anemone; SP, sea urchin; XL, frog.@(((:tag . "NNP") (:stem . "Species") (:form . "Species") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "abbreviation") (:form . "abbreviations")\n (:end . 21) (:start . 8) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 25) (:start . 22)\n (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 28) (:start . 26)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 36)\n (:start . 29) (:id . 46))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 37) (:start . 36)\n (:id . 47))\n ((:tag . "NN") (:stem . "aa") (:form . "AA") (:end . 40) (:start . 38)\n (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n (:id . 49))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 48)\n (:start . 42) (:id . 50))\n ((:tag . "NN") (:stem . "fever") (:form . "fever") (:end . 54) (:start . 49)\n (:id . 51))\n ((:tag . "NN") (:stem . "mosquito") (:form . "mosquito") (:end . 63)\n (:start . 55) (:id . 52))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 64) (:start . 63)\n (:id . 53))\n ((:tag . "NNP") (:stem . "AG") (:form . "AG") (:end . 67) (:start . 65)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n (:id . 55))\n ((:tag . "JJ") (:stem . "african") (:form . "African") (:end . 76)\n (:start . 69) (:id . 56))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 84)\n (:start . 77) (:id . 57))\n ((:tag . "NN") (:stem . "mosquito") (:form . "mosquito") (:end . 93)\n (:start . 85) (:id . 58))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 94) (:start . 93)\n (:id . 59))\n ((:tag . "NNP") (:stem . "BF") (:form . "BF") (:end . 97) (:start . 95)\n (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n (:id . 61))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 107)\n (:start . 99) (:id . 62))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 108) (:start . 107)\n (:id . 63))\n ((:tag . "NNP") (:stem . "CL") (:form . "CL") (:end . 111) (:start . 109)\n (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n (:id . 65))\n ((:tag . "NN") (:stem . "bull") (:form . "bull") (:end . 117) (:start . 113)\n (:id . 66))\n ((:tag . "NN") (:stem . "shark") (:form . "shark") (:end . 123)\n (:start . 118) (:id . 67))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 124) (:start . 123)\n (:id . 68))\n ((:tag . "NNP") (:stem . "DP") (:form . "DP") (:end . 127) (:start . 125)\n (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n (:id . 70))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 131) (:start . 129)\n (:id . 71))\n ((:tag . "NN") (:stem . "pseudoobscura") (:form . "pseudoobscura")\n (:end . 145) (:start . 132) (:id . 72))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 151)\n (:start . 146) (:id . 73))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 155) (:start . 152)\n (:id . 74))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 156) (:start . 155)\n (:id . 75))\n ((:tag . "NNP") (:stem . "FR") (:form . "FR") (:end . 159) (:start . 157)\n (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n (:id . 77))\n ((:tag . "NN") (:stem . "fugu") (:form . "fugu") (:end . 165) (:start . 161)\n (:id . 78))\n ((:tag . "NN") (:stem . "fish") (:form . "fish") (:end . 170) (:start . 166)\n (:id . 79))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 171) (:start . 170)\n (:id . 80))\n ((:tag . "NNP") (:stem . "HM") (:form . "HM") (:end . 174) (:start . 172)\n (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n (:id . 82))\n ((:tag . "NN") (:stem . "hydra") (:form . "hydra") (:end . 181)\n (:start . 176) (:id . 83))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 182) (:start . 181)\n (:id . 84))\n ((:tag . "NNP") (:stem . "HS") (:form . "HS") (:end . 185) (:start . 183)\n (:id . 85))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 186) (:start . 185)\n (:id . 86))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 192)\n (:start . 187) (:id . 87))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 193) (:start . 192)\n (:id . 88))\n ((:tag . "NNP") (:stem . "NV") (:form . "NV") (:end . 196) (:start . 194)\n (:id . 89))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n (:id . 90))\n ((:tag . "NN") (:stem . "starlet") (:form . "starlet") (:end . 205)\n (:start . 198) (:id . 91))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 209) (:start . 206)\n (:id . 92))\n ((:tag . "NN") (:stem . "anemone") (:form . "anemone") (:end . 217)\n (:start . 210) (:id . 93))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 218) (:start . 217)\n (:id . 94))\n ((:tag . "NNP") (:stem . "SP") (:form . "SP") (:end . 221) (:start . 219)\n (:id . 95))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 222) (:start . 221)\n (:id . 96))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 226) (:start . 223)\n (:id . 97))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 233)\n (:start . 227) (:id . 98))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 234) (:start . 233)\n (:id . 99))\n ((:tag . "NNP") (:stem . "XL") (:form . "XL") (:end . 237) (:start . 235)\n (:id . 100))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 238) (:start . 237)\n (:id . 101))\n ((:tag . "NN") (:stem . "frog") (:form . "frog") (:end . 243) (:start . 239)\n (:id . 102))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 244) (:start . 243)\n (:id . 103)))@@@1@62@((:identifiers (:sid . :s6.96) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101836@unknown@formal@none@1@S@(Transib1 through Transib5 are from D. melanogaster fruit fly.)@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Transib1") (:form . "Transib1") (:end . 9)\n (:start . 1) (:id . 43))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 17)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "transib5") (:form . "Transib5") (:end . 26)\n (:start . 18) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 35) (:start . 31)\n (:id . 47))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 38) (:start . 36)\n (:id . 48))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 51)\n (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 57) (:start . 52)\n (:id . 50))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 61) (:start . 58)\n (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 62) (:start . 61)\n (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s6.97) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101837@unknown@formal@none@1@S@Common Structural Hallmarks of the Transib TPase and RAG1 Core@(((:tag . "JJ") (:stem . "common") (:form . "Common") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "structural") (:form . "Structural") (:end . 17)\n (:start . 7) (:id . 43))\n ((:tag . "NNP") (:stem . "Hallmark") (:form . "Hallmarks") (:end . 27)\n (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 42)\n (:start . 35) (:id . 47))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 48) (:start . 43)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n (:id . 49))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 57) (:start . 53)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Core") (:form . "Core") (:end . 62) (:start . 58)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s6.98) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101838@unknown@formal@none@1@S@All three core residues from the catalytic DDE triad in the RAG1 proteins (residues 603, 711, and 965) that are necessary for V(D)J recombination [21,22] are conserved in the Transib TPases (Figures 3 and Figure S3).@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 28) (:start . 24)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n (:id . 47))\n ((:tag . "JJ") (:stem . "catalytic") (:form . "catalytic") (:end . 42)\n (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "dde") (:form . "DDE") (:end . 46) (:start . 43)\n (:id . 49))\n ((:tag . "NN") (:stem . "triad") (:form . "triad") (:end . 52) (:start . 47)\n (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n (:id . 52))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 64) (:start . 60)\n (:id . 53))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 73)\n (:start . 65) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n (:id . 55))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 83)\n (:start . 75) (:id . 56))\n ((:tag . "CD") (:stem . "603") (:form . "603") (:end . 87) (:start . 84)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n (:id . 58))\n ((:tag . "CD") (:stem . "711") (:form . "711") (:end . 92) (:start . 89)\n (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n (:id . 61))\n ((:tag . "CD") (:stem . "965") (:form . "965") (:end . 101) (:start . 98)\n (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n (:id . 63))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 107) (:start . 103)\n (:id . 64))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 111) (:start . 108)\n (:id . 65))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 121)\n (:start . 112) (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 125) (:start . 122)\n (:id . 67))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 131)\n (:start . 126) (:id . 68))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 145) (:start . 132) (:id . 69))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 147) (:start . 146)\n (:id . 70))\n ((:tag . "CD") (:stem . "21,22") (:form . "21,22") (:end . 152)\n (:start . 147) (:id . 71))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 153) (:start . 152)\n (:id . 72))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 157) (:start . 154)\n (:id . 73))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 167)\n (:start . 158) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 170) (:start . 168)\n (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 174) (:start . 171)\n (:id . 76))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 182)\n (:start . 175) (:id . 77))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 189)\n (:start . 183) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 191) (:start . 190)\n (:id . 79))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 198)\n (:start . 191) (:id . 80))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 200) (:start . 199)\n (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 204) (:start . 201)\n (:id . 82))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 211)\n (:start . 205) (:id . 83))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 214) (:start . 212)\n (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 215) (:start . 214)\n (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n (:id . 86)))@@@1@45@((:identifiers (:sid . :s6.99) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101840@unknown@formal@none@1@S@Moreover, each catalytic residue is a part of a motif that is conserved in the Transib TPases and RAG1 (motifs 4, 6, and 10 in Figures 3 and Figure S3).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "JJ") (:stem . "catalytic") (:form . "catalytic") (:end . 24)\n (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 32)\n (:start . 25) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 35) (:start . 33)\n (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n (:id . 48))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 42) (:start . 38)\n (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 47) (:start . 46)\n (:id . 51))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 53) (:start . 48)\n (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 58) (:start . 54)\n (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 61) (:start . 59)\n (:id . 54))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 71)\n (:start . 62) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n (:id . 57))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 86)\n (:start . 79) (:id . 58))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 93) (:start . 87)\n (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n (:id . 60))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 102) (:start . 98)\n (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n (:id . 62))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 110)\n (:start . 104) (:id . 63))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 112) (:start . 111)\n (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n (:id . 65))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 115) (:start . 114)\n (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n (:id . 68))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 123) (:start . 121)\n (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 126) (:start . 124)\n (:id . 70))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 134)\n (:start . 127) (:id . 71))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 136) (:start . 135)\n (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n (:id . 73))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 147)\n (:start . 141) (:id . 74))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 150) (:start . 148)\n (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s6.101) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101841@unknown@formal@none@1@S@The RAG1 core is composed of the N-terminal region and the central and C-terminal domains ([26,27].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "VBN") (:stem . "compose") (:form . "composed") (:end . 25)\n (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n (:id . 48))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 43)\n (:start . 33) (:id . 49))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 50)\n (:start . 44) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n (:id . 52))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 66)\n (:start . 59) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n (:id . 54))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 81)\n (:start . 71) (:id . 55))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 89)\n (:start . 82) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 92) (:start . 91)\n (:id . 58))\n ((:tag . "CD") (:stem . "26,27") (:form . "26,27") (:end . 97) (:start . 92)\n (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 98) (:start . 97)\n (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.102) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101842@unknown@formal@none@1@S@The N-terminal region includes the RSS nonamer-binding regions (residues 387–480), referred to as NBR [28,29].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 21)\n (:start . 15) (:id . 44))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 30)\n (:start . 22) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 46))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSS") (:end . 38) (:start . 35)\n (:id . 47))\n ((:tag . "JJ") (:stem . "nonamer-binding") (:form . "nonamer-binding")\n (:end . 54) (:start . 39) (:id . 48))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 62)\n (:start . 55) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 64) (:start . 63)\n (:id . 50))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 72)\n (:start . 64) (:id . 51))\n ((:tag . "CD") (:stem . "387–480") (:form . "387–480") (:end . 80)\n (:start . 73) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n (:id . 54))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 91)\n (:start . 83) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 97) (:start . 95)\n (:id . 57))\n ((:tag . "NNP") (:stem . "NBR") (:form . "NBR") (:end . 101) (:start . 98)\n (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 103) (:start . 102)\n (:id . 59))\n ((:tag . "CD") (:stem . "28,29") (:form . "28,29") (:end . 108)\n (:start . 103) (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 109) (:start . 108)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.103) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101843@unknown@formal@none@1@S@The two terminal motifs of RAG1 NBR are conserved in the Transib TPases (Figure S3), which indicates that they may be important for their binding to the Transib TIRs during transposition (the RSS-like structure of TIRs is described below; Figure 4).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 16)\n (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 23)\n (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 31) (:start . 27)\n (:id . 47))\n ((:tag . "NNP") (:stem . "NBR") (:form . "NBR") (:end . 35) (:start . 32)\n (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 39) (:start . 36)\n (:id . 49))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 49)\n (:start . 40) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n (:id . 52))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 64)\n (:start . 57) (:id . 53))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 71) (:start . 65)\n (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 79)\n (:start . 73) (:id . 56))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 82) (:start . 80)\n (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 90) (:start . 85)\n (:id . 60))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 100)\n (:start . 91) (:id . 61))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 105) (:start . 101)\n (:id . 62))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 110) (:start . 106)\n (:id . 63))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 114) (:start . 111)\n (:id . 64))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 117) (:start . 115)\n (:id . 65))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 127)\n (:start . 118) (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 131) (:start . 128)\n (:id . 67))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 137)\n (:start . 132) (:id . 68))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 145)\n (:start . 138) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 148) (:start . 146)\n (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n (:id . 71))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 160)\n (:start . 153) (:id . 72))\n ((:tag . "NNP") (:stem . "TIR") (:form . "TIRs") (:end . 165) (:start . 161)\n (:id . 73))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 172)\n (:start . 166) (:id . 74))\n ((:tag . "NN") (:stem . "transposition") (:form . "transposition")\n (:end . 186) (:start . 173) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 188) (:start . 187)\n (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 191) (:start . 188)\n (:id . 77))\n ((:tag . "JJ") (:stem . "rss-like") (:form . "RSS-like") (:end . 200)\n (:start . 192) (:id . 78))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 210)\n (:start . 201) (:id . 79))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 213) (:start . 211)\n (:id . 80))\n ((:tag . "NNP") (:stem . "TIR") (:form . "TIRs") (:end . 218) (:start . 214)\n (:id . 81))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 221) (:start . 219)\n (:id . 82))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 231)\n (:start . 222) (:id . 83))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 237)\n (:start . 232) (:id . 84))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 238) (:start . 237)\n (:id . 85))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 245)\n (:start . 239) (:id . 86))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 247) (:start . 246)\n (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 248) (:start . 247)\n (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 249) (:start . 248)\n (:id . 89)))@@@1@48@((:hcues ((:id . :x6.104.1) (:span 111 114))\n ((:id . :x6.104.2) (:span 91 105)))\n (:hscopes ((:id . :x6.104.1) (:span 111 237))\n ((:id . :x6.104.2) (:span 91 237)))\n (:identifiers (:sid . :s6.104) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101844@unknown@formal@none@1@S@The central domain of the RAG1 core (residues 531–763) includes two aspartic acid residues from the DDE triad and is also thought to be involved in binding to the RSS heptamer and RAG2 [30,31].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 18)\n (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 46))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 30) (:start . 26)\n (:id . 47))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 35) (:start . 31)\n (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n (:id . 49))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 45)\n (:start . 37) (:id . 50))\n ((:tag . "CD") (:stem . "531–763") (:form . "531–763") (:end . 53)\n (:start . 46) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 54) (:start . 53)\n (:id . 52))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 63)\n (:start . 55) (:id . 53))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 67) (:start . 64)\n (:id . 54))\n ((:tag . "JJ") (:stem . "aspartic") (:form . "aspartic") (:end . 76)\n (:start . 68) (:id . 55))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 81) (:start . 77)\n (:id . 56))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 90)\n (:start . 82) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 95) (:start . 91)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n (:id . 59))\n ((:tag . "NNP") (:stem . "DDE") (:form . "DDE") (:end . 103) (:start . 100)\n (:id . 60))\n ((:tag . "NN") (:stem . "triad") (:form . "triad") (:end . 109)\n (:start . 104) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 116) (:start . 114)\n (:id . 63))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 121) (:start . 117)\n (:id . 64))\n ((:tag . "VBN") (:stem . "think") (:form . "thought") (:end . 129)\n (:start . 122) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 132) (:start . 130)\n (:id . 66))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 135) (:start . 133)\n (:id . 67))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 144)\n (:start . 136) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 147) (:start . 145)\n (:id . 69))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 155)\n (:start . 148) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 158) (:start . 156)\n (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 162) (:start . 159)\n (:id . 72))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSS") (:end . 166) (:start . 163)\n (:id . 73))\n ((:tag . "NN") (:stem . "heptamer") (:form . "heptamer") (:end . 175)\n (:start . 167) (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 179) (:start . 176)\n (:id . 75))\n ((:tag . "NN") (:stem . "rag2") (:form . "RAG2") (:end . 184) (:start . 180)\n (:id . 76))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 186) (:start . 185)\n (:id . 77))\n ((:tag . "CD") (:stem . "30,31") (:form . "30,31") (:end . 191)\n (:start . 186) (:id . 78))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 192) (:start . 191)\n (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n (:id . 80)))@@@1@39@((:hcues ((:id . :x6.105.1) (:span 122 129)))\n (:hscopes ((:id . :x6.105.1) (:span 114 184)))\n (:identifiers (:sid . :s6.105) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101845@unknown@formal@none@1@S@The C-terminal domain of RAG1 (residues 764–1011) is the portion of RAG1 that is most conserved between RAG1 and Transib TPases.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 21)\n (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n (:id . 45))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 29) (:start . 25)\n (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 31) (:start . 30)\n (:id . 47))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 39)\n (:start . 31) (:id . 48))\n ((:tag . "CD") (:stem . "764–1011") (:form . "764–1011") (:end . 48)\n (:start . 40) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 49) (:start . 48)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 52) (:start . 50)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n (:id . 52))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 64)\n (:start . 57) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n (:id . 54))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 72) (:start . 68)\n (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 77) (:start . 73)\n (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 80) (:start . 78)\n (:id . 57))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 85) (:start . 81)\n (:id . 58))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 95)\n (:start . 86) (:id . 59))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 103)\n (:start . 96) (:id . 60))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 108) (:start . 104)\n (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n (:id . 62))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 120)\n (:start . 113) (:id . 63))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 127)\n (:start . 121) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s6.106) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101846@unknown@formal@none@1@S@In addition to the catalytic activity attributed to the last residue of the DDE triad, this domain has a strong nonspecific DNA-binding affinity because it binds to coding DNA upstream of the RSS heptamer, and is thought to be involved in RAG1 dimerization [26,27].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "JJ") (:stem . "catalytic") (:form . "catalytic") (:end . 28)\n (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 37)\n (:start . 29) (:id . 47))\n ((:tag . "VBN") (:stem . "attribute") (:form . "attributed") (:end . 48)\n (:start . 38) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n (:id . 50))\n ((:tag . "JJ") (:stem . "last") (:form . "last") (:end . 60) (:start . 56)\n (:id . 51))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 68)\n (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n (:id . 54))\n ((:tag . "NNP") (:stem . "DDE") (:form . "DDE") (:end . 79) (:start . 76)\n (:id . 55))\n ((:tag . "NN") (:stem . "triad") (:form . "triad") (:end . 85) (:start . 80)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n (:id . 57))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 91) (:start . 87)\n (:id . 58))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 98)\n (:start . 92) (:id . 59))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 102) (:start . 99)\n (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 104) (:start . 103)\n (:id . 61))\n ((:tag . "JJ") (:stem . "strong") (:form . "strong") (:end . 111)\n (:start . 105) (:id . 62))\n ((:tag . "JJ") (:stem . "nonspecific") (:form . "nonspecific") (:end . 123)\n (:start . 112) (:id . 63))\n ((:tag . "JJ") (:stem . "dna-binding") (:form . "DNA-binding") (:end . 135)\n (:start . 124) (:id . 64))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 144)\n (:start . 136) (:id . 65))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 152)\n (:start . 145) (:id . 66))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 155) (:start . 153)\n (:id . 67))\n ((:tag . "VBZ") (:stem . "bind") (:form . "binds") (:end . 161)\n (:start . 156) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 164) (:start . 162)\n (:id . 69))\n ((:tag . "VBG") (:stem . "cod") (:form . "coding") (:end . 171)\n (:start . 165) (:id . 70))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 175) (:start . 172)\n (:id . 71))\n ((:tag . "RB") (:stem . "upstream") (:form . "upstream") (:end . 184)\n (:start . 176) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 187) (:start . 185)\n (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 191) (:start . 188)\n (:id . 74))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSS") (:end . 195) (:start . 192)\n (:id . 75))\n ((:tag . "NN") (:stem . "heptamer") (:form . "heptamer") (:end . 204)\n (:start . 196) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 205) (:start . 204)\n (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 209) (:start . 206)\n (:id . 78))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 212) (:start . 210)\n (:id . 79))\n ((:tag . "VBN") (:stem . "think") (:form . "thought") (:end . 220)\n (:start . 213) (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 223) (:start . 221)\n (:id . 81))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 226) (:start . 224)\n (:id . 82))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 235)\n (:start . 227) (:id . 83))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 238) (:start . 236)\n (:id . 84))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 243) (:start . 239)\n (:id . 85))\n ((:tag . "NN") (:stem . "dimerization") (:form . "dimerization") (:end . 256)\n (:start . 244) (:id . 86))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 258) (:start . 257)\n (:id . 87))\n ((:tag . "CD") (:stem . "26,27") (:form . "26,27") (:end . 263)\n (:start . 258) (:id . 88))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 264) (:start . 263)\n (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 265) (:start . 264)\n (:id . 90)))@@@1@49@((:hcues ((:id . :x6.107.1) (:span 213 220)))\n (:hscopes ((:id . :x6.107.1) (:span 210 256)))\n (:identifiers (:sid . :s6.107) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101847@unknown@formal@none@1@S@This domain is predicted to function analogously in Transib transposons.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 24)\n (:start . 15) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "VB") (:stem . "function") (:form . "function") (:end . 36)\n (:start . 28) (:id . 47))\n ((:tag . "RB") (:stem . "analogously") (:form . "analogously") (:end . 48)\n (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n (:id . 49))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 59)\n (:start . 52) (:id . 50))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 71)\n (:start . 60) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n (:id . 52)))@@@1@11@((:hcues ((:id . :x6.108.1) (:span 15 24)))\n (:hscopes ((:id . :x6.108.1) (:span 0 71)))\n (:identifiers (:sid . :s6.108) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101848@unknown@formal@none@1@S@Several other motifs conserved in Transib TPases and RAG1 include aa residues that have been shown experimentally to be important for specific functions in V(D)J recombination (Figure S3).@(((:tag . "JJ") (:stem . "several") (:form . "Several") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 13) (:start . 8)\n (:id . 43))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 20)\n (:start . 14) (:id . 44))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 30)\n (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 41)\n (:start . 34) (:id . 47))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 48) (:start . 42)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n (:id . 49))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 57) (:start . 53)\n (:id . 50))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 65)\n (:start . 58) (:id . 51))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 68) (:start . 66)\n (:id . 52))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 77)\n (:start . 69) (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 82) (:start . 78)\n (:id . 54))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 87) (:start . 83)\n (:id . 55))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 92) (:start . 88)\n (:id . 56))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 98) (:start . 93)\n (:id . 57))\n ((:tag . "RB") (:stem . "experimentally") (:form . "experimentally")\n (:end . 113) (:start . 99) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 116) (:start . 114)\n (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 119) (:start . 117)\n (:id . 60))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 129)\n (:start . 120) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 133) (:start . 130)\n (:id . 62))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 142)\n (:start . 134) (:id . 63))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 152)\n (:start . 143) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 155) (:start . 153)\n (:id . 65))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 161)\n (:start . 156) (:id . 66))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 175) (:start . 162) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 177) (:start . 176)\n (:id . 68))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 183)\n (:start . 177) (:id . 69))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 186) (:start . 184)\n (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 187) (:start . 186)\n (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n (:id . 72)))@@@1@31@((:identifiers (:sid . :s6.109) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101850@unknown@formal@none@1@S@Among the most conserved motifs, motif 5 (see Figures 3 and Figure S3) is of particular interest because its function is not known yet but is expected to play a role both V(D)J recombination and Transib transposition.@(((:tag . "IN") (:stem . "among") (:form . "Among") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 24)\n (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 31)\n (:start . 25) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n (:id . 47))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 38) (:start . 33)\n (:id . 48))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 40) (:start . 39)\n (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n (:id . 50))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 45) (:start . 42)\n (:id . 51))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 53)\n (:start . 46) (:id . 52))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 55) (:start . 54)\n (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 66)\n (:start . 60) (:id . 55))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 69) (:start . 67)\n (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 73) (:start . 71)\n (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n (:id . 59))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 87)\n (:start . 77) (:id . 60))\n ((:tag . "NN") (:stem . "interest") (:form . "interest") (:end . 96)\n (:start . 88) (:id . 61))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 104)\n (:start . 97) (:id . 62))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 108) (:start . 105)\n (:id . 63))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 117)\n (:start . 109) (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 120) (:start . 118)\n (:id . 65))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 124) (:start . 121)\n (:id . 66))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 130)\n (:start . 125) (:id . 67))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 134) (:start . 131)\n (:id . 68))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 138) (:start . 135)\n (:id . 69))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 141) (:start . 139)\n (:id . 70))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 150)\n (:start . 142) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 153) (:start . 151)\n (:id . 72))\n ((:tag . "VB") (:stem . "play") (:form . "play") (:end . 158) (:start . 154)\n (:id . 73))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 160) (:start . 159)\n (:id . 74))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 165) (:start . 161)\n (:id . 75))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 170) (:start . 166)\n (:id . 76))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 176)\n (:start . 171) (:id . 77))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 190) (:start . 177) (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 194) (:start . 191)\n (:id . 79))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 202)\n (:start . 195) (:id . 80))\n ((:tag . "NN") (:stem . "transposition") (:form . "transposition")\n (:end . 216) (:start . 203) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 217) (:start . 216)\n (:id . 82)))@@@1@41@((:hcues ((:id . :x6.111.1) (:span 142 150))\n ((:id . :x6.111.2) (:span 121 130)))\n (:hscopes ((:id . :x6.111.1) (:span 139 216))\n ((:id . :x6.111.2) (:span 105 134)))\n (:identifiers (:sid . :s6.111) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101851@unknown@formal@none@1@S@In conjunction with detailed studies of the Transib superfamily, we also analyzed the remaining nine known superfamilies of DNA transposons defined by diverse TPases (see Table 1 in [24]).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "conjunction") (:form . "conjunction") (:end . 14)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "JJ") (:stem . "detailed") (:form . "detailed") (:end . 28)\n (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 36)\n (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 51)\n (:start . 44) (:id . 49))\n ((:tag . "NN") (:stem . "superfamily") (:form . "superfamily") (:end . 63)\n (:start . 52) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n (:id . 51))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 67) (:start . 65)\n (:id . 52))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 72) (:start . 68)\n (:id . 53))\n ((:tag . "VBD") (:stem . "analyze") (:form . "analyzed") (:end . 81)\n (:start . 73) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n (:id . 55))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 95)\n (:start . 86) (:id . 56))\n ((:tag . "CD") (:stem . "nine") (:form . "nine") (:end . 100) (:start . 96)\n (:id . 57))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 106)\n (:start . 101) (:id . 58))\n ((:tag . "NNS") (:stem . "superfamily") (:form . "superfamilies")\n (:end . 120) (:start . 107) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n (:id . 60))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 127) (:start . 124)\n (:id . 61))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 139)\n (:start . 128) (:id . 62))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 147)\n (:start . 140) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 150) (:start . 148)\n (:id . 64))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 158)\n (:start . 151) (:id . 65))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 165)\n (:start . 159) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n (:id . 67))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 170) (:start . 167)\n (:id . 68))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 176)\n (:start . 171) (:id . 69))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 178) (:start . 177)\n (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 181) (:start . 179)\n (:id . 71))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 183) (:start . 182)\n (:id . 72))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 185) (:start . 183)\n (:id . 73))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 186) (:start . 185)\n (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 187) (:start . 186)\n (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s6.112) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101852@unknown@formal@none@1@S@Some of these TPases, including Mariner, Harbinger, P, and hAT, also contain the catalytic DDE triad [23].@(((:tag . "DT") (:stem . "some") (:form . "Some") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 20) (:start . 14)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n (:id . 46))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 31)\n (:start . 22) (:id . 47))\n ((:tag . "NNP") (:stem . "Mariner") (:form . "Mariner") (:end . 39)\n (:start . 32) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n (:id . 49))\n ((:tag . "NNP") (:stem . "Harbinger") (:form . "Harbinger") (:end . 50)\n (:start . 41) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n (:id . 51))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 53) (:start . 52)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n (:id . 54))\n ((:tag . "NN") (:stem . "hat") (:form . "hAT") (:end . 62) (:start . 59)\n (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n (:id . 56))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 68) (:start . 64)\n (:id . 57))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 76)\n (:start . 69) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n (:id . 59))\n ((:tag . "JJ") (:stem . "catalytic") (:form . "catalytic") (:end . 90)\n (:start . 81) (:id . 60))\n ((:tag . "NN") (:stem . "dde") (:form . "DDE") (:end . 94) (:start . 91)\n (:id . 61))\n ((:tag . "NN") (:stem . "triad") (:form . "triad") (:end . 100) (:start . 95)\n (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 102) (:start . 101)\n (:id . 63))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 104) (:start . 102)\n (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 105) (:start . 104)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s6.113) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101853@unknown@formal@none@1@S@However, based on PSI-BLAST searches, no significant similarities between these nine TPases and RAG1 protein were found (data not shown).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 17) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 27)\n (:start . 18) (:id . 46))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 36)\n (:start . 28) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n (:id . 48))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 40) (:start . 38)\n (:id . 49))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 52)\n (:start . 41) (:id . 50))\n ((:tag . "NNS") (:stem . "similarity") (:form . "similarities") (:end . 65)\n (:start . 53) (:id . 51))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 73)\n (:start . 66) (:id . 52))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 79) (:start . 74)\n (:id . 53))\n ((:tag . "CD") (:stem . "nine") (:form . "nine") (:end . 84) (:start . 80)\n (:id . 54))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 91) (:start . 85)\n (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n (:id . 56))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 100) (:start . 96)\n (:id . 57))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 108)\n (:start . 101) (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 113) (:start . 109)\n (:id . 59))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 119)\n (:start . 114) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n (:id . 61))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 125)\n (:start . 121) (:id . 62))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 129) (:start . 126)\n (:id . 63))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 135)\n (:start . 130) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n (:id . 66)))@@@1@25@((:ncues ((:id . :x6.114.1) (:span 126 129))\n ((:id . :x6.114.2) (:span 38 40)))\n (:nscopes ((:id . :x6.114.1) (:span 120 136))\n ((:id . :x6.114.2) (:span 38 119)))\n (:identifiers (:sid . :s6.114) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101854@unknown@formal@none@1@S@Therefore, given that the only significant similarity of the RAG1 core was to the Transib TPase, the RAG1 core was re-confirmed as belonging to the Transib superfamily.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 16) (:start . 11)\n (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 46))\n ((:tag . "JJ") (:stem . "only") (:form . "only") (:end . 30) (:start . 26)\n (:id . 47))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 42)\n (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 53)\n (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n (:id . 51))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 65) (:start . 61)\n (:id . 52))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 70) (:start . 66)\n (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 74) (:start . 71)\n (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 77) (:start . 75)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n (:id . 56))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 89)\n (:start . 82) (:id . 57))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 95) (:start . 90)\n (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n (:id . 60))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 105) (:start . 101)\n (:id . 61))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 110) (:start . 106)\n (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 114) (:start . 111)\n (:id . 63))\n ((:tag . "VBN") (:stem . "re-confirme") (:form . "re-confirmed") (:end . 127)\n (:start . 115) (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 130) (:start . 128)\n (:id . 65))\n ((:tag . "VBG") (:stem . "belong") (:form . "belonging") (:end . 140)\n (:start . 131) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 143) (:start . 141)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 147) (:start . 144)\n (:id . 68))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 155)\n (:start . 148) (:id . 69))\n ((:tag . "NN") (:stem . "superfamily") (:form . "superfamily") (:end . 167)\n (:start . 156) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s6.115) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101855@unknown@formal@none@1@S@In addition to the statistically significant similarity between the approximately 600-aa RAG1 core and Transib TPases, there are two other lines of evidence suggesting evolution of the V(D)J machinery from Transib DNA transposons.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "RB") (:stem . "statistically") (:form . "statistically")\n (:end . 32) (:start . 19) (:id . 46))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 44)\n (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 55)\n (:start . 45) (:id . 48))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 63)\n (:start . 56) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n (:id . 50))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 81) (:start . 68) (:id . 51))\n ((:tag . "JJ") (:stem . "600-aa") (:form . "600-aa") (:end . 88)\n (:start . 82) (:id . 52))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 93) (:start . 89)\n (:id . 53))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 98) (:start . 94)\n (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 110)\n (:start . 103) (:id . 56))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 117)\n (:start . 111) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n (:id . 58))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 124)\n (:start . 119) (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 128) (:start . 125)\n (:id . 60))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 132) (:start . 129)\n (:id . 61))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 138)\n (:start . 133) (:id . 62))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 144)\n (:start . 139) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 147) (:start . 145)\n (:id . 64))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 156)\n (:start . 148) (:id . 65))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 167)\n (:start . 157) (:id . 66))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 177)\n (:start . 168) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 180) (:start . 178)\n (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 184) (:start . 181)\n (:id . 69))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 190)\n (:start . 185) (:id . 70))\n ((:tag . "NN") (:stem . "machinery") (:form . "machinery") (:end . 200)\n (:start . 191) (:id . 71))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 205) (:start . 201)\n (:id . 72))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 213)\n (:start . 206) (:id . 73))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 217) (:start . 214)\n (:id . 74))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 229)\n (:start . 218) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 230) (:start . 229)\n (:id . 76)))@@@1@35@((:hcues ((:id . :x6.116.1) (:span 157 167)))\n (:hscopes ((:id . :x6.116.1) (:span 157 229)))\n (:identifiers (:sid . :s6.116) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101856@unknown@formal@none@1@S@They include the characteristic TSDs and structure of the TIRs discussed in the next two sections.@(((:tag . "PRP") (:stem . "they") (:form . "They") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n (:end . 31) (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "tsd") (:form . "TSDs") (:end . 36) (:start . 32)\n (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n (:id . 47))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 50)\n (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n (:id . 50))\n ((:tag . "NNS") (:stem . "tir") (:form . "TIRs") (:end . 62) (:start . 58)\n (:id . 51))\n ((:tag . "VBN") (:stem . "discuss") (:form . "discussed") (:end . 72)\n (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 75) (:start . 73)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n (:id . 54))\n ((:tag . "JJ") (:stem . "next") (:form . "next") (:end . 84) (:start . 80)\n (:id . 55))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 88) (:start . 85)\n (:id . 56))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 97)\n (:start . 89) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s6.117) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101857@unknown@formal@none@1@S@Multiple Alignment of Ten Conserved Motifs in the RAG1 Core Proteins and Transib TPases@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "alignment") (:form . "Alignment") (:end . 18)\n (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 44))\n ((:tag . "CD") (:stem . "ten") (:form . "Ten") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "VBN") (:stem . "conserve") (:form . "Conserved") (:end . 35)\n (:start . 26) (:id . 46))\n ((:tag . "NNS") (:stem . "motif") (:form . "Motifs") (:end . 42)\n (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 54) (:start . 50)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Core") (:form . "Core") (:end . 59) (:start . 55)\n (:id . 51))\n ((:tag . "NNPS") (:stem . "Proteins") (:form . "Proteins") (:end . 68)\n (:start . 60) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 80)\n (:start . 73) (:id . 54))\n ((:tag . "NNPS") (:stem . "TPas") (:form . "TPases") (:end . 87)\n (:start . 81) (:id . 55)))@@@1@14@((:identifiers (:sid . :s6.118) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5101858@unknown@formal@none@1@S@The motifs are underlined and numbered from 1 to 10.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "VBN") (:stem . "underline") (:form . "underlined") (:end . 25)\n (:start . 15) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 29) (:start . 26)\n (:id . 46))\n ((:tag . "VBN") (:stem . "number") (:form . "numbered") (:end . 38)\n (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 43) (:start . 39)\n (:id . 48))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 45) (:start . 44)\n (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n (:id . 50))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 51) (:start . 49)\n (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 52) (:start . 51)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s6.119) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101860@unknown@formal@none@1@S@Distances between the motifs are indicated in numbers of aa residues.@(((:tag . "NNS") (:stem . "distance") (:form . "Distances") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 17)\n (:start . 10) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n (:id . 44))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 28)\n (:start . 22) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 32) (:start . 29)\n (:id . 46))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 42)\n (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n (:id . 48))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 53)\n (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n (:id . 50))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 59) (:start . 57)\n (:id . 51))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 68)\n (:start . 60) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s6.121) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101861@unknown@formal@none@1@S@Black circles denote conserved residues that form the RAG1/Transib catalytic DDE triad.@(((:tag . "JJ") (:stem . "black") (:form . "Black") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "circle") (:form . "circles") (:end . 13)\n (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "denote") (:form . "denote") (:end . 20)\n (:start . 14) (:id . 44))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 30)\n (:start . 21) (:id . 45))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 39)\n (:start . 31) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 44) (:start . 40)\n (:id . 47))\n ((:tag . "VBP") (:stem . "form") (:form . "form") (:end . 49) (:start . 45)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n (:id . 49))\n ((:tag . "NNP") (:stem . "RAG1/Transib") (:form . "RAG1/Transib") (:end . 66)\n (:start . 54) (:id . 50))\n ((:tag . "JJ") (:stem . "catalytic") (:form . "catalytic") (:end . 76)\n (:start . 67) (:id . 51))\n ((:tag . "NN") (:stem . "dde") (:form . "DDE") (:end . 80) (:start . 77)\n (:id . 52))\n ((:tag . "NN") (:stem . "triad") (:form . "triad") (:end . 86) (:start . 81)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.122) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101862@unknown@formal@none@1@S@The RAG1 proteins are as follows: RAG1_XL (GenBank GI no. 2501723, Xenopus laevis, frog), RAG1_HS (4557841, Homo sapiens, human), RAG1_GG (131826, Gallus gallus, chicken), RAG1_CL (1470117, Carcharhinus leucas, bull shark), RAG1_FR (4426834, Fugu rubripes, fugu fish).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 17)\n (:start . 9) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 21) (:start . 18)\n (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 24) (:start . 22)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 32)\n (:start . 25) (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 33) (:start . 32)\n (:id . 48))\n ((:tag . "NNP") (:stem . "RAG1_XL") (:form . "RAG1_XL") (:end . 41)\n (:start . 34) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 43) (:start . 42)\n (:id . 50))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 50)\n (:start . 43) (:id . 51))\n ((:tag . "NNP") (:stem . "GI") (:form . "GI") (:end . 53) (:start . 51)\n (:id . 52))\n ((:tag . "NNP") (:stem . "no.") (:form . "no.") (:end . 57) (:start . 54)\n (:id . 53))\n ((:tag . "CD") (:stem . "2501723") (:form . "2501723") (:end . 65)\n (:start . 58) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Xenopus") (:form . "Xenopus") (:end . 74)\n (:start . 67) (:id . 56))\n ((:tag . "NNP") (:stem . "laevis") (:form . "laevis") (:end . 81)\n (:start . 75) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n (:id . 58))\n ((:tag . "NN") (:stem . "frog") (:form . "frog") (:end . 87) (:start . 83)\n (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 88) (:start . 87)\n (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n (:id . 61))\n ((:tag . "NNP") (:stem . "RAG1_HS") (:form . "RAG1_HS") (:end . 97)\n (:start . 90) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 99) (:start . 98)\n (:id . 63))\n ((:tag . "CD") (:stem . "4557841") (:form . "4557841") (:end . 106)\n (:start . 99) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n (:id . 65))\n ((:tag . "NNP") (:stem . "Homo") (:form . "Homo") (:end . 112) (:start . 108)\n (:id . 66))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 120)\n (:start . 113) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n (:id . 68))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 127)\n (:start . 122) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 128) (:start . 127)\n (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n (:id . 71))\n ((:tag . "NNP") (:stem . "RAG1_GG") (:form . "RAG1_GG") (:end . 137)\n (:start . 130) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n (:id . 73))\n ((:tag . "CD") (:stem . "131826") (:form . "131826") (:end . 145)\n (:start . 139) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n (:id . 75))\n ((:tag . "NNP") (:stem . "Gallus") (:form . "Gallus") (:end . 153)\n (:start . 147) (:id . 76))\n ((:tag . "NN") (:stem . "gallus") (:form . "gallus") (:end . 160)\n (:start . 154) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n (:id . 78))\n ((:tag . "NN") (:stem . "chicken") (:form . "chicken") (:end . 169)\n (:start . 162) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 170) (:start . 169)\n (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n (:id . 81))\n ((:tag . "NNP") (:stem . "RAG1_CL") (:form . "RAG1_CL") (:end . 179)\n (:start . 172) (:id . 82))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 181) (:start . 180)\n (:id . 83))\n ((:tag . "CD") (:stem . "1470117") (:form . "1470117") (:end . 188)\n (:start . 181) (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n (:id . 85))\n ((:tag . "NNP") (:stem . "Carcharhinus") (:form . "Carcharhinus")\n (:end . 202) (:start . 190) (:id . 86))\n ((:tag . "NNS") (:stem . "leuca") (:form . "leucas") (:end . 209)\n (:start . 203) (:id . 87))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 210) (:start . 209)\n (:id . 88))\n ((:tag . "NN") (:stem . "bull") (:form . "bull") (:end . 215) (:start . 211)\n (:id . 89))\n ((:tag . "NN") (:stem . "shark") (:form . "shark") (:end . 221)\n (:start . 216) (:id . 90))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 222) (:start . 221)\n (:id . 91))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 223) (:start . 222)\n (:id . 92))\n ((:tag . "NNP") (:stem . "RAG1_FR") (:form . "RAG1_FR") (:end . 231)\n (:start . 224) (:id . 93))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 233) (:start . 232)\n (:id . 94))\n ((:tag . "CD") (:stem . "4426834") (:form . "4426834") (:end . 240)\n (:start . 233) (:id . 95))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 241) (:start . 240)\n (:id . 96))\n ((:tag . "NNP") (:stem . "Fugu") (:form . "Fugu") (:end . 246) (:start . 242)\n (:id . 97))\n ((:tag . "NNS") (:stem . "rubripe") (:form . "rubripes") (:end . 255)\n (:start . 247) (:id . 98))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 256) (:start . 255)\n (:id . 99))\n ((:tag . "NN") (:stem . "fugu") (:form . "fugu") (:end . 261) (:start . 257)\n (:id . 100))\n ((:tag . "NN") (:stem . "fish") (:form . "fish") (:end . 266) (:start . 262)\n (:id . 101))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 267) (:start . 266)\n (:id . 102))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 268) (:start . 267)\n (:id . 103)))@@@1@62@((:identifiers (:sid . :s6.123) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101863@unknown@formal@none@1@S@Coloring scheme [43] reflects physiochemical properties of amino acids: black shading marks hydrophobic residues, blue indicates charged (white font), positively charged (red font), and negatively charged (green font); red indicates proline (blue font) and glycine (green font); gray indicates aliphatic (red font) and aromatic (blue font); green indicates polar (black font) and amphoteric (red font); and yellow indicates tiny (blue font) and small (green font).@(((:tag . "VBG") (:stem . "color") (:form . "Coloring") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 15) (:start . 9)\n (:id . 43))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 17) (:start . 16)\n (:id . 44))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 20) (:start . 19)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "reflect") (:form . "reflects") (:end . 29)\n (:start . 21) (:id . 47))\n ((:tag . "JJ") (:stem . "physiochemical") (:form . "physiochemical")\n (:end . 44) (:start . 30) (:id . 48))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 55)\n (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n (:id . 50))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 64) (:start . 59)\n (:id . 51))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 70) (:start . 65)\n (:id . 52))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 71) (:start . 70)\n (:id . 53))\n ((:tag . "JJ") (:stem . "black") (:form . "black") (:end . 77) (:start . 72)\n (:id . 54))\n ((:tag . "NN") (:stem . "shading") (:form . "shading") (:end . 85)\n (:start . 78) (:id . 55))\n ((:tag . "VBZ") (:stem . "mark") (:form . "marks") (:end . 91) (:start . 86)\n (:id . 56))\n ((:tag . "JJ") (:stem . "hydrophobic") (:form . "hydrophobic") (:end . 103)\n (:start . 92) (:id . 57))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 112)\n (:start . 104) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n (:id . 59))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 118) (:start . 114)\n (:id . 60))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 128)\n (:start . 119) (:id . 61))\n ((:tag . "VBN") (:stem . "charge") (:form . "charged") (:end . 136)\n (:start . 129) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 138) (:start . 137)\n (:id . 63))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 143)\n (:start . 138) (:id . 64))\n ((:tag . "NN") (:stem . "font") (:form . "font") (:end . 148) (:start . 144)\n (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n (:id . 67))\n ((:tag . "RB") (:stem . "positively") (:form . "positively") (:end . 161)\n (:start . 151) (:id . 68))\n ((:tag . "VBN") (:stem . "charge") (:form . "charged") (:end . 169)\n (:start . 162) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 171) (:start . 170)\n (:id . 70))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 174) (:start . 171)\n (:id . 71))\n ((:tag . "NN") (:stem . "font") (:form . "font") (:end . 179) (:start . 175)\n (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 181) (:start . 180)\n (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 185) (:start . 182)\n (:id . 75))\n ((:tag . "RB") (:stem . "negatively") (:form . "negatively") (:end . 196)\n (:start . 186) (:id . 76))\n ((:tag . "VBN") (:stem . "charge") (:form . "charged") (:end . 204)\n (:start . 197) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 206) (:start . 205)\n (:id . 78))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 211)\n (:start . 206) (:id . 79))\n ((:tag . "NN") (:stem . "font") (:form . "font") (:end . 216) (:start . 212)\n (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 217) (:start . 216)\n (:id . 81))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 218) (:start . 217)\n (:id . 82))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 222) (:start . 219)\n (:id . 83))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 232)\n (:start . 223) (:id . 84))\n ((:tag . "NN") (:stem . "proline") (:form . "proline") (:end . 240)\n (:start . 233) (:id . 85))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 242) (:start . 241)\n (:id . 86))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 246) (:start . 242)\n (:id . 87))\n ((:tag . "NN") (:stem . "font") (:form . "font") (:end . 251) (:start . 247)\n (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 252) (:start . 251)\n (:id . 89))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 256) (:start . 253)\n (:id . 90))\n ((:tag . "NN") (:stem . "glycine") (:form . "glycine") (:end . 264)\n (:start . 257) (:id . 91))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 266) (:start . 265)\n (:id . 92))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 271)\n (:start . 266) (:id . 93))\n ((:tag . "NN") (:stem . "font") (:form . "font") (:end . 276) (:start . 272)\n (:id . 94))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 277) (:start . 276)\n (:id . 95))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 278) (:start . 277)\n (:id . 96))\n ((:tag . "NN") (:stem . "gray") (:form . "gray") (:end . 283) (:start . 279)\n (:id . 97))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 293)\n (:start . 284) (:id . 98))\n ((:tag . "JJ") (:stem . "aliphatic") (:form . "aliphatic") (:end . 303)\n (:start . 294) (:id . 99))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 305) (:start . 304)\n (:id . 100))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 308) (:start . 305)\n (:id . 101))\n ((:tag . "NN") (:stem . "font") (:form . "font") (:end . 313) (:start . 309)\n (:id . 102))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 314) (:start . 313)\n (:id . 103))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 318) (:start . 315)\n (:id . 104))\n ((:tag . "JJ") (:stem . "aromatic") (:form . "aromatic") (:end . 327)\n (:start . 319) (:id . 105))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 329) (:start . 328)\n (:id . 106))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 333) (:start . 329)\n (:id . 107))\n ((:tag . "NN") (:stem . "font") (:form . "font") (:end . 338) (:start . 334)\n (:id . 108))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 339) (:start . 338)\n (:id . 109))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 340) (:start . 339)\n (:id . 110))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 346)\n (:start . 341) (:id . 111))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 356)\n (:start . 347) (:id . 112))\n ((:tag . "JJ") (:stem . "polar") (:form . "polar") (:end . 362)\n (:start . 357) (:id . 113))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 364) (:start . 363)\n (:id . 114))\n ((:tag . "JJ") (:stem . "black") (:form . "black") (:end . 369)\n (:start . 364) (:id . 115))\n ((:tag . "NN") (:stem . "font") (:form . "font") (:end . 374) (:start . 370)\n (:id . 116))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 375) (:start . 374)\n (:id . 117))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 379) (:start . 376)\n (:id . 118))\n ((:tag . "JJ") (:stem . "amphoteric") (:form . "amphoteric") (:end . 390)\n (:start . 380) (:id . 119))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 392) (:start . 391)\n (:id . 120))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 395) (:start . 392)\n (:id . 121))\n ((:tag . "NN") (:stem . "font") (:form . "font") (:end . 400) (:start . 396)\n (:id . 122))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 401) (:start . 400)\n (:id . 123))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 402) (:start . 401)\n (:id . 124))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 406) (:start . 403)\n (:id . 125))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 413)\n (:start . 407) (:id . 126))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 423)\n (:start . 414) (:id . 127))\n ((:tag . "JJ") (:stem . "tiny") (:form . "tiny") (:end . 428) (:start . 424)\n (:id . 128))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 430) (:start . 429)\n (:id . 129))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 434) (:start . 430)\n (:id . 130))\n ((:tag . "NN") (:stem . "font") (:form . "font") (:end . 439) (:start . 435)\n (:id . 131))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 440) (:start . 439)\n (:id . 132))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 444) (:start . 441)\n (:id . 133))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 450)\n (:start . 445) (:id . 134))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 452) (:start . 451)\n (:id . 135))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 457)\n (:start . 452) (:id . 136))\n ((:tag . "NN") (:stem . "font") (:form . "font") (:end . 462) (:start . 458)\n (:id . 137))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 463) (:start . 462)\n (:id . 138))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 464) (:start . 463)\n (:id . 139)))@@@1@98@((:identifiers (:sid . :s6.124) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101864@unknown@formal@none@1@S@The species abbreviations for the Transib transposons are as follows: AA, yellow fever mosquito; AG, African malaria mosquito; DP, D. pseudoobscura fruit fly.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "species") (:form . "species") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "abbreviation") (:form . "abbreviations")\n (:end . 25) (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 29) (:start . 26)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 41)\n (:start . 34) (:id . 47))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 53)\n (:start . 42) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 57) (:start . 54)\n (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 60) (:start . 58)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 68)\n (:start . 61) (:id . 51))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 69) (:start . 68)\n (:id . 52))\n ((:tag . "NN") (:stem . "aa") (:form . "AA") (:end . 72) (:start . 70)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n (:id . 54))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 80)\n (:start . 74) (:id . 55))\n ((:tag . "NN") (:stem . "fever") (:form . "fever") (:end . 86) (:start . 81)\n (:id . 56))\n ((:tag . "NN") (:stem . "mosquito") (:form . "mosquito") (:end . 95)\n (:start . 87) (:id . 57))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 96) (:start . 95)\n (:id . 58))\n ((:tag . "NNP") (:stem . "AG") (:form . "AG") (:end . 99) (:start . 97)\n (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n (:id . 60))\n ((:tag . "JJ") (:stem . "african") (:form . "African") (:end . 108)\n (:start . 101) (:id . 61))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 116)\n (:start . 109) (:id . 62))\n ((:tag . "NN") (:stem . "mosquito") (:form . "mosquito") (:end . 125)\n (:start . 117) (:id . 63))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 126) (:start . 125)\n (:id . 64))\n ((:tag . "NNP") (:stem . "DP") (:form . "DP") (:end . 129) (:start . 127)\n (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n (:id . 66))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 133) (:start . 131)\n (:id . 67))\n ((:tag . "NN") (:stem . "pseudoobscura") (:form . "pseudoobscura")\n (:end . 147) (:start . 134) (:id . 68))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 153)\n (:start . 148) (:id . 69))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 157) (:start . 154)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s6.125) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101865@unknown@formal@none@1@S@(Transib1 through Transib5 are from the fruitfly D. melanogaster.)@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Transib1") (:form . "Transib1") (:end . 9)\n (:start . 1) (:id . 43))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 17)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "transib5") (:form . "Transib5") (:end . 26)\n (:start . 18) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 35) (:start . 31)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "JJ") (:stem . "fruitfly") (:form . "fruitfly") (:end . 48)\n (:start . 40) (:id . 49))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 51) (:start . 49)\n (:id . 50))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 64)\n (:start . 52) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 66) (:start . 65)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s6.126) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101866@unknown@formal@none@1@S@Structural Similarities between the Transib TIRs and V(D)J RSS Signals@(((:tag . "JJ") (:stem . "structural") (:form . "Structural") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "similarity") (:form . "Similarities") (:end . 23)\n (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 31)\n (:start . 24) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 43)\n (:start . 36) (:id . 46))\n ((:tag . "NNP") (:stem . "TIR") (:form . "TIRs") (:end . 48) (:start . 44)\n (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n (:id . 48))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 58) (:start . 53)\n (:id . 49))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSS") (:end . 62) (:start . 59)\n (:id . 50))\n ((:tag . "NNPS") (:stem . "Signal") (:form . "Signals") (:end . 70)\n (:start . 63) (:id . 51)))@@@1@10@((:identifiers (:sid . :s6.127) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5101867@unknown@formal@none@1@S@The species abbreviations are: AA, yellow fever mosquito; AG, African malaria mosquito; DM, D. melanogaster fruit fly DP, D. pseudoobscura fruit fly; SP, sea urchin.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "species") (:form . "species") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "abbreviation") (:form . "abbreviations")\n (:end . 25) (:start . 12) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n (:id . 45))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 30) (:start . 29)\n (:id . 46))\n ((:tag . "NN") (:stem . "aa") (:form . "AA") (:end . 33) (:start . 31)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n (:id . 48))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 41)\n (:start . 35) (:id . 49))\n ((:tag . "NN") (:stem . "fever") (:form . "fever") (:end . 47) (:start . 42)\n (:id . 50))\n ((:tag . "NN") (:stem . "mosquito") (:form . "mosquito") (:end . 56)\n (:start . 48) (:id . 51))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 57) (:start . 56)\n (:id . 52))\n ((:tag . "NNP") (:stem . "AG") (:form . "AG") (:end . 60) (:start . 58)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n (:id . 54))\n ((:tag . "JJ") (:stem . "african") (:form . "African") (:end . 69)\n (:start . 62) (:id . 55))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 77)\n (:start . 70) (:id . 56))\n ((:tag . "NN") (:stem . "mosquito") (:form . "mosquito") (:end . 86)\n (:start . 78) (:id . 57))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 87) (:start . 86)\n (:id . 58))\n ((:tag . "NNP") (:stem . "DM") (:form . "DM") (:end . 90) (:start . 88)\n (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n (:id . 60))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 94) (:start . 92)\n (:id . 61))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n (:end . 107) (:start . 95) (:id . 62))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 113)\n (:start . 108) (:id . 63))\n ((:tag . "NNP") (:stem . "fly") (:form . "fly") (:end . 117) (:start . 114)\n (:id . 64))\n ((:tag . "NNP") (:stem . "DP") (:form . "DP") (:end . 120) (:start . 118)\n (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n (:id . 66))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 124) (:start . 122)\n (:id . 67))\n ((:tag . "NN") (:stem . "pseudoobscura") (:form . "pseudoobscura")\n (:end . 138) (:start . 125) (:id . 68))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 144)\n (:start . 139) (:id . 69))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 148) (:start . 145)\n (:id . 70))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 149) (:start . 148)\n (:id . 71))\n ((:tag . "NNP") (:stem . "SP") (:form . "SP") (:end . 152) (:start . 150)\n (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n (:id . 73))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 157) (:start . 154)\n (:id . 74))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 164)\n (:start . 158) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s6.128) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101868@unknown@formal@none@1@S@(Transib1 through Transib5 are from the fruit fly D. melanogaster.)@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Transib1") (:form . "Transib1") (:end . 9)\n (:start . 1) (:id . 43))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 17)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "transib5") (:form . "Transib5") (:end . 26)\n (:start . 18) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 35) (:start . 31)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 45) (:start . 40)\n (:id . 49))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 49) (:start . 46)\n (:id . 50))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 52) (:start . 50)\n (:id . 51))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 65)\n (:start . 53) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.129) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101870@unknown@formal@none@1@S@The RSS23 consensus sequence is shown immediately under the TIRs consensus sequence.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "rss23") (:form . "RSS23") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 19)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 28)\n (:start . 20) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 31) (:start . 29)\n (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 37) (:start . 32)\n (:id . 47))\n ((:tag . "RB") (:stem . "immediately") (:form . "immediately") (:end . 49)\n (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 55) (:start . 50)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n (:id . 50))\n ((:tag . "NNP") (:stem . "TIR") (:form . "TIRs") (:end . 64) (:start . 60)\n (:id . 51))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 74)\n (:start . 65) (:id . 52))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 83)\n (:start . 75) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.131) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101871@unknown@formal@none@1@S@The most conserved nucleotides in the RSS23 heptamer and nonamer, which are necessary for efficient V(D)J recombination, are highlighted.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 18)\n (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "nucleotide") (:form . "nucleotides") (:end . 30)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n (:id . 47))\n ((:tag . "NN") (:stem . "rss23") (:form . "RSS23") (:end . 43) (:start . 38)\n (:id . 48))\n ((:tag . "NN") (:stem . "heptamer") (:form . "heptamer") (:end . 52)\n (:start . 44) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n (:id . 50))\n ((:tag . "NN") (:stem . "nonamer") (:form . "nonamer") (:end . 64)\n (:start . 57) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 71) (:start . 66)\n (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 75) (:start . 72)\n (:id . 54))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 85)\n (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 89) (:start . 86)\n (:id . 56))\n ((:tag . "JJ") (:stem . "efficient") (:form . "efficient") (:end . 99)\n (:start . 90) (:id . 57))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 105)\n (:start . 100) (:id . 58))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 119) (:start . 106) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 124) (:start . 121)\n (:id . 61))\n ((:tag . "VBN") (:stem . "highlight") (:form . "highlighted") (:end . 136)\n (:start . 125) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.132) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101872@unknown@formal@none@1@S@The 23 ± 1 bp variable spacer is marked by Ns.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 6) (:start . 4)\n (:id . 43))\n ((:tag . "SYM") (:stem . "±") (:form . "±") (:end . 8) (:start . 7)\n (:id . 44))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 10) (:start . 9)\n (:id . 45))\n ((:tag . "NN") (:stem . "bp") (:form . "bp") (:end . 13) (:start . 11)\n (:id . 46))\n ((:tag . "JJ") (:stem . "variable") (:form . "variable") (:end . 22)\n (:start . 14) (:id . 47))\n ((:tag . "NN") (:stem . "spacer") (:form . "spacer") (:end . 29)\n (:start . 23) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 32) (:start . 30)\n (:id . 49))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 39) (:start . 33)\n (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 42) (:start . 40)\n (:id . 51))\n ((:tag . "NNP") (:stem . "N") (:form . "Ns") (:end . 45) (:start . 43)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 46) (:start . 45)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s6.133) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101873@unknown@formal@none@1@S@(B) Non-gapped alignment of consensus sequences of 5? TIRs from 21 families of Transib transposons.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "non-gapped") (:form . "Non-gapped") (:end . 14)\n (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 24)\n (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n (:id . 47))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 37)\n (:start . 28) (:id . 48))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 47)\n (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n (:id . 50))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 52) (:start . 51)\n (:id . 51))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 53) (:start . 52)\n (:id . 52))\n ((:tag . "NNS") (:stem . "tir") (:form . "TIRs") (:end . 58) (:start . 54)\n (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 63) (:start . 59)\n (:id . 54))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 66) (:start . 64)\n (:id . 55))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 75)\n (:start . 67) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n (:id . 57))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 86)\n (:start . 79) (:id . 58))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 98)\n (:start . 87) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.134) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101874@unknown@formal@none@1@S@(C) The 12/23 rule follows from the basic structure of TIRs of the consensus sequences of transposons that belong to the Transib5, Transib2_AG, TransibN1_AG, TransibN2_AG, and TransibN3_AG families.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 7) (:start . 4)\n (:id . 45))\n ((:tag . "CD") (:stem . "12/23") (:form . "12/23") (:end . 13) (:start . 8)\n (:id . 46))\n ((:tag . "NN") (:stem . "rule") (:form . "rule") (:end . 18) (:start . 14)\n (:id . 47))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 26)\n (:start . 19) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 31) (:start . 27)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n (:id . 50))\n ((:tag . "JJ") (:stem . "basic") (:form . "basic") (:end . 41) (:start . 36)\n (:id . 51))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 51)\n (:start . 42) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n (:id . 53))\n ((:tag . "NNS") (:stem . "tir") (:form . "TIRs") (:end . 59) (:start . 55)\n (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n (:id . 56))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 76)\n (:start . 67) (:id . 57))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 86)\n (:start . 77) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n (:id . 59))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 101)\n (:start . 90) (:id . 60))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 106) (:start . 102)\n (:id . 61))\n ((:tag . "VBP") (:stem . "belong") (:form . "belong") (:end . 113)\n (:start . 107) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 116) (:start . 114)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n (:id . 64))\n ((:tag . "NNP") (:stem . "Transib5") (:form . "Transib5") (:end . 129)\n (:start . 121) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n (:id . 66))\n ((:tag . "NNP") (:stem . "Transib2_AG") (:form . "Transib2_AG") (:end . 142)\n (:start . 131) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n (:id . 68))\n ((:tag . "NNP") (:stem . "TransibN1_AG") (:form . "TransibN1_AG")\n (:end . 156) (:start . 144) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 157) (:start . 156)\n (:id . 70))\n ((:tag . "NNP") (:stem . "TransibN2_AG") (:form . "TransibN2_AG")\n (:end . 170) (:start . 158) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 175) (:start . 172)\n (:id . 73))\n ((:tag . "NNP") (:stem . "TransibN3_AG") (:form . "TransibN3_AG")\n (:end . 188) (:start . 176) (:id . 74))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 197)\n (:start . 189) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s6.135) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101875@unknown@formal@none@1@S@The 5? TIRs of these transposons are aligned with the corresponding 3? TIRs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 5) (:start . 4)\n (:id . 43))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 6) (:start . 5) (:id . 44))\n ((:tag . "NNS") (:stem . "tir") (:form . "TIRs") (:end . 11) (:start . 7)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 46))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 20) (:start . 15)\n (:id . 47))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 32)\n (:start . 21) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 36) (:start . 33)\n (:id . 49))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 44)\n (:start . 37) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 49) (:start . 45)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n (:id . 52))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 67)\n (:start . 54) (:id . 53))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 69) (:start . 68)\n (:id . 54))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 70) (:start . 69)\n (:id . 55))\n ((:tag . "NNS") (:stem . "tir") (:form . "TIRs") (:end . 75) (:start . 71)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s6.136) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101876@unknown@formal@none@1@S@Structures of the 5? and 3? TIRs resemble RSS12 and RSS23, respectively.@(((:tag . "NNP") (:stem . "Structure") (:form . "Structures") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 19) (:start . 18)\n (:id . 45))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 20) (:start . 19)\n (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n (:id . 47))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 26) (:start . 25)\n (:id . 48))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 27) (:start . 26)\n (:id . 49))\n ((:tag . "NNPS") (:stem . "TIR") (:form . "TIRs") (:end . 32) (:start . 28)\n (:id . 50))\n ((:tag . "JJ") (:stem . "resemble") (:form . "resemble") (:end . 41)\n (:start . 33) (:id . 51))\n ((:tag . "NN") (:stem . "rss12") (:form . "RSS12") (:end . 47) (:start . 42)\n (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n (:id . 53))\n ((:tag . "NNP") (:stem . "RSS23") (:form . "RSS23") (:end . 57) (:start . 52)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n (:id . 55))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 71)\n (:start . 59) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s6.137) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101877@unknown@formal@none@1@S@Similar Length of TSDs and Target Site Composition in Transib and RAG1/2-Mediated Transpositions@(((:tag . "JJ") (:stem . "similar") (:form . "Similar") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Length") (:form . "Length") (:end . 14)\n (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n (:id . 44))\n ((:tag . "NNP") (:stem . "TSD") (:form . "TSDs") (:end . 22) (:start . 18)\n (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "VB") (:stem . "target") (:form . "Target") (:end . 33)\n (:start . 27) (:id . 47))\n ((:tag . "NNP") (:stem . "Site") (:form . "Site") (:end . 38) (:start . 34)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Composition") (:form . "Composition") (:end . 50)\n (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 61)\n (:start . 54) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n (:id . 52))\n ((:tag . "JJ") (:stem . "rag1/2-mediated") (:form . "RAG1/2-Mediated")\n (:end . 81) (:start . 66) (:id . 53))\n ((:tag . "NNPS") (:stem . "Transposition") (:form . "Transpositions")\n (:end . 96) (:start . 82) (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.138) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101878@unknown@formal@none@1@S@It has been known that RAG1-mediated transposition in vitro, both intermolecular and intramolecular, is most frequently accompanied by 5-bp TSDs [12,13].@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 17) (:start . 12)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n (:id . 46))\n ((:tag . "JJ") (:stem . "rag1-mediated") (:form . "RAG1-mediated")\n (:end . 36) (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "transposition") (:form . "transposition")\n (:end . 50) (:start . 37) (:id . 48))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n (:id . 49))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 59) (:start . 54)\n (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n (:id . 51))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 65) (:start . 61)\n (:id . 52))\n ((:tag . "JJ") (:stem . "intermolecular") (:form . "intermolecular")\n (:end . 80) (:start . 66) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n (:id . 54))\n ((:tag . "JJ") (:stem . "intramolecular") (:form . "intramolecular")\n (:end . 99) (:start . 85) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 103) (:start . 101)\n (:id . 57))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 108) (:start . 104)\n (:id . 58))\n ((:tag . "RB") (:stem . "frequently") (:form . "frequently") (:end . 119)\n (:start . 109) (:id . 59))\n ((:tag . "VBN") (:stem . "accompany") (:form . "accompanied") (:end . 131)\n (:start . 120) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 134) (:start . 132)\n (:id . 61))\n ((:tag . "JJ") (:stem . "5-bp") (:form . "5-bp") (:end . 139) (:start . 135)\n (:id . 62))\n ((:tag . "NNS") (:stem . "tsd") (:form . "TSDs") (:end . 144) (:start . 140)\n (:id . 63))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 146) (:start . 145)\n (:id . 64))\n ((:tag . "CD") (:stem . "12,13") (:form . "12,13") (:end . 151)\n (:start . 146) (:id . 65))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 152) (:start . 151)\n (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s6.139) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101880@unknown@formal@none@1@S@Also, 69% of 36 TSDs recovered during RAG-mediated intramolecular transpositions were 5 bp in length; of the remaining ones, 28% were 4 bp and 3% were 3 bp long.@(((:tag . "RB") (:stem . "also") (:form . "Also") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "CD") (:stem . "69") (:form . "69") (:end . 8) (:start . 6)\n (:id . 44))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 9) (:start . 8)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n (:id . 46))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 15) (:start . 13)\n (:id . 47))\n ((:tag . "NNS") (:stem . "tsd") (:form . "TSDs") (:end . 20) (:start . 16)\n (:id . 48))\n ((:tag . "VBN") (:stem . "recover") (:form . "recovered") (:end . 30)\n (:start . 21) (:id . 49))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 37)\n (:start . 31) (:id . 50))\n ((:tag . "JJ") (:stem . "rag-mediated") (:form . "RAG-mediated") (:end . 50)\n (:start . 38) (:id . 51))\n ((:tag . "JJ") (:stem . "intramolecular") (:form . "intramolecular")\n (:end . 65) (:start . 51) (:id . 52))\n ((:tag . "NNS") (:stem . "transposition") (:form . "transpositions")\n (:end . 80) (:start . 66) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 85) (:start . 81)\n (:id . 54))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 87) (:start . 86)\n (:id . 55))\n ((:tag . "NN") (:stem . "bp") (:form . "bp") (:end . 90) (:start . 88)\n (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 93) (:start . 91)\n (:id . 57))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 100)\n (:start . 94) (:id . 58))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 101) (:start . 100)\n (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n (:id . 61))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 118)\n (:start . 109) (:id . 62))\n ((:tag . "NNS") (:stem . "one") (:form . "ones") (:end . 123) (:start . 119)\n (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n (:id . 64))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 127) (:start . 125)\n (:id . 65))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 128) (:start . 127)\n (:id . 66))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 133) (:start . 129)\n (:id . 67))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 135) (:start . 134)\n (:id . 68))\n ((:tag . "NN") (:stem . "bp") (:form . "bp") (:end . 138) (:start . 136)\n (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n (:id . 70))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 144) (:start . 143)\n (:id . 71))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 145) (:start . 144)\n (:id . 72))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 150) (:start . 146)\n (:id . 73))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 152) (:start . 151)\n (:id . 74))\n ((:tag . "NN") (:stem . "bp") (:form . "bp") (:end . 155) (:start . 153)\n (:id . 75))\n ((:tag . "RB") (:stem . "long") (:form . "long") (:end . 160) (:start . 156)\n (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s6.141) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101881@unknown@formal@none@1@S@In another study [13], six of six TSDs detected in the intermolecular transposition were 5 bp long.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 16) (:start . 11)\n (:id . 44))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 18) (:start . 17)\n (:id . 45))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 20) (:start . 18)\n (:id . 46))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 21) (:start . 20)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n (:id . 48))\n ((:tag . "CD") (:stem . "six") (:form . "six") (:end . 26) (:start . 23)\n (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 50))\n ((:tag . "CD") (:stem . "six") (:form . "six") (:end . 33) (:start . 30)\n (:id . 51))\n ((:tag . "NNS") (:stem . "tsd") (:form . "TSDs") (:end . 38) (:start . 34)\n (:id . 52))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 47)\n (:start . 39) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n (:id . 55))\n ((:tag . "JJ") (:stem . "intermolecular") (:form . "intermolecular")\n (:end . 69) (:start . 55) (:id . 56))\n ((:tag . "NN") (:stem . "transposition") (:form . "transposition")\n (:end . 83) (:start . 70) (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 88) (:start . 84)\n (:id . 58))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 90) (:start . 89)\n (:id . 59))\n ((:tag . "NN") (:stem . "bp") (:form . "bp") (:end . 93) (:start . 91)\n (:id . 60))\n ((:tag . "RB") (:stem . "long") (:form . "long") (:end . 98) (:start . 94)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.142) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101882@unknown@formal@none@1@S@Intramolecular transposition mediated by murine RAG1/2 proteins was also studied recently in vivo in yeast [14].@(((:tag . "JJ") (:stem . "intramolecular") (:form . "Intramolecular")\n (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "transposition") (:form . "transposition")\n (:end . 28) (:start . 15) (:id . 43))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 37)\n (:start . 29) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 40) (:start . 38)\n (:id . 45))\n ((:tag . "JJ") (:stem . "murine") (:form . "murine") (:end . 47)\n (:start . 41) (:id . 46))\n ((:tag . "NN") (:stem . "rag1/2") (:form . "RAG1/2") (:end . 54)\n (:start . 48) (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 63)\n (:start . 55) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 67) (:start . 64)\n (:id . 49))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 72) (:start . 68)\n (:id . 50))\n ((:tag . "VBN") (:stem . "study") (:form . "studied") (:end . 80)\n (:start . 73) (:id . 51))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 89)\n (:start . 81) (:id . 52))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n (:id . 53))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 97) (:start . 93)\n (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 100) (:start . 98)\n (:id . 55))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 106)\n (:start . 101) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 108) (:start . 107)\n (:id . 57))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 110) (:start . 108)\n (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 111) (:start . 110)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.143) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101883@unknown@formal@none@1@S@Again, 60% of TSDs recovered in 26 events were 5 bp long [14].@(((:tag . "RB") (:stem . "again") (:form . "Again") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 9) (:start . 7)\n (:id . 44))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 10) (:start . 9)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 46))\n ((:tag . "NNS") (:stem . "tsd") (:form . "TSDs") (:end . 18) (:start . 14)\n (:id . 47))\n ((:tag . "VBN") (:stem . "recover") (:form . "recovered") (:end . 28)\n (:start . 19) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n (:id . 49))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 34) (:start . 32)\n (:id . 50))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 41)\n (:start . 35) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 46) (:start . 42)\n (:id . 52))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 48) (:start . 47)\n (:id . 53))\n ((:tag . "NN") (:stem . "bp") (:form . "bp") (:end . 51) (:start . 49)\n (:id . 54))\n ((:tag . "RB") (:stem . "long") (:form . "long") (:end . 56) (:start . 52)\n (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 58) (:start . 57)\n (:id . 56))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 60) (:start . 58)\n (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 61) (:start . 60)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 62) (:start . 61)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s6.144) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101884@unknown@formal@none@1@S@Given the predominance of 5-bp TSDs, it is striking that Transib transposons belong to the only superfamily of eukaryotic DNA transposons with 5-bp TSDs generated upon insertions into the genome [17,24].@(((:tag . "VBN") (:stem . "give") (:form . "Given") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "predominance") (:form . "predominance") (:end . 22)\n (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n (:id . 45))\n ((:tag . "JJ") (:stem . "5-bp") (:form . "5-bp") (:end . 30) (:start . 26)\n (:id . 46))\n ((:tag . "NNS") (:stem . "tsd") (:form . "TSDs") (:end . 35) (:start . 31)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n (:id . 48))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 39) (:start . 37)\n (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 42) (:start . 40)\n (:id . 50))\n ((:tag . "JJ") (:stem . "striking") (:form . "striking") (:end . 51)\n (:start . 43) (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 56) (:start . 52)\n (:id . 52))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 64)\n (:start . 57) (:id . 53))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 76)\n (:start . 65) (:id . 54))\n ((:tag . "VBP") (:stem . "belong") (:form . "belong") (:end . 83)\n (:start . 77) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 86) (:start . 84)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n (:id . 57))\n ((:tag . "JJ") (:stem . "only") (:form . "only") (:end . 95) (:start . 91)\n (:id . 58))\n ((:tag . "NN") (:stem . "superfamily") (:form . "superfamily") (:end . 107)\n (:start . 96) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n (:id . 60))\n ((:tag . "JJ") (:stem . "eukaryotic") (:form . "eukaryotic") (:end . 121)\n (:start . 111) (:id . 61))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 125) (:start . 122)\n (:id . 62))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 137)\n (:start . 126) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 142) (:start . 138)\n (:id . 64))\n ((:tag . "JJ") (:stem . "5-bp") (:form . "5-bp") (:end . 147) (:start . 143)\n (:id . 65))\n ((:tag . "NNS") (:stem . "tsd") (:form . "TSDs") (:end . 152) (:start . 148)\n (:id . 66))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 162)\n (:start . 153) (:id . 67))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 167) (:start . 163)\n (:id . 68))\n ((:tag . "NNS") (:stem . "insertion") (:form . "insertions") (:end . 178)\n (:start . 168) (:id . 69))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 183) (:start . 179)\n (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 187) (:start . 184)\n (:id . 71))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 194)\n (:start . 188) (:id . 72))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 196) (:start . 195)\n (:id . 73))\n ((:tag . "CD") (:stem . "17,24") (:form . "17,24") (:end . 201)\n (:start . 196) (:id . 74))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 202) (:start . 201)\n (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s6.145) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101885@unknown@formal@none@1@S@To illustrate the characteristic 5-bp TSDs, we show copies of Transib transposons with intact 5? and 3? TIRs from diverse families of Transib transposons present in the D. melanogaster, D. pseudoobscura, A. gambiae, and S. purpuratus genomes (Figure S4).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "illustrate") (:form . "illustrate") (:end . 13)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n (:end . 32) (:start . 18) (:id . 45))\n ((:tag . "JJ") (:stem . "5-bp") (:form . "5-bp") (:end . 37) (:start . 33)\n (:id . 46))\n ((:tag . "NNS") (:stem . "tsd") (:form . "TSDs") (:end . 42) (:start . 38)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 46) (:start . 44)\n (:id . 49))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 51) (:start . 47)\n (:id . 50))\n ((:tag . "NNS") (:stem . "copy") (:form . "copies") (:end . 58) (:start . 52)\n (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n (:id . 52))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 69)\n (:start . 62) (:id . 53))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 81)\n (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 86) (:start . 82)\n (:id . 55))\n ((:tag . "JJ") (:stem . "intact") (:form . "intact") (:end . 93)\n (:start . 87) (:id . 56))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 95) (:start . 94)\n (:id . 57))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 96) (:start . 95)\n (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n (:id . 59))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 102) (:start . 101)\n (:id . 60))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 103) (:start . 102)\n (:id . 61))\n ((:tag . "NNS") (:stem . "tir") (:form . "TIRs") (:end . 108) (:start . 104)\n (:id . 62))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 113) (:start . 109)\n (:id . 63))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 121)\n (:start . 114) (:id . 64))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 130)\n (:start . 122) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 133) (:start . 131)\n (:id . 66))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 141)\n (:start . 134) (:id . 67))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 153)\n (:start . 142) (:id . 68))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 161)\n (:start . 154) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 164) (:start . 162)\n (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n (:id . 71))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 171) (:start . 169)\n (:id . 72))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n (:end . 184) (:start . 172) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 185) (:start . 184)\n (:id . 74))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 188) (:start . 186)\n (:id . 75))\n ((:tag . "NNP") (:stem . "pseudoobscura") (:form . "pseudoobscura")\n (:end . 202) (:start . 189) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 203) (:start . 202)\n (:id . 77))\n ((:tag . "NNP") (:stem . "A.") (:form . "A.") (:end . 206) (:start . 204)\n (:id . 78))\n ((:tag . "NNP") (:stem . "gambiae") (:form . "gambiae") (:end . 214)\n (:start . 207) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 215) (:start . 214)\n (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 219) (:start . 216)\n (:id . 81))\n ((:tag . "NNP") (:stem . "S.") (:form . "S.") (:end . 222) (:start . 220)\n (:id . 82))\n ((:tag . "NN") (:stem . "purpuratus") (:form . "purpuratus") (:end . 233)\n (:start . 223) (:id . 83))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 241)\n (:start . 234) (:id . 84))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 243) (:start . 242)\n (:id . 85))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 249)\n (:start . 243) (:id . 86))\n ((:tag . "NNP") (:stem . "S4") (:form . "S4") (:end . 252) (:start . 250)\n (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 253) (:start . 252)\n (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 254) (:start . 253)\n (:id . 89)))@@@1@48@((:identifiers (:sid . :s6.146) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101886@unknown@formal@none@1@S@Moreover, some families show high target site specificity, e.g., Transib-N1_AG and Transib-N2_AG integrate preferentially at cCASTGg and cCAWTGc, respectively (TSDs are capitalized).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 28) (:start . 24)\n (:id . 46))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 40)\n (:start . 34) (:id . 48))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 45) (:start . 41)\n (:id . 49))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 57)\n (:start . 46) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n (:id . 51))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 63) (:start . 59)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Transib-N1_AG") (:form . "Transib-N1_AG")\n (:end . 78) (:start . 65) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Transib-N2_AG") (:form . "Transib-N2_AG")\n (:end . 96) (:start . 83) (:id . 56))\n ((:tag . "NN") (:stem . "integrate") (:form . "integrate") (:end . 106)\n (:start . 97) (:id . 57))\n ((:tag . "RB") (:stem . "preferentially") (:form . "preferentially")\n (:end . 121) (:start . 107) (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 124) (:start . 122)\n (:id . 59))\n ((:tag . "NN") (:stem . "ccastgg") (:form . "cCASTGg") (:end . 132)\n (:start . 125) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 136) (:start . 133)\n (:id . 61))\n ((:tag . "NN") (:stem . "ccawtgc") (:form . "cCAWTGc") (:end . 144)\n (:start . 137) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n (:id . 63))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 158)\n (:start . 146) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 160) (:start . 159)\n (:id . 65))\n ((:tag . "NNS") (:stem . "tsd") (:form . "TSDs") (:end . 164) (:start . 160)\n (:id . 66))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 168) (:start . 165)\n (:id . 67))\n ((:tag . "VBN") (:stem . "capitalize") (:form . "capitalized") (:end . 180)\n (:start . 169) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 181) (:start . 180)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s6.147) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101887@unknown@formal@none@1@S@RAG1/2-mediated transpositions also show significant target specificity, presumably reflecting the original specificity of the Transib TPase [12].@(((:tag . "JJ") (:stem . "rag1/2-mediated") (:form . "RAG1/2-mediated")\n (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "transposition") (:form . "transpositions")\n (:end . 30) (:start . 16) (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 35) (:start . 31)\n (:id . 44))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 40) (:start . 36)\n (:id . 45))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 52)\n (:start . 41) (:id . 46))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 59)\n (:start . 53) (:id . 47))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 71)\n (:start . 60) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n (:id . 49))\n ((:tag . "RB") (:stem . "presumably") (:form . "presumably") (:end . 83)\n (:start . 73) (:id . 50))\n ((:tag . "VBG") (:stem . "reflect") (:form . "reflecting") (:end . 94)\n (:start . 84) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n (:id . 52))\n ((:tag . "JJ") (:stem . "original") (:form . "original") (:end . 107)\n (:start . 99) (:id . 53))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 119)\n (:start . 108) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n (:id . 56))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 134)\n (:start . 127) (:id . 57))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 140)\n (:start . 135) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 142) (:start . 141)\n (:id . 59))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 144) (:start . 142)\n (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 145) (:start . 144)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n (:id . 62)))@@@1@21@((:hcues ((:id . :x6.148.1) (:span 73 83)))\n (:hscopes ((:id . :x6.148.1) (:span 73 140)))\n (:identifiers (:sid . :s6.148) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101888@unknown@formal@none@1@S@Indigenous properties of the Transib TPase, that were not related directly to RAG1 functions, including those responsible for the precise 5-bp length of TSDs, might have been altered during evolution of RAG1, leading to occasional 4-bp and 3-bp TSDs that are atypical for Transib transposons.@(((:tag . "JJ") (:stem . "indigenous") (:form . "Indigenous") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 21)\n (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 36)\n (:start . 29) (:id . 46))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 42) (:start . 37)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 48) (:start . 44)\n (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 53) (:start . 49)\n (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 57) (:start . 54)\n (:id . 51))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 65)\n (:start . 58) (:id . 52))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 74)\n (:start . 66) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 77) (:start . 75)\n (:id . 54))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 82) (:start . 78)\n (:id . 55))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 92)\n (:start . 83) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n (:id . 57))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 103)\n (:start . 94) (:id . 58))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 109)\n (:start . 104) (:id . 59))\n ((:tag . "JJ") (:stem . "responsible") (:form . "responsible") (:end . 121)\n (:start . 110) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 125) (:start . 122)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n (:id . 62))\n ((:tag . "JJ") (:stem . "precise") (:form . "precise") (:end . 137)\n (:start . 130) (:id . 63))\n ((:tag . "JJ") (:stem . "5-bp") (:form . "5-bp") (:end . 142) (:start . 138)\n (:id . 64))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 149)\n (:start . 143) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 152) (:start . 150)\n (:id . 66))\n ((:tag . "NNP") (:stem . "TSD") (:form . "TSDs") (:end . 157) (:start . 153)\n (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n (:id . 68))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 164)\n (:start . 159) (:id . 69))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 169) (:start . 165)\n (:id . 70))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 174) (:start . 170)\n (:id . 71))\n ((:tag . "VBN") (:stem . "alter") (:form . "altered") (:end . 182)\n (:start . 175) (:id . 72))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 189)\n (:start . 183) (:id . 73))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 199)\n (:start . 190) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 202) (:start . 200)\n (:id . 75))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 207) (:start . 203)\n (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 208) (:start . 207)\n (:id . 77))\n ((:tag . "VBG") (:stem . "lead") (:form . "leading") (:end . 216)\n (:start . 209) (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 219) (:start . 217)\n (:id . 79))\n ((:tag . "JJ") (:stem . "occasional") (:form . "occasional") (:end . 230)\n (:start . 220) (:id . 80))\n ((:tag . "JJ") (:stem . "4-bp") (:form . "4-bp") (:end . 235) (:start . 231)\n (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 239) (:start . 236)\n (:id . 82))\n ((:tag . "JJ") (:stem . "3-bp") (:form . "3-bp") (:end . 244) (:start . 240)\n (:id . 83))\n ((:tag . "NNS") (:stem . "tsd") (:form . "TSDs") (:end . 249) (:start . 245)\n (:id . 84))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 254) (:start . 250)\n (:id . 85))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 258) (:start . 255)\n (:id . 86))\n ((:tag . "JJ") (:stem . "atypical") (:form . "atypical") (:end . 267)\n (:start . 259) (:id . 87))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 271) (:start . 268)\n (:id . 88))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 279)\n (:start . 272) (:id . 89))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 291)\n (:start . 280) (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 292) (:start . 291)\n (:id . 91)))@@@1@50@((:hcues ((:id . :x6.149.2) (:span 159 164)))\n (:ncues ((:id . :x6.149.1) (:span 54 57)))\n (:hscopes ((:id . :x6.149.2) (:span 0 207)))\n (:nscopes ((:id . :x6.149.1) (:span 54 157)))\n (:identifiers (:sid . :s6.149) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101890@unknown@formal@none@1@S@Structure of Transib TIRs@(((:tag . "NN") (:stem . "structure") (:form . "Structure") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 20)\n (:start . 13) (:id . 44))\n ((:tag . "NNPS") (:stem . "TIR") (:form . "TIRs") (:end . 25) (:start . 21)\n (:id . 45)))@@@1@4@((:identifiers (:sid . :s6.151) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101891@unknown@formal@none@1@S@The structure and conservation patterns of the 38-bp termini of Transib transposons from 21 different families closely resemble those of RSSs, suggesting that the latter were derived from termini of ancient Transib transposons (Figures 4 and S4).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 30)\n (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 39)\n (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n (:id . 48))\n ((:tag . "JJ") (:stem . "38-bp") (:form . "38-bp") (:end . 52) (:start . 47)\n (:id . 49))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 60)\n (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n (:id . 51))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 71)\n (:start . 64) (:id . 52))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 83)\n (:start . 72) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 88) (:start . 84)\n (:id . 54))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 91) (:start . 89)\n (:id . 55))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 101)\n (:start . 92) (:id . 56))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 110)\n (:start . 102) (:id . 57))\n ((:tag . "RB") (:stem . "closely") (:form . "closely") (:end . 118)\n (:start . 111) (:id . 58))\n ((:tag . "VBP") (:stem . "resemble") (:form . "resemble") (:end . 127)\n (:start . 119) (:id . 59))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 133)\n (:start . 128) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 136) (:start . 134)\n (:id . 61))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSSs") (:end . 141) (:start . 137)\n (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 142) (:start . 141)\n (:id . 63))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 153)\n (:start . 143) (:id . 64))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 158) (:start . 154)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 162) (:start . 159)\n (:id . 66))\n ((:tag . "JJ") (:stem . "latter") (:form . "latter") (:end . 169)\n (:start . 163) (:id . 67))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 174) (:start . 170)\n (:id . 68))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 182)\n (:start . 175) (:id . 69))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 187) (:start . 183)\n (:id . 70))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 195)\n (:start . 188) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 198) (:start . 196)\n (:id . 72))\n ((:tag . "JJ") (:stem . "ancient") (:form . "ancient") (:end . 206)\n (:start . 199) (:id . 73))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 214)\n (:start . 207) (:id . 74))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 226)\n (:start . 215) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 228) (:start . 227)\n (:id . 76))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 235)\n (:start . 228) (:id . 77))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 237) (:start . 236)\n (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 241) (:start . 238)\n (:id . 79))\n ((:tag . "NN") (:stem . "s4") (:form . "S4") (:end . 244) (:start . 242)\n (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 245) (:start . 244)\n (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 246) (:start . 245)\n (:id . 82)))@@@1@41@((:hcues ((:id . :x6.152.1) (:span 143 153)))\n (:hscopes ((:id . :x6.152.1) (:span 143 226)))\n (:identifiers (:sid . :s6.152) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101892@unknown@formal@none@1@S@The 38-bp consensus TIR of Transib transposons consists of a conserved 5?- CACAATG heptamer separated by a variable 23-bp spacer from an AAAAAAATC-3? nonamer.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "38-bp") (:form . "38-bp") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 19)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "tir") (:form . "TIR") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 34)\n (:start . 27) (:id . 47))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 46)\n (:start . 35) (:id . 48))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 55)\n (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 60) (:start . 59)\n (:id . 51))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 70)\n (:start . 61) (:id . 52))\n ((:tag . "CD") (:stem . "5?-") (:form . "5?-") (:end . 74) (:start . 71)\n (:id . 53))\n ((:tag . "NN") (:stem . "cacaatg") (:form . "CACAATG") (:end . 82)\n (:start . 75) (:id . 54))\n ((:tag . "NN") (:stem . "heptamer") (:form . "heptamer") (:end . 91)\n (:start . 83) (:id . 55))\n ((:tag . "VBN") (:stem . "separate") (:form . "separated") (:end . 101)\n (:start . 92) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 104) (:start . 102)\n (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 106) (:start . 105)\n (:id . 58))\n ((:tag . "JJ") (:stem . "variable") (:form . "variable") (:end . 115)\n (:start . 107) (:id . 59))\n ((:tag . "JJ") (:stem . "23-bp") (:form . "23-bp") (:end . 121)\n (:start . 116) (:id . 60))\n ((:tag . "NN") (:stem . "spacer") (:form . "spacer") (:end . 128)\n (:start . 122) (:id . 61))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 133) (:start . 129)\n (:id . 62))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 136) (:start . 134)\n (:id . 63))\n ((:tag . "NN") (:stem . "aaaaaaatc-3") (:form . "AAAAAAATC-3") (:end . 148)\n (:start . 137) (:id . 64))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 149) (:start . 148)\n (:id . 65))\n ((:tag . "NN") (:stem . "nonamer") (:form . "nonamer") (:end . 157)\n (:start . 150) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s6.153) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101893@unknown@formal@none@1@S@This corresponds closely to the structure of RSSs, which are composed of the conserved heptamers 5?- CACAGTG separated by a variable 22-bp spacers from ACAAAAACC-like nonamers [1,5–7].@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "correspond") (:form . "corresponds") (:end . 16)\n (:start . 5) (:id . 43))\n ((:tag . "RB") (:stem . "closely") (:form . "closely") (:end . 24)\n (:start . 17) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n (:id . 46))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 41)\n (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n (:id . 48))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSSs") (:end . 49) (:start . 45)\n (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 56) (:start . 51)\n (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 60) (:start . 57)\n (:id . 52))\n ((:tag . "VBN") (:stem . "compose") (:form . "composed") (:end . 69)\n (:start . 61) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n (:id . 55))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 86)\n (:start . 77) (:id . 56))\n ((:tag . "NNS") (:stem . "heptamer") (:form . "heptamers") (:end . 96)\n (:start . 87) (:id . 57))\n ((:tag . "CD") (:stem . "5?-") (:form . "5?-") (:end . 100) (:start . 97)\n (:id . 58))\n ((:tag . "NN") (:stem . "cacagtg") (:form . "CACAGTG") (:end . 108)\n (:start . 101) (:id . 59))\n ((:tag . "VBN") (:stem . "separate") (:form . "separated") (:end . 118)\n (:start . 109) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 121) (:start . 119)\n (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 123) (:start . 122)\n (:id . 62))\n ((:tag . "JJ") (:stem . "variable") (:form . "variable") (:end . 132)\n (:start . 124) (:id . 63))\n ((:tag . "JJ") (:stem . "22-bp") (:form . "22-bp") (:end . 138)\n (:start . 133) (:id . 64))\n ((:tag . "NNS") (:stem . "spacer") (:form . "spacers") (:end . 146)\n (:start . 139) (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 151) (:start . 147)\n (:id . 66))\n ((:tag . "JJ") (:stem . "acaaaaacc-like") (:form . "ACAAAAACC-like")\n (:end . 166) (:start . 152) (:id . 67))\n ((:tag . "NNS") (:stem . "nonamer") (:form . "nonamers") (:end . 175)\n (:start . 167) (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 177) (:start . 176)\n (:id . 69))\n ((:tag . "CD") (:stem . "1,5–7") (:form . "1,5–7") (:end . 182)\n (:start . 177) (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 183) (:start . 182)\n (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n (:id . 72)))@@@1@31@((:identifiers (:sid . :s6.154) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101894@unknown@formal@none@1@S@Only bases at positions 1 through 3 in the heptamer and at positions 5 and 6 in the nonamer are universally conserved in RSSs and absolutely essential for efficient V(D)J recombination [5–7].@(((:tag . "RB") (:stem . "only") (:form . "Only") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "base") (:form . "bases") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 23)\n (:start . 14) (:id . 45))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 25) (:start . 24)\n (:id . 46))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 33)\n (:start . 26) (:id . 47))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 35) (:start . 34)\n (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n (:id . 50))\n ((:tag . "NN") (:stem . "heptamer") (:form . "heptamer") (:end . 51)\n (:start . 43) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 58) (:start . 56)\n (:id . 53))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 68)\n (:start . 59) (:id . 54))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 70) (:start . 69)\n (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n (:id . 56))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 76) (:start . 75)\n (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n (:id . 59))\n ((:tag . "NN") (:stem . "nonamer") (:form . "nonamer") (:end . 91)\n (:start . 84) (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 95) (:start . 92)\n (:id . 61))\n ((:tag . "RB") (:stem . "universally") (:form . "universally") (:end . 107)\n (:start . 96) (:id . 62))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 117)\n (:start . 108) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 120) (:start . 118)\n (:id . 64))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSSs") (:end . 125) (:start . 121)\n (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n (:id . 66))\n ((:tag . "RB") (:stem . "absolutely") (:form . "absolutely") (:end . 140)\n (:start . 130) (:id . 67))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 150)\n (:start . 141) (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 154) (:start . 151)\n (:id . 69))\n ((:tag . "JJ") (:stem . "efficient") (:form . "efficient") (:end . 164)\n (:start . 155) (:id . 70))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 170)\n (:start . 165) (:id . 71))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 184) (:start . 171) (:id . 72))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 186) (:start . 185)\n (:id . 73))\n ((:tag . "CD") (:stem . "5–7") (:form . "5–7") (:end . 189) (:start . 186)\n (:id . 74))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 190) (:start . 189)\n (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s6.155) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101895@unknown@formal@none@1@S@The corresponding positions are perfectly conserved in all Transib transposons (Figure 4A and 4B; excluding the 85% conserved position 34 in the Transib consensus that corresponds to position 5 in the RSS nonamer).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "corresponding") (:form . "corresponding")\n (:end . 17) (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 27)\n (:start . 18) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 31) (:start . 28)\n (:id . 45))\n ((:tag . "RB") (:stem . "perfectly") (:form . "perfectly") (:end . 41)\n (:start . 32) (:id . 46))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 51)\n (:start . 42) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n (:id . 48))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 58) (:start . 55)\n (:id . 49))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 66)\n (:start . 59) (:id . 50))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 78)\n (:start . 67) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 80) (:start . 79)\n (:id . 52))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 86)\n (:start . 80) (:id . 53))\n ((:tag . "NN") (:stem . "4a") (:form . "4A") (:end . 89) (:start . 87)\n (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n (:id . 55))\n ((:tag . "NN") (:stem . "4b") (:form . "4B") (:end . 96) (:start . 94)\n (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 97) (:start . 96)\n (:id . 57))\n ((:tag . "VBG") (:stem . "exclude") (:form . "excluding") (:end . 107)\n (:start . 98) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n (:id . 59))\n ((:tag . "CD") (:stem . "85") (:form . "85") (:end . 114) (:start . 112)\n (:id . 60))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 115) (:start . 114)\n (:id . 61))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 125)\n (:start . 116) (:id . 62))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 134)\n (:start . 126) (:id . 63))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 137) (:start . 135)\n (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 140) (:start . 138)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n (:id . 66))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 152)\n (:start . 145) (:id . 67))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 162)\n (:start . 153) (:id . 68))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 167) (:start . 163)\n (:id . 69))\n ((:tag . "VBZ") (:stem . "correspond") (:form . "corresponds") (:end . 179)\n (:start . 168) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 182) (:start . 180)\n (:id . 71))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 191)\n (:start . 183) (:id . 72))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 193) (:start . 192)\n (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 196) (:start . 194)\n (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 200) (:start . 197)\n (:id . 75))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSS") (:end . 204) (:start . 201)\n (:id . 76))\n ((:tag . "NN") (:stem . "nonamer") (:form . "nonamer") (:end . 212)\n (:start . 205) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 213) (:start . 212)\n (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n (:id . 79)))@@@1@38@((:identifiers (:sid . :s6.156) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101896@unknown@formal@none@1@S@The probability of the observed match between the RSS and Transib termini to occur by chance is less than 10-3 (see Materials and Methods).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 31)\n (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 37) (:start . 32)\n (:id . 47))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 45)\n (:start . 38) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSS") (:end . 53) (:start . 50)\n (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n (:id . 51))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 65)\n (:start . 58) (:id . 52))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 73)\n (:start . 66) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 76) (:start . 74)\n (:id . 54))\n ((:tag . "VB") (:stem . "occur") (:form . "occur") (:end . 82) (:start . 77)\n (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 85) (:start . 83)\n (:id . 56))\n ((:tag . "NN") (:stem . "chance") (:form . "chance") (:end . 92)\n (:start . 86) (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 95) (:start . 93)\n (:id . 58))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 100) (:start . 96)\n (:id . 59))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 105) (:start . 101)\n (:id . 60))\n ((:tag . "CD") (:stem . "10-3") (:form . "10-3") (:end . 110) (:start . 106)\n (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n (:id . 62))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 115) (:start . 112)\n (:id . 63))\n ((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 125)\n (:start . 116) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n (:id . 65))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 137)\n (:start . 130) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s6.157) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101897@unknown@formal@none@1@S@Although most Transib families are represented by transposons flanked by TIRs similar to RSS23 (Figure 4A), several families include transposons with 5? and 3? termini similar to RSS12 and RSS23, respectively (Figure 4C).@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 13) (:start . 9)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 21)\n (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 30)\n (:start . 22) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 34) (:start . 31)\n (:id . 46))\n ((:tag . "VBN") (:stem . "represent") (:form . "represented") (:end . 46)\n (:start . 35) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 49) (:start . 47)\n (:id . 48))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 61)\n (:start . 50) (:id . 49))\n ((:tag . "VBN") (:stem . "flank") (:form . "flanked") (:end . 69)\n (:start . 62) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 72) (:start . 70)\n (:id . 51))\n ((:tag . "NNS") (:stem . "tir") (:form . "TIRs") (:end . 77) (:start . 73)\n (:id . 52))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 85)\n (:start . 78) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n (:id . 54))\n ((:tag . "NNP") (:stem . "RSS23") (:form . "RSS23") (:end . 94) (:start . 89)\n (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n (:id . 56))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 102)\n (:start . 96) (:id . 57))\n ((:tag . "NN") (:stem . "4a") (:form . "4A") (:end . 105) (:start . 103)\n (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n (:id . 60))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 115)\n (:start . 108) (:id . 61))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 124)\n (:start . 116) (:id . 62))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 132)\n (:start . 125) (:id . 63))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 144)\n (:start . 133) (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 149) (:start . 145)\n (:id . 65))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 151) (:start . 150)\n (:id . 66))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 152) (:start . 151)\n (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n (:id . 68))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 158) (:start . 157)\n (:id . 69))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 159) (:start . 158)\n (:id . 70))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 167)\n (:start . 160) (:id . 71))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 175)\n (:start . 168) (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 178) (:start . 176)\n (:id . 73))\n ((:tag . "NN") (:stem . "rss12") (:form . "RSS12") (:end . 184)\n (:start . 179) (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 188) (:start . 185)\n (:id . 75))\n ((:tag . "NNP") (:stem . "RSS23") (:form . "RSS23") (:end . 194)\n (:start . 189) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 195) (:start . 194)\n (:id . 77))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 208)\n (:start . 196) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 210) (:start . 209)\n (:id . 79))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 216)\n (:start . 210) (:id . 80))\n ((:tag . "NN") (:stem . "4c") (:form . "4C") (:end . 219) (:start . 217)\n (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 220) (:start . 219)\n (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 221) (:start . 220)\n (:id . 83)))@@@1@42@((:identifiers (:sid . :s6.158) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101898@unknown@formal@none@1@S@Therefore, even the 12/23 rule [1] can be derived directly from the sequence structure of known Transib transposons.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "CD") (:stem . "12/23") (:form . "12/23") (:end . 25) (:start . 20)\n (:id . 46))\n ((:tag . "NN") (:stem . "rule") (:form . "rule") (:end . 30) (:start . 26)\n (:id . 47))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 32) (:start . 31)\n (:id . 48))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 33) (:start . 32)\n (:id . 49))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 34) (:start . 33)\n (:id . 50))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 38) (:start . 35)\n (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 41) (:start . 39)\n (:id . 52))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 49)\n (:start . 42) (:id . 53))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 58)\n (:start . 50) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 63) (:start . 59)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n (:id . 56))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 76)\n (:start . 68) (:id . 57))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 86)\n (:start . 77) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n (:id . 59))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 95) (:start . 90)\n (:id . 60))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 103)\n (:start . 96) (:id . 61))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 115)\n (:start . 104) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.159) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101900@unknown@formal@none@1@S@Using RAG1 proteins as query sequences in a WU BLAST search against sea urchin contigs sequenced at Baylor College (see Materials and Methods), we identified eight proteins approximately 30% identical to portions of the RAG1 core and approximately 50% identical to each other (see Figures 2, 5, and S5).@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 19)\n (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 22) (:start . 20)\n (:id . 45))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 28) (:start . 23)\n (:id . 46))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 38)\n (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 43) (:start . 42)\n (:id . 49))\n ((:tag . "NNP") (:stem . "WU") (:form . "WU") (:end . 46) (:start . 44)\n (:id . 50))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 52) (:start . 47)\n (:id . 51))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 59)\n (:start . 53) (:id . 52))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 67)\n (:start . 60) (:id . 53))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 71) (:start . 68)\n (:id . 54))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 78)\n (:start . 72) (:id . 55))\n ((:tag . "NNS") (:stem . "contig") (:form . "contigs") (:end . 86)\n (:start . 79) (:id . 56))\n ((:tag . "VBN") (:stem . "sequence") (:form . "sequenced") (:end . 96)\n (:start . 87) (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 99) (:start . 97)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Baylor") (:form . "Baylor") (:end . 106)\n (:start . 100) (:id . 59))\n ((:tag . "NNP") (:stem . "College") (:form . "College") (:end . 114)\n (:start . 107) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 116) (:start . 115)\n (:id . 61))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 119) (:start . 116)\n (:id . 62))\n ((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 129)\n (:start . 120) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 133) (:start . 130)\n (:id . 64))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 141)\n (:start . 134) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n (:id . 67))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 146) (:start . 144)\n (:id . 68))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 157)\n (:start . 147) (:id . 69))\n ((:tag . "CD") (:stem . "eight") (:form . "eight") (:end . 163)\n (:start . 158) (:id . 70))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 172)\n (:start . 164) (:id . 71))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 186) (:start . 173) (:id . 72))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 189) (:start . 187)\n (:id . 73))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 190) (:start . 189)\n (:id . 74))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 200)\n (:start . 191) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 203) (:start . 201)\n (:id . 76))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 212)\n (:start . 204) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 215) (:start . 213)\n (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 219) (:start . 216)\n (:id . 79))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 224) (:start . 220)\n (:id . 80))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 229) (:start . 225)\n (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 233) (:start . 230)\n (:id . 82))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 247) (:start . 234) (:id . 83))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 250) (:start . 248)\n (:id . 84))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 251) (:start . 250)\n (:id . 85))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 261)\n (:start . 252) (:id . 86))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 264) (:start . 262)\n (:id . 87))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 269) (:start . 265)\n (:id . 88))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 275)\n (:start . 270) (:id . 89))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 277) (:start . 276)\n (:id . 90))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 280) (:start . 277)\n (:id . 91))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 288)\n (:start . 281) (:id . 92))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 290) (:start . 289)\n (:id . 93))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 291) (:start . 290)\n (:id . 94))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 293) (:start . 292)\n (:id . 95))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 294) (:start . 293)\n (:id . 96))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 298) (:start . 295)\n (:id . 97))\n ((:tag . "NN") (:stem . "s5") (:form . "S5") (:end . 301) (:start . 299)\n (:id . 98))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 302) (:start . 301)\n (:id . 99))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 303) (:start . 302)\n (:id . 100)))@@@1@59@((:identifiers (:sid . :s6.161) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101901@unknown@formal@none@1@S@Only one protein is present in two copies, which are 94% identical to each other at the DNA level (contigs 81987 and 6797).@(((:tag . "RB") (:stem . "only") (:form . "Only") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 16)\n (:start . 9) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 27)\n (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n (:id . 47))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 34) (:start . 31)\n (:id . 48))\n ((:tag . "NNS") (:stem . "copy") (:form . "copies") (:end . 41) (:start . 35)\n (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 48) (:start . 43)\n (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 52) (:start . 49)\n (:id . 52))\n ((:tag . "CD") (:stem . "94") (:form . "94") (:end . 55) (:start . 53)\n (:id . 53))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 56) (:start . 55)\n (:id . 54))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 66)\n (:start . 57) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 69) (:start . 67)\n (:id . 56))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 74) (:start . 70)\n (:id . 57))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 80) (:start . 75)\n (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 83) (:start . 81)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n (:id . 60))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 91) (:start . 88)\n (:id . 61))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 97) (:start . 92)\n (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 99) (:start . 98)\n (:id . 63))\n ((:tag . "NNS") (:stem . "contig") (:form . "contigs") (:end . 106)\n (:start . 99) (:id . 64))\n ((:tag . "CD") (:stem . "81987") (:form . "81987") (:end . 112)\n (:start . 107) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n (:id . 66))\n ((:tag . "CD") (:stem . "6797") (:form . "6797") (:end . 121) (:start . 117)\n (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 122) (:start . 121)\n (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s6.162) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101902@unknown@formal@none@1@S@Both copies appear to be encoded by pseudogenes damaged by a stop codon at the same position of each protein.@(((:tag . "DT") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "copy") (:form . "copies") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 18)\n (:start . 12) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 24) (:start . 22)\n (:id . 46))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 32)\n (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 35) (:start . 33)\n (:id . 48))\n ((:tag . "NNS") (:stem . "pseudogene") (:form . "pseudogenes") (:end . 47)\n (:start . 36) (:id . 49))\n ((:tag . "VBN") (:stem . "damage") (:form . "damaged") (:end . 55)\n (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 58) (:start . 56)\n (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 60) (:start . 59)\n (:id . 52))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 65) (:start . 61)\n (:id . 53))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 71) (:start . 66)\n (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 74) (:start . 72)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n (:id . 56))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 83) (:start . 79)\n (:id . 57))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 92)\n (:start . 84) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n (:id . 59))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 100) (:start . 96)\n (:id . 60))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 108)\n (:start . 101) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n (:id . 62)))@@@1@21@((:hcues ((:id . :x6.163.1) (:span 12 18)))\n (:hscopes ((:id . :x6.163.1) (:span 0 108)))\n (:identifiers (:sid . :s6.163) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101903@unknown@formal@none@1@S@Interestingly, the 6,690-bp contig 6797 harbours two additional defective pseudogenes coding for different RAG1 core–like proteins (Figure 5).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 44))\n ((:tag . "CD") (:stem . "6,690-bp") (:form . "6,690-bp") (:end . 27)\n (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "contig") (:form . "contig") (:end . 34)\n (:start . 28) (:id . 46))\n ((:tag . "CD") (:stem . "6797") (:form . "6797") (:end . 39) (:start . 35)\n (:id . 47))\n ((:tag . "VBZ") (:stem . "harbour") (:form . "harbours") (:end . 48)\n (:start . 40) (:id . 48))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 52) (:start . 49)\n (:id . 49))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 63)\n (:start . 53) (:id . 50))\n ((:tag . "JJ") (:stem . "defective") (:form . "defective") (:end . 73)\n (:start . 64) (:id . 51))\n ((:tag . "NNS") (:stem . "pseudogene") (:form . "pseudogenes") (:end . 85)\n (:start . 74) (:id . 52))\n ((:tag . "VBG") (:stem . "cod") (:form . "coding") (:end . 92) (:start . 86)\n (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 96) (:start . 93)\n (:id . 54))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 106)\n (:start . 97) (:id . 55))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 111) (:start . 107)\n (:id . 56))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 121)\n (:start . 112) (:id . 57))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 130)\n (:start . 122) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 132) (:start . 131)\n (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 138)\n (:start . 132) (:id . 60))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 140) (:start . 139)\n (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 141) (:start . 140)\n (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.164) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101904@unknown@formal@none@1@S@We also identified a 597-aa protein sequence encoded by a single open reading frame (contig 29068, positions 1157–2944), which is 28% identical to nearly the entire RAG1 core (positions 461–1002 in the human RAG1, Figure S5).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 18)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n (:id . 45))\n ((:tag . "JJ") (:stem . "597-aa") (:form . "597-aa") (:end . 27)\n (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 35)\n (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 44)\n (:start . 36) (:id . 48))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 52)\n (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 55) (:start . 53)\n (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n (:id . 51))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 64)\n (:start . 58) (:id . 52))\n ((:tag . "JJ") (:stem . "open") (:form . "open") (:end . 69) (:start . 65)\n (:id . 53))\n ((:tag . "NN") (:stem . "reading") (:form . "reading") (:end . 77)\n (:start . 70) (:id . 54))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 83) (:start . 78)\n (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n (:id . 56))\n ((:tag . "NN") (:stem . "contig") (:form . "contig") (:end . 91)\n (:start . 85) (:id . 57))\n ((:tag . "CD") (:stem . "29068") (:form . "29068") (:end . 97) (:start . 92)\n (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n (:id . 59))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 108)\n (:start . 99) (:id . 60))\n ((:tag . "CD") (:stem . "1157–2944") (:form . "1157–2944") (:end . 118)\n (:start . 109) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 119) (:start . 118)\n (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n (:id . 63))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 126)\n (:start . 121) (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 129) (:start . 127)\n (:id . 65))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 132) (:start . 130)\n (:id . 66))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 133) (:start . 132)\n (:id . 67))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 143)\n (:start . 134) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 146) (:start . 144)\n (:id . 69))\n ((:tag . "RB") (:stem . "nearly") (:form . "nearly") (:end . 153)\n (:start . 147) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 157) (:start . 154)\n (:id . 71))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 164)\n (:start . 158) (:id . 72))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 169) (:start . 165)\n (:id . 73))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 174) (:start . 170)\n (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 176) (:start . 175)\n (:id . 75))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 185)\n (:start . 176) (:id . 76))\n ((:tag . "CD") (:stem . "461–1002") (:form . "461–1002") (:end . 194)\n (:start . 186) (:id . 77))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 197) (:start . 195)\n (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 201) (:start . 198)\n (:id . 79))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 207)\n (:start . 202) (:id . 80))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 212) (:start . 208)\n (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 213) (:start . 212)\n (:id . 82))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 220)\n (:start . 214) (:id . 83))\n ((:tag . "NNP") (:stem . "S5") (:form . "S5") (:end . 223) (:start . 221)\n (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 224) (:start . 223)\n (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n (:id . 86)))@@@1@45@((:identifiers (:sid . :s6.165) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101905@unknown@formal@none@1@S@Extensive analysis of the flanks failed to show any hallmarks of putative transposons that might be associated with this RAG1-like protein, and we did not find any evidence indicating that other RAG1 core–like proteins are encoded by transposable elements (Figure 5).@(((:tag . "JJ") (:stem . "extensive") (:form . "Extensive") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 18)\n (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "NNS") (:stem . "flank") (:form . "flanks") (:end . 32)\n (:start . 26) (:id . 46))\n ((:tag . "VBD") (:stem . "fail") (:form . "failed") (:end . 39) (:start . 33)\n (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 42) (:start . 40)\n (:id . 48))\n ((:tag . "VB") (:stem . "show") (:form . "show") (:end . 47) (:start . 43)\n (:id . 49))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 51) (:start . 48)\n (:id . 50))\n ((:tag . "NNS") (:stem . "hallmark") (:form . "hallmarks") (:end . 61)\n (:start . 52) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n (:id . 52))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 73)\n (:start . 65) (:id . 53))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 85)\n (:start . 74) (:id . 54))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 90) (:start . 86)\n (:id . 55))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 96) (:start . 91)\n (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 99) (:start . 97)\n (:id . 57))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 110)\n (:start . 100) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 115) (:start . 111)\n (:id . 59))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 120) (:start . 116)\n (:id . 60))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 130)\n (:start . 121) (:id . 61))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 138)\n (:start . 131) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n (:id . 64))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 146) (:start . 144)\n (:id . 65))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 150) (:start . 147)\n (:id . 66))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 154) (:start . 151)\n (:id . 67))\n ((:tag . "VB") (:stem . "find") (:form . "find") (:end . 159) (:start . 155)\n (:id . 68))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 163) (:start . 160)\n (:id . 69))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 172)\n (:start . 164) (:id . 70))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 183)\n (:start . 173) (:id . 71))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 188) (:start . 184)\n (:id . 72))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 194)\n (:start . 189) (:id . 73))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 199) (:start . 195)\n (:id . 74))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 209)\n (:start . 200) (:id . 75))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 218)\n (:start . 210) (:id . 76))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 222) (:start . 219)\n (:id . 77))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 230)\n (:start . 223) (:id . 78))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 233) (:start . 231)\n (:id . 79))\n ((:tag . "JJ") (:stem . "transposable") (:form . "transposable") (:end . 246)\n (:start . 234) (:id . 80))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 255)\n (:start . 247) (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 257) (:start . 256)\n (:id . 82))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 263)\n (:start . 257) (:id . 83))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 265) (:start . 264)\n (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 266) (:start . 265)\n (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 267) (:start . 266)\n (:id . 86)))@@@1@45@((:hcues ((:id . :x6.166.1) (:span 173 188)) ((:id . :x6.166.3) (:span 91 96))\n ((:id . :x6.166.4) (:span 65 73)))\n (:ncues ((:id . :x6.166.2) (:span 151 154))\n ((:id . :x6.166.5) (:span 33 39)))\n (:hscopes ((:id . :x6.166.1) (:span 173 255))\n ((:id . :x6.166.3) (:span 86 138)) ((:id . :x6.166.4) (:span 65 138)))\n (:nscopes ((:id . :x6.166.2) (:span 151 255))\n ((:id . :x6.166.5) (:span 33 138)))\n (:identifiers (:sid . :s6.166) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101906@unknown@formal@none@1@S@Using FGENESH [33], we detected that the RAG1 core–like open reading frame (ORF) in the contig 29068 forms a terminal exon (positions 1154–2947) of an incomplete hypothetical gene composed of two exons (internal and terminal; see Figure S6).@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . 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"open") (:form . "open") (:end . 60) (:start . 56)\n (:id . 54))\n ((:tag . "NN") (:stem . "reading") (:form . "reading") (:end . 68)\n (:start . 61) (:id . 55))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 74) (:start . 69)\n (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 76) (:start . 75)\n (:id . 57))\n ((:tag . "NNP") (:stem . "ORF") (:form . "ORF") (:end . 79) (:start . 76)\n (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 83) (:start . 81)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n (:id . 61))\n ((:tag . "NN") (:stem . "contig") (:form . "contig") (:end . 94)\n (:start . 88) (:id . 62))\n ((:tag . "CD") (:stem . "29068") (:form . "29068") (:end . 100) (:start . 95)\n (:id . 63))\n ((:tag . "VBZ") (:stem . "form") (:form . "forms") (:end . 106)\n (:start . 101) (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 108) (:start . 107)\n (:id . 65))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 117)\n (:start . 109) (:id . 66))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 122) (:start . 118)\n (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 124) (:start . 123)\n (:id . 68))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 133)\n (:start . 124) (:id . 69))\n ((:tag . "CD") (:stem . "1154–2947") (:form . "1154–2947") (:end . 143)\n (:start . 134) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 144) (:start . 143)\n (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 147) (:start . 145)\n (:id . 72))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 150) (:start . 148)\n (:id . 73))\n ((:tag . "JJ") (:stem . "incomplete") (:form . "incomplete") (:end . 161)\n (:start . 151) (:id . 74))\n ((:tag . "JJ") (:stem . "hypothetical") (:form . "hypothetical") (:end . 174)\n (:start . 162) (:id . 75))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 179) (:start . 175)\n (:id . 76))\n ((:tag . "VBN") (:stem . "compose") (:form . "composed") (:end . 188)\n (:start . 180) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 191) (:start . 189)\n (:id . 78))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 195) (:start . 192)\n (:id . 79))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 201)\n (:start . 196) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 203) (:start . 202)\n (:id . 81))\n ((:tag . "JJ") (:stem . "internal") (:form . "internal") (:end . 211)\n (:start . 203) (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 215) (:start . 212)\n (:id . 83))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 224)\n (:start . 216) (:id . 84))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 225) (:start . 224)\n (:id . 85))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 229) (:start . 226)\n (:id . 86))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 236)\n (:start . 230) (:id . 87))\n ((:tag . "NNP") (:stem . "S6") (:form . "S6") (:end . 239) (:start . 237)\n (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 240) (:start . 239)\n (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 241) (:start . 240)\n (:id . 90)))@@@1@49@((:identifiers (:sid . :s6.167) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101907@unknown@formal@none@1@S@The 3? terminal portion of the internal exon encodes a protein sequence that appears to be marginally similar to an approximately 50-aa fragment of the RAG1 core (positions 394–454 in human RAG1; Figure S5).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 5) (:start . 4)\n (:id . 43))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 6) (:start . 5) (:id . 44))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 15)\n (:start . 7) (:id . 45))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 23)\n (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n (:id . 48))\n ((:tag . "JJ") (:stem . "internal") (:form . "internal") (:end . 39)\n (:start . 31) (:id . 49))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 44) (:start . 40)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 52)\n (:start . 45) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n (:id . 52))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 62)\n (:start . 55) (:id . 53))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 71)\n (:start . 63) (:id . 54))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 76) (:start . 72)\n (:id . 55))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 84)\n (:start . 77) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 87) (:start . 85)\n (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 90) (:start . 88)\n (:id . 58))\n ((:tag . "RB") (:stem . "marginally") (:form . "marginally") (:end . 101)\n (:start . 91) (:id . 59))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 109)\n (:start . 102) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 112) (:start . 110)\n (:id . 61))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 115) (:start . 113)\n (:id . 62))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 129) (:start . 116) (:id . 63))\n ((:tag . "JJ") (:stem . "50-aa") (:form . "50-aa") (:end . 135)\n (:start . 130) (:id . 64))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 144)\n (:start . 136) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 147) (:start . 145)\n (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n (:id . 67))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 156) (:start . 152)\n (:id . 68))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 161) (:start . 157)\n (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 163) (:start . 162)\n (:id . 70))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 172)\n (:start . 163) (:id . 71))\n ((:tag . "CD") (:stem . "394–454") (:form . "394–454") (:end . 180)\n (:start . 173) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 183) (:start . 181)\n (:id . 73))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 189)\n (:start . 184) (:id . 74))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 194) (:start . 190)\n (:id . 75))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 195) (:start . 194)\n (:id . 76))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 202)\n (:start . 196) (:id . 77))\n ((:tag . "NNP") (:stem . "S5") (:form . "S5") (:end . 205) (:start . 203)\n (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 206) (:start . 205)\n (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n (:id . 80)))@@@1@39@((:hcues ((:id . :x6.168.1) (:span 77 84)))\n (:hscopes ((:id . :x6.168.1) (:span 72 194)))\n (:identifiers (:sid . :s6.168) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101908@unknown@formal@none@1@S@The RAG1 core–like protein in whole genome shotgun (WGS) contig 12509 (Figure 5) also seems to be encoded by the last exon starting at position 1650 of a hypothetical RAG1-like gene.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 18)\n (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 26)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 35) (:start . 30)\n (:id . 47))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 42)\n (:start . 36) (:id . 48))\n ((:tag . "NN") (:stem . "shotgun") (:form . "shotgun") (:end . 50)\n (:start . 43) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n (:id . 50))\n ((:tag . "NNP") (:stem . "WGS") (:form . "WGS") (:end . 55) (:start . 52)\n (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 56) (:start . 55)\n (:id . 52))\n ((:tag . "NN") (:stem . "contig") (:form . "contig") (:end . 63)\n (:start . 57) (:id . 53))\n ((:tag . "CD") (:stem . "12509") (:form . "12509") (:end . 69) (:start . 64)\n (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 77)\n (:start . 71) (:id . 56))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 79) (:start . 78)\n (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n (:id . 58))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 85) (:start . 81)\n (:id . 59))\n ((:tag . "VBZ") (:stem . "seem") (:form . "seems") (:end . 91) (:start . 86)\n (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n (:id . 61))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 97) (:start . 95)\n (:id . 62))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 105)\n (:start . 98) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 108) (:start . 106)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n (:id . 65))\n ((:tag . "JJ") (:stem . "last") (:form . "last") (:end . 117) (:start . 113)\n (:id . 66))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 122) (:start . 118)\n (:id . 67))\n ((:tag . "VBG") (:stem . "start") (:form . "starting") (:end . 131)\n (:start . 123) (:id . 68))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 134) (:start . 132)\n (:id . 69))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 143)\n (:start . 135) (:id . 70))\n ((:tag . "CD") (:stem . "1650") (:form . "1650") (:end . 148) (:start . 144)\n (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 153) (:start . 152)\n (:id . 73))\n ((:tag . "JJ") (:stem . "hypothetical") (:form . "hypothetical") (:end . 166)\n (:start . 154) (:id . 74))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 176)\n (:start . 167) (:id . 75))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 181) (:start . 177)\n (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n (:id . 77)))@@@1@36@((:hcues ((:id . :x6.169.1) (:span 154 166))\n ((:id . :x6.169.2) (:span 86 91)))\n (:hscopes ((:id . :x6.169.1) (:span 154 181))\n ((:id . :x6.169.2) (:span 0 181)))\n (:identifiers (:sid . :s6.169) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101910@unknown@formal@none@1@S@Remarkably, the acceptor splice site positions in the sea urchin RAG1 core–like proteins closely correspond to those in RAG1 from teleosts (i.e., most of the living ray-finned or bony fish), in which RAG1 is split by an intron at position homologous to Gly460 in human RAG1 [34].@(((:tag . "RB") (:stem . "remarkably") (:form . "Remarkably") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "acceptor") (:form . "acceptor") (:end . 24)\n (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "splice") (:form . "splice") (:end . 31)\n (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 36) (:start . 32)\n (:id . 47))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 46)\n (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n (:id . 50))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 57) (:start . 54)\n (:id . 51))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 64)\n (:start . 58) (:id . 52))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 69) (:start . 65)\n (:id . 53))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 79)\n (:start . 70) (:id . 54))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 88)\n (:start . 80) (:id . 55))\n ((:tag . "RB") (:stem . "closely") (:form . "closely") (:end . 96)\n (:start . 89) (:id . 56))\n ((:tag . "VBP") (:stem . "correspond") (:form . "correspond") (:end . 107)\n (:start . 97) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n (:id . 58))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 116)\n (:start . 111) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 119) (:start . 117)\n (:id . 60))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 124) (:start . 120)\n (:id . 61))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 129) (:start . 125)\n (:id . 62))\n ((:tag . "NNS") (:stem . "teleost") (:form . "teleosts") (:end . 138)\n (:start . 130) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 140) (:start . 139)\n (:id . 64))\n ((:tag . "FW") (:stem . "i.e.") (:form . 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",") (:form . ",") (:end . 190) (:start . 189)\n (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 193) (:start . 191)\n (:id . 77))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 199)\n (:start . 194) (:id . 78))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 204) (:start . 200)\n (:id . 79))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 207) (:start . 205)\n (:id . 80))\n ((:tag . "VBN") (:stem . "split") (:form . "split") (:end . 213)\n (:start . 208) (:id . 81))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 216) (:start . 214)\n (:id . 82))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 219) (:start . 217)\n (:id . 83))\n ((:tag . "NN") (:stem . "intron") (:form . "intron") (:end . 226)\n (:start . 220) (:id . 84))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 229) (:start . 227)\n (:id . 85))\n ((:tag . "NN") (:stem . "position") (:form . 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(:end . 279) (:start . 278)\n (:id . 96)))@@@1@55@((:identifiers (:sid . :s6.171) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101911@unknown@formal@none@1@S@Using the same RAG1 query sequences in a TBLASTN search against WGS trace sequences from the lancelet (Branchiostoma floridae) genome recently sequenced at the Joint Genome Institute (see Materials and Methods), we found that the lancelet genome encodes protein sequences approximately 35% identical to the RAG1 core (Figure S5; RAG1L_BF; BLASTP E-value is equal to 10-34).@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 19) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . 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")") (:end . 210) (:start . 209)\n (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 211) (:start . 210)\n (:id . 77))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 214) (:start . 212)\n (:id . 78))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 220)\n (:start . 215) (:id . 79))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 225) (:start . 221)\n (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 229) (:start . 226)\n (:id . 81))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 238)\n (:start . 230) (:id . 82))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 245)\n (:start . 239) (:id . 83))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 253)\n (:start . 246) (:id . 84))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 261)\n (:start . 254) (:id . 85))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 271)\n (:start . 262) (:id . 86))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 285) (:start . 272) (:id . 87))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 288) (:start . 286)\n (:id . 88))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 289) (:start . 288)\n (:id . 89))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 299)\n (:start . 290) (:id . 90))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 302) (:start . 300)\n (:id . 91))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 306) (:start . 303)\n (:id . 92))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 311) (:start . 307)\n (:id . 93))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 316) (:start . 312)\n (:id . 94))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 318) (:start . 317)\n (:id . 95))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 324)\n (:start . 318) (:id . 96))\n ((:tag . "NNP") (:stem . "S5") (:form . "S5") (:end . 327) (:start . 325)\n (:id . 97))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 328) (:start . 327)\n (:id . 98))\n ((:tag . "NNP") (:stem . "RAG1L_BF") (:form . "RAG1L_BF") (:end . 337)\n (:start . 329) (:id . 99))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 338) (:start . 337)\n (:id . 100))\n ((:tag . "NNP") (:stem . "BLASTP") (:form . "BLASTP") (:end . 345)\n (:start . 339) (:id . 101))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-value") (:end . 353)\n (:start . 346) (:id . 102))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 356) (:start . 354)\n (:id . 103))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 362)\n (:start . 357) (:id . 104))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 365) (:start . 363)\n (:id . 105))\n ((:tag . "CD") (:stem . "10-34") (:form . "10-34") (:end . 371)\n (:start . 366) (:id . 106))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 372) (:start . 371)\n (:id . 107))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 373) (:start . 372)\n (:id . 108)))@@@1@67@((:identifiers (:sid . :s6.172) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101912@unknown@formal@none@1@S@Again, as in the case of the sea urchin sequences, the lancelet RAG1 core–like elements show no hallmarks of transposons (data not shown).@(((:tag . "RB") (:stem . "again") (:form . "Again") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 9) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 12) (:start . 10)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 46))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 21) (:start . 17)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n (:id . 49))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 32) (:start . 29)\n (:id . 50))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 39)\n (:start . 33) (:id . 51))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 49)\n (:start . 40) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n (:id . 54))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 63)\n (:start . 55) (:id . 55))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 68) (:start . 64)\n (:id . 56))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 78)\n (:start . 69) (:id . 57))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 87)\n (:start . 79) (:id . 58))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 92) (:start . 88)\n (:id . 59))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 95) (:start . 93)\n (:id . 60))\n ((:tag . "NNS") (:stem . "hallmark") (:form . "hallmarks") (:end . 105)\n (:start . 96) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 108) (:start . 106)\n (:id . 62))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 120)\n (:start . 109) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 122) (:start . 121)\n (:id . 64))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 126)\n (:start . 122) (:id . 65))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 130) (:start . 127)\n (:id . 66))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 136)\n (:start . 131) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 137) (:start . 136)\n (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n (:id . 69)))@@@1@28@((:ncues ((:id . :x6.173.1) (:span 127 130))\n ((:id . :x6.173.2) (:span 93 95)))\n (:nscopes ((:id . :x6.173.1) (:span 121 137))\n ((:id . :x6.173.2) (:span 93 120)))\n (:identifiers (:sid . :s6.173) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101913@unknown@formal@none@1@S@However, unlike highly conserved RAG1 proteins, the RAG1 core–like proteins are remarkably diverse (see Figure 2).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "unlike") (:form . "unlike") (:end . 15) (:start . 9)\n (:id . 44))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 22)\n (:start . 16) (:id . 45))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 32)\n (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 37) (:start . 33)\n (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 46)\n (:start . 38) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n (:id . 50))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 56) (:start . 52)\n (:id . 51))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 66)\n (:start . 57) (:id . 52))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 75)\n (:start . 67) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 79) (:start . 76)\n (:id . 54))\n ((:tag . "RB") (:stem . "remarkably") (:form . "remarkably") (:end . 90)\n (:start . 80) (:id . 55))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 98)\n (:start . 91) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n (:id . 57))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 103) (:start . 100)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 110)\n (:start . 104) (:id . 59))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 112) (:start . 111)\n (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.174) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101914@unknown@formal@none@1@S@During the second review of the manuscript of this article, we were kindly informed by Dr.@(((:tag . "IN") (:stem . "during") (:form . "During") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n (:id . 43))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 17)\n (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "review") (:form . "review") (:end . 24)\n (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n (:id . 47))\n ((:tag . "NN") (:stem . "manuscript") (:form . "manuscript") (:end . 42)\n (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n (:id . 49))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 50) (:start . 46)\n (:id . 50))\n ((:tag . "NN") (:stem . "article") (:form . "article") (:end . 58)\n (:start . 51) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 62) (:start . 60)\n (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 67) (:start . 63)\n (:id . 54))\n ((:tag . "RB") (:stem . "kindly") (:form . "kindly") (:end . 74)\n (:start . 68) (:id . 55))\n ((:tag . "VBN") (:stem . "inform") (:form . "informed") (:end . 83)\n (:start . 75) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 86) (:start . 84)\n (:id . 57))\n ((:tag . "NNP") (:stem . "Dr") (:form . "Dr") (:end . 89) (:start . 87)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s6.175) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101915@unknown@formal@none@1@S@Hervé Philippe of a RAG1 core–like sequence present the starlet sea anemone (Nematostella vectensis).@(((:tag . "NNP") (:stem . "Hervé") (:form . "Hervé") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Philippe") (:form . "Philippe") (:end . 14)\n (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 19) (:start . 18)\n (:id . 45))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 24) (:start . 20)\n (:id . 46))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 34)\n (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 43)\n (:start . 35) (:id . 48))\n ((:tag . "VBP") (:stem . "present") (:form . "present") (:end . 51)\n (:start . 44) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n (:id . 50))\n ((:tag . "NN") (:stem . "starlet") (:form . "starlet") (:end . 63)\n (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 67) (:start . 64)\n (:id . 52))\n ((:tag . "NN") (:stem . "anemone") (:form . "anemone") (:end . 75)\n (:start . 68) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 77) (:start . 76)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Nematostella") (:form . "Nematostella") (:end . 89)\n (:start . 77) (:id . 55))\n ((:tag . "NN") (:stem . "vectensis") (:form . "vectensis") (:end . 99)\n (:start . 90) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s6.176) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101916@unknown@formal@none@1@S@After that, we screened all available Trace Archives (Materials and Methods) and detected additional RAG1-like proteins.@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 14) (:start . 12)\n (:id . 45))\n ((:tag . "VBD") (:stem . "screen") (:form . "screened") (:end . 23)\n (:start . 15) (:id . 46))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 27) (:start . 24)\n (:id . 47))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 37)\n (:start . 28) (:id . 48))\n ((:tag . "NNP") (:stem . "Trace") (:form . "Trace") (:end . 43) (:start . 38)\n (:id . 49))\n ((:tag . "NNPS") (:stem . "Archives") (:form . "Archives") (:end . 52)\n (:start . 44) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n (:id . 51))\n ((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 63)\n (:start . 54) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n (:id . 53))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 75)\n (:start . 68) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 76) (:start . 75)\n (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n (:id . 56))\n ((:tag . "VBD") (:stem . "detect") (:form . "detected") (:end . 89)\n (:start . 81) (:id . 57))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 100)\n (:start . 90) (:id . 58))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 110)\n (:start . 101) (:id . 59))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 119)\n (:start . 111) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.177) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101917@unknown@formal@none@1@S@In starlet sea anemone, several approximately 1000-bp WGS trace sequences were found (e.g., GenBank Trace Archive IDs 668021618, 558173651, 568641192, and 599572062), which encode protein, called RAG1L_NV, that is approximately 30% identical to the human RAG1 core (positions 284–802, TBLASTN, 10-26 < E < 10-7).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "starlet") (:form . "starlet") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "anemone") (:form . "anemone") (:end . 22)\n (:start . 15) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n (:id . 46))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 31)\n (:start . 24) (:id . 47))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 45) (:start . 32) (:id . 48))\n ((:tag . "JJ") (:stem . "1000-bp") (:form . "1000-bp") (:end . 53)\n (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "wgs") (:form . "WGS") (:end . 57) (:start . 54)\n (:id . 50))\n ((:tag . "NN") (:stem . "trace") (:form . "trace") (:end . 63) (:start . 58)\n (:id . 51))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 73)\n (:start . 64) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 78) (:start . 74)\n (:id . 53))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 84) (:start . 79)\n (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n (:id . 55))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 90) (:start . 86)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n (:id . 57))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 99)\n (:start . 92) (:id . 58))\n ((:tag . "NNP") (:stem . "Trace") (:form . "Trace") (:end . 105)\n (:start . 100) (:id . 59))\n ((:tag . "NNP") (:stem . "Archive") (:form . "Archive") (:end . 113)\n (:start . 106) (:id . 60))\n ((:tag . "NNP") (:stem . "IDs") (:form . "IDs") (:end . 117) (:start . 114)\n (:id . 61))\n ((:tag . "CD") (:stem . "668021618") (:form . "668021618") (:end . 127)\n (:start . 118) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n (:id . 63))\n ((:tag . "CD") (:stem . "558173651") (:form . "558173651") (:end . 138)\n (:start . 129) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n (:id . 65))\n ((:tag . "CD") (:stem . "568641192") (:form . "568641192") (:end . 149)\n (:start . 140) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 154) (:start . 151)\n (:id . 68))\n ((:tag . "CD") (:stem . "599572062") (:form . "599572062") (:end . 164)\n (:start . 155) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 165) (:start . 164)\n (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n (:id . 71))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 172)\n (:start . 167) (:id . 72))\n ((:tag . "VBP") (:stem . "encode") (:form . "encode") (:end . 179)\n (:start . 173) (:id . 73))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 187)\n (:start . 180) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 188) (:start . 187)\n (:id . 75))\n ((:tag . "VBN") (:stem . "call") (:form . "called") (:end . 195)\n (:start . 189) (:id . 76))\n ((:tag . "NNP") (:stem . "RAG1L_NV") (:form . "RAG1L_NV") (:end . 204)\n (:start . 196) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 205) (:start . 204)\n (:id . 78))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 210) (:start . 206)\n (:id . 79))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 213) (:start . 211)\n (:id . 80))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 227) (:start . 214) (:id . 81))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 230) (:start . 228)\n (:id . 82))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 231) (:start . 230)\n (:id . 83))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 241)\n (:start . 232) (:id . 84))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 244) (:start . 242)\n (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 248) (:start . 245)\n (:id . 86))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 254)\n (:start . 249) (:id . 87))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 259) (:start . 255)\n (:id . 88))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 264) (:start . 260)\n (:id . 89))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 266) (:start . 265)\n (:id . 90))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 275)\n (:start . 266) (:id . 91))\n ((:tag . "CD") (:stem . "284–802") (:form . "284–802") (:end . 283)\n (:start . 276) (:id . 92))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 284) (:start . 283)\n (:id . 93))\n ((:tag . "NNP") (:stem . "TBLASTN") (:form . "TBLASTN") (:end . 292)\n (:start . 285) (:id . 94))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 293) (:start . 292)\n (:id . 95))\n ((:tag . "CD") (:stem . "10-26") (:form . "10-26") (:end . 299)\n (:start . 294) (:id . 96))\n ((:tag . "SYM") (:stem . "<") (:form . "<") (:end . 301) (:start . 300)\n (:id . 97))\n ((:tag . "NN") (:stem . "e") (:form . "E") (:end . 303) (:start . 302)\n (:id . 98))\n ((:tag . "SYM") (:stem . "<") (:form . "<") (:end . 305) (:start . 304)\n (:id . 99))\n ((:tag . "CD") (:stem . "10-7") (:form . "10-7") (:end . 310) (:start . 306)\n (:id . 100))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 311) (:start . 310)\n (:id . 101))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 312) (:start . 311)\n (:id . 102)))@@@1@61@((:identifiers (:sid . :s6.178) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101918@unknown@formal@none@1@S@We also found several approximately 1000-bp WGS trace sequences of Hydra magnipapillata (Trace Archive IDs 688654311, 647073738, 666995387, 687186526, 688683890, and 688948453), coding for protein sequences 26%-30% identical to the RAG1 core (positions 753-995, E-value is approximately equal to 10-7 in a BLASTX search against GenBank).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 21)\n (:start . 14) (:id . 45))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 35) (:start . 22) (:id . 46))\n ((:tag . "JJ") (:stem . "1000-bp") (:form . "1000-bp") (:end . 43)\n (:start . 36) (:id . 47))\n ((:tag . "NN") (:stem . "wgs") (:form . "WGS") (:end . 47) (:start . 44)\n (:id . 48))\n ((:tag . "NN") (:stem . "trace") (:form . "trace") (:end . 53) (:start . 48)\n (:id . 49))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 63)\n (:start . 54) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n (:id . 51))\n ((:tag . "NNP") (:stem . "Hydra") (:form . "Hydra") (:end . 72) (:start . 67)\n (:id . 52))\n ((:tag . "NN") (:stem . "magnipapillata") (:form . "magnipapillata")\n (:end . 87) (:start . 73) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Trace") (:form . "Trace") (:end . 94) (:start . 89)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Archive") (:form . "Archive") (:end . 102)\n (:start . 95) (:id . 56))\n ((:tag . "NNP") (:stem . "IDs") (:form . "IDs") (:end . 106) (:start . 103)\n (:id . 57))\n ((:tag . "CD") (:stem . "688654311") (:form . "688654311") (:end . 116)\n (:start . 107) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n (:id . 59))\n ((:tag . "CD") (:stem . "647073738") (:form . "647073738") (:end . 127)\n (:start . 118) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n (:id . 61))\n ((:tag . "CD") (:stem . "666995387") (:form . "666995387") (:end . 138)\n (:start . 129) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n (:id . 63))\n ((:tag . "CD") (:stem . "687186526") (:form . "687186526") (:end . 149)\n (:start . 140) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n (:id . 65))\n ((:tag . "CD") (:stem . "688683890") (:form . "688683890") (:end . 160)\n (:start . 151) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 165) (:start . 162)\n (:id . 68))\n ((:tag . "CD") (:stem . "688948453") (:form . "688948453") (:end . 175)\n (:start . 166) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 176) (:start . 175)\n (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 177) (:start . 176)\n (:id . 71))\n ((:tag . "VBG") (:stem . "cod") (:form . "coding") (:end . 184)\n (:start . 178) (:id . 72))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 188) (:start . 185)\n (:id . 73))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 196)\n (:start . 189) (:id . 74))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 206)\n (:start . 197) (:id . 75))\n ((:tag . "CD") (:stem . "26%-30") (:form . "26%-30") (:end . 213)\n (:start . 207) (:id . 76))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 214) (:start . 213)\n (:id . 77))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 224)\n (:start . 215) (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 227) (:start . 225)\n (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 231) (:start . 228)\n (:id . 80))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 236) (:start . 232)\n (:id . 81))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 241) (:start . 237)\n (:id . 82))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 243) (:start . 242)\n (:id . 83))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 252)\n (:start . 243) (:id . 84))\n ((:tag . "CD") (:stem . "753-995") (:form . "753-995") (:end . 260)\n (:start . 253) (:id . 85))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 261) (:start . 260)\n (:id . 86))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-value") (:end . 269)\n (:start . 262) (:id . 87))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 272) (:start . 270)\n (:id . 88))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 286) (:start . 273) (:id . 89))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 292)\n (:start . 287) (:id . 90))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 295) (:start . 293)\n (:id . 91))\n ((:tag . "CD") (:stem . "10-7") (:form . "10-7") (:end . 300) (:start . 296)\n (:id . 92))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 303) (:start . 301)\n (:id . 93))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 305) (:start . 304)\n (:id . 94))\n ((:tag . "NNP") (:stem . "BLASTX") (:form . "BLASTX") (:end . 312)\n (:start . 306) (:id . 95))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 319)\n (:start . 313) (:id . 96))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 327)\n (:start . 320) (:id . 97))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 335)\n (:start . 328) (:id . 98))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 336) (:start . 335)\n (:id . 99))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 337) (:start . 336)\n (:id . 100)))@@@1@59@((:identifiers (:sid . :s6.179) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101920@unknown@formal@none@1@S@Remarkably, the hydra RAG1L_NM protein turned out to be significantly similar to the Transib TPase (26% identity; E-value is approximately equal to 10-14 in a BLASTX search against GenBank proteins combined with the Transib TPase sequences).@(((:tag . "RB") (:stem . "remarkably") (:form . "Remarkably") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "hydra") (:form . "hydra") (:end . 21) (:start . 16)\n (:id . 45))\n ((:tag . "NNP") (:stem . "RAG1L_NM") (:form . "RAG1L_NM") (:end . 30)\n (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 38)\n (:start . 31) (:id . 47))\n ((:tag . "VBD") (:stem . "turn") (:form . "turned") (:end . 45) (:start . 39)\n (:id . 48))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 49) (:start . 46)\n (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 55) (:start . 53)\n (:id . 51))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 69) (:start . 56) (:id . 52))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 77)\n (:start . 70) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 80) (:start . 78)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 92)\n (:start . 85) (:id . 56))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 98) (:start . 93)\n (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n (:id . 58))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 102) (:start . 100)\n (:id . 59))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 103) (:start . 102)\n (:id . 60))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 112)\n (:start . 104) (:id . 61))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 113) (:start . 112)\n (:id . 62))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-value") (:end . 121)\n (:start . 114) (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 124) (:start . 122)\n (:id . 64))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 138) (:start . 125) (:id . 65))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 144)\n (:start . 139) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 147) (:start . 145)\n (:id . 67))\n ((:tag . "CD") (:stem . "10-14") (:form . "10-14") (:end . 153)\n (:start . 148) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 156) (:start . 154)\n (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 158) (:start . 157)\n (:id . 70))\n ((:tag . "NNP") (:stem . "BLASTX") (:form . "BLASTX") (:end . 165)\n (:start . 159) (:id . 71))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 172)\n (:start . 166) (:id . 72))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 180)\n (:start . 173) (:id . 73))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 188)\n (:start . 181) (:id . 74))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 197)\n (:start . 189) (:id . 75))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 206)\n (:start . 198) (:id . 76))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 211) (:start . 207)\n (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 215) (:start . 212)\n (:id . 78))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 223)\n (:start . 216) (:id . 79))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 229)\n (:start . 224) (:id . 80))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 239)\n (:start . 230) (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 240) (:start . 239)\n (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 241) (:start . 240)\n (:id . 83)))@@@1@42@((:identifiers (:sid . :s6.181) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101921@unknown@formal@none@1@S@Therefore, the hydra RAG1 core–like protein provides the first direct link between the RAG1 core and Transib TPase.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "hydra") (:form . "hydra") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 25) (:start . 21)\n (:id . 46))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 35)\n (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 43)\n (:start . 36) (:id . 48))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 52)\n (:start . 44) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n (:id . 50))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 62) (:start . 57)\n (:id . 51))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 69)\n (:start . 63) (:id . 52))\n ((:tag . "NN") (:stem . "link") (:form . "link") (:end . 74) (:start . 70)\n (:id . 53))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 82)\n (:start . 75) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n (:id . 55))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 91) (:start . 87)\n (:id . 56))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 96) (:start . 92)\n (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 108)\n (:start . 101) (:id . 59))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 114)\n (:start . 109) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.182) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101922@unknown@formal@none@1@S@Schematic Structure of the Sea Urchin RAG1-Like Sequences@(((:tag . "JJ") (:stem . "schematic") (:form . "Schematic") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Structure") (:form . "Structure") (:end . 19)\n (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Sea") (:form . "Sea") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Urchin") (:form . "Urchin") (:end . 37)\n (:start . 31) (:id . 47))\n ((:tag . "NNP") (:stem . "RAG1-Like") (:form . "RAG1-Like") (:end . 47)\n (:start . 38) (:id . 48))\n ((:tag . "NNP") (:stem . "Sequence") (:form . "Sequences") (:end . 57)\n (:start . 48) (:id . 49)))@@@1@8@((:identifiers (:sid . :s6.183) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5101923@unknown@formal@none@1@S@Contig accession numbers are shown in the left column.@(((:tag . "NNP") (:stem . "Contig") (:form . "Contig") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "accession") (:form . "accession") (:end . 16)\n (:start . 7) (:id . 43))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 24)\n (:start . 17) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 28) (:start . 25)\n (:id . 45))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 34) (:start . 29)\n (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n (:id . 48))\n ((:tag . "JJ") (:stem . "left") (:form . "left") (:end . 46) (:start . 42)\n (:id . 49))\n ((:tag . "NN") (:stem . "column") (:form . "column") (:end . 53)\n (:start . 47) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 54) (:start . 53)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s6.184) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101924@unknown@formal@none@1@S@Inverted complement contigs are marked by “c” followed by the contig number.@(((:tag . "VBN") (:stem . "invert") (:form . "Inverted") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "complement") (:form . "complement") (:end . 19)\n (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "contig") (:form . "contigs") (:end . 27)\n (:start . 20) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 31) (:start . 28)\n (:id . 45))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 38) (:start . 32)\n (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 41) (:start . 39)\n (:id . 47))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 43) (:start . 42)\n (:id . 48))\n ((:tag . "NN") (:stem . "c") (:form . "c") (:end . 44) (:start . 43)\n (:id . 49))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 45) (:start . 44)\n (:id . 50))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 54)\n (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 57) (:start . 55)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n (:id . 53))\n ((:tag . "NN") (:stem . "contig") (:form . "contig") (:end . 68)\n (:start . 62) (:id . 54))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 75)\n (:start . 69) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s6.185) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101925@unknown@formal@none@1@S@In each contig, RAG1-like proteins (white rectangle) are schematically aligned with the human RAG1 core (top rectangle).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "contig") (:form . "contig") (:end . 14) (:start . 8)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n (:id . 45))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 25)\n (:start . 16) (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 34)\n (:start . 26) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n (:id . 48))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 41) (:start . 36)\n (:id . 49))\n ((:tag . "NN") (:stem . "rectangle") (:form . "rectangle") (:end . 51)\n (:start . 42) (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 56) (:start . 53)\n (:id . 52))\n ((:tag . "RB") (:stem . "schematically") (:form . "schematically")\n (:end . 70) (:start . 57) (:id . 53))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 78)\n (:start . 71) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 83) (:start . 79)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n (:id . 56))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 93) (:start . 88)\n (:id . 57))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 98) (:start . 94)\n (:id . 58))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 103) (:start . 99)\n (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 105) (:start . 104)\n (:id . 60))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 108) (:start . 105)\n (:id . 61))\n ((:tag . "NN") (:stem . "rectangle") (:form . "rectangle") (:end . 118)\n (:start . 109) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 119) (:start . 118)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s6.186) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101926@unknown@formal@none@1@S@Nucleotide positions of the RAG1-like sequences are shown beneath the white rectangles.@(((:tag . "NN") (:stem . "nucleotide") (:form . "Nucleotide") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 20)\n (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n (:id . 45))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 37)\n (:start . 28) (:id . 46))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 47)\n (:start . 38) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 51) (:start . 48)\n (:id . 48))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 57) (:start . 52)\n (:id . 49))\n ((:tag . "IN") (:stem . "beneath") (:form . "beneath") (:end . 65)\n (:start . 58) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n (:id . 51))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 75) (:start . 70)\n (:id . 52))\n ((:tag . "NNS") (:stem . "rectangle") (:form . "rectangles") (:end . 86)\n (:start . 76) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.187) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101927@unknown@formal@none@1@S@Three pairs of recently duplicated sequences (nucleotide identity is higher than 95%) are underlined by red, green, and black lines, respectively.@(((:tag . "CD") (:stem . "three") (:form . "Three") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "VBN") (:stem . "duplicate") (:form . "duplicated") (:end . 34)\n (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 44)\n (:start . 35) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 46) (:start . 45)\n (:id . 48))\n ((:tag . "NN") (:stem . "nucleotide") (:form . "nucleotide") (:end . 56)\n (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 65)\n (:start . 57) (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 68) (:start . 66)\n (:id . 51))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 75) (:start . 69)\n (:id . 52))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 80) (:start . 76)\n (:id . 53))\n ((:tag . "CD") (:stem . "95") (:form . "95") (:end . 83) (:start . 81)\n (:id . 54))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 84) (:start . 83)\n (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 89) (:start . 86)\n (:id . 57))\n ((:tag . "VBN") (:stem . "underline") (:form . "underlined") (:end . 100)\n (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 103) (:start . 101)\n (:id . 59))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 107) (:start . 104)\n (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n (:id . 61))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 114)\n (:start . 109) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 119) (:start . 116)\n (:id . 64))\n ((:tag . "JJ") (:stem . "black") (:form . "black") (:end . 125)\n (:start . 120) (:id . 65))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 131)\n (:start . 126) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n (:id . 67))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 145)\n (:start . 133) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s6.188) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101928@unknown@formal@none@1@S@Transposable and repetitive elements detected in the flanking regions are marked by painted rectangles.@(((:tag . "JJ") (:stem . "transposable") (:form . "Transposable") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n (:id . 43))\n ((:tag . "JJ") (:stem . "repetitive") (:form . "repetitive") (:end . 27)\n (:start . 17) (:id . 44))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 36)\n (:start . 28) (:id . 45))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 45)\n (:start . 37) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n (:id . 48))\n ((:tag . "NN") (:stem . "flanking") (:form . "flanking") (:end . 61)\n (:start . 53) (:id . 49))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 69)\n (:start . 62) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 73) (:start . 70)\n (:id . 51))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 80) (:start . 74)\n (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 83) (:start . 81)\n (:id . 53))\n ((:tag . "VBN") (:stem . "paint") (:form . "painted") (:end . 91)\n (:start . 84) (:id . 54))\n ((:tag . "NNS") (:stem . "rectangle") (:form . "rectangles") (:end . 102)\n (:start . 92) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s6.189) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101930@unknown@formal@none@1@S@Asterisks denote stop codons in the corresponding RAG1-like sequences.@(((:tag . "NNP") (:stem . "Asterisk") (:form . "Asterisks") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "denote") (:form . "denote") (:end . 16)\n (:start . 10) (:id . 43))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 21) (:start . 17)\n (:id . 44))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 28)\n (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n (:id . 47))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 49)\n (:start . 36) (:id . 48))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 59)\n (:start . 50) (:id . 49))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 69)\n (:start . 60) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s6.191) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101931@unknown@formal@none@1@S@BLASTP E-values characterizing similarities between the sea urchin and RAG1 proteins are shown above the white rectangles.@(((:tag . "NNP") (:stem . "BLASTP") (:form . "BLASTP") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-values") (:end . 15)\n (:start . 7) (:id . 43))\n ((:tag . "VBG") (:stem . "characterize") (:form . "characterizing")\n (:end . 30) (:start . 16) (:id . 44))\n ((:tag . "NNS") (:stem . "similarity") (:form . "similarities") (:end . 43)\n (:start . 31) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 51)\n (:start . 44) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n (:id . 47))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 59) (:start . 56)\n (:id . 48))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 66)\n (:start . 60) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n (:id . 50))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 75) (:start . 71)\n (:id . 51))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 84)\n (:start . 76) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 88) (:start . 85)\n (:id . 53))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 94) (:start . 89)\n (:id . 54))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 100) (:start . 95)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n (:id . 56))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 110)\n (:start . 105) (:id . 57))\n ((:tag . "NNS") (:stem . "rectangle") (:form . "rectangles") (:end . 121)\n (:start . 111) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s6.192) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101932@unknown@formal@none@1@S@Multiple alignment of these protein sequences is reported in Figure S5.@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 18)\n (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 27) (:start . 22)\n (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 35)\n (:start . 28) (:id . 46))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 45)\n (:start . 36) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 48) (:start . 46)\n (:id . 48))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 57)\n (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 67)\n (:start . 61) (:id . 51))\n ((:tag . "NNP") (:stem . "S5") (:form . "S5") (:end . 70) (:start . 68)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s6.193) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101933@unknown@formal@none@1@S@N-Terminal–Like Domain of RAG1 in the Sea Urchin, Lancelet, Starlet Sea Anemone, and Hydra Genomes@(((:tag . "NNP") (:stem . "N-Terminal–Like") (:form . "N-Terminal–Like")\n (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Domain") (:form . "Domain") (:end . 22)\n (:start . 16) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n (:id . 44))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 30) (:start . 26)\n (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Sea") (:form . "Sea") (:end . 41) (:start . 38)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Urchin") (:form . "Urchin") (:end . 48)\n (:start . 42) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Lancelet") (:form . "Lancelet") (:end . 58)\n (:start . 50) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n (:id . 52))\n ((:tag . "NNP") (:stem . "Starlet") (:form . "Starlet") (:end . 67)\n (:start . 60) (:id . 53))\n ((:tag . "NNP") (:stem . "Sea") (:form . "Sea") (:end . 71) (:start . 68)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Anemone") (:form . "Anemone") (:end . 79)\n (:start . 72) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n (:id . 57))\n ((:tag . "NNP") (:stem . "Hydra") (:form . "Hydra") (:end . 90) (:start . 85)\n (:id . 58))\n ((:tag . "NNPS") (:stem . "Genome") (:form . "Genomes") (:end . 98)\n (:start . 91) (:id . 59)))@@@1@18@((:identifiers (:sid . :s6.194) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101934@unknown@formal@none@1@S@A separate analysis of the assembled sea urchin sequences yielded seven sequences encoding three diverse proteins that were significantly similar to the 380-aa N-terminal domain of RAG1 (BLASTX, E < 10-4), excluding the 100-aa N-terminus (Figure 6).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 10)\n (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 19)\n (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "VBN") (:stem . "assemble") (:form . "assembled") (:end . 36)\n (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 40) (:start . 37)\n (:id . 48))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 47)\n (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 57)\n (:start . 48) (:id . 50))\n ((:tag . "VBD") (:stem . "yield") (:form . "yielded") (:end . 65)\n (:start . 58) (:id . 51))\n ((:tag . "CD") (:stem . "seven") (:form . "seven") (:end . 71) (:start . 66)\n (:id . 52))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 81)\n (:start . 72) (:id . 53))\n ((:tag . "VBG") (:stem . "encode") (:form . "encoding") (:end . 90)\n (:start . 82) (:id . 54))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 96) (:start . 91)\n (:id . 55))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 104)\n (:start . 97) (:id . 56))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 113)\n (:start . 105) (:id . 57))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 118) (:start . 114)\n (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 123) (:start . 119)\n (:id . 59))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 137) (:start . 124) (:id . 60))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 145)\n (:start . 138) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 148) (:start . 146)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n (:id . 63))\n ((:tag . "JJ") (:stem . "380-aa") (:form . "380-aa") (:end . 159)\n (:start . 153) (:id . 64))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 170)\n (:start . 160) (:id . 65))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 177)\n (:start . 171) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 180) (:start . 178)\n (:id . 67))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 185) (:start . 181)\n (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 187) (:start . 186)\n (:id . 69))\n ((:tag . "NNP") (:stem . "BLASTX") (:form . "BLASTX") (:end . 193)\n (:start . 187) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 194) (:start . 193)\n (:id . 71))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 196) (:start . 195)\n (:id . 72))\n ((:tag . "SYM") (:stem . "<") (:form . "<") (:end . 198) (:start . 197)\n (:id . 73))\n ((:tag . "CD") (:stem . "10-4") (:form . "10-4") (:end . 203) (:start . 199)\n (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 204) (:start . 203)\n (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 205) (:start . 204)\n (:id . 76))\n ((:tag . "VBG") (:stem . "exclude") (:form . "excluding") (:end . 215)\n (:start . 206) (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 219) (:start . 216)\n (:id . 78))\n ((:tag . "JJ") (:stem . "100-aa") (:form . "100-aa") (:end . 226)\n (:start . 220) (:id . 79))\n ((:tag . "NNP") (:stem . "N-terminus") (:form . "N-terminus") (:end . 237)\n (:start . 227) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 239) (:start . 238)\n (:id . 81))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 245)\n (:start . 239) (:id . 82))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 247) (:start . 246)\n (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 248) (:start . 247)\n (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 249) (:start . 248)\n (:id . 85)))@@@1@44@((:identifiers (:sid . :s6.195) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101935@unknown@formal@none@1@S@The first 305-aa protein is encoded by contig 1226, and its recently duplicated copies are on contigs 1219 and 1222 (approximately 95% identical to each other at the protein level).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "305-aa") (:form . "305-aa") (:end . 16)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 24)\n (:start . 17) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 35)\n (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 38) (:start . 36)\n (:id . 48))\n ((:tag . "NN") (:stem . "contig") (:form . "contig") (:end . 45)\n (:start . 39) (:id . 49))\n ((:tag . "CD") (:stem . "1226") (:form . "1226") (:end . 50) (:start . 46)\n (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n (:id . 52))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 59) (:start . 56)\n (:id . 53))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 68)\n (:start . 60) (:id . 54))\n ((:tag . "VBN") (:stem . "duplicate") (:form . "duplicated") (:end . 79)\n (:start . 69) (:id . 55))\n ((:tag . "NNS") (:stem . "copy") (:form . "copies") (:end . 86) (:start . 80)\n (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 90) (:start . 87)\n (:id . 57))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 93) (:start . 91)\n (:id . 58))\n ((:tag . "NNS") (:stem . "contig") (:form . "contigs") (:end . 101)\n (:start . 94) (:id . 59))\n ((:tag . "CD") (:stem . "1219") (:form . "1219") (:end . 106) (:start . 102)\n (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n (:id . 61))\n ((:tag . "CD") (:stem . "1222") (:form . "1222") (:end . 115) (:start . 111)\n (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n (:id . 63))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 130) (:start . 117) (:id . 64))\n ((:tag . "CD") (:stem . "95") (:form . "95") (:end . 133) (:start . 131)\n (:id . 65))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 134) (:start . 133)\n (:id . 66))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 144)\n (:start . 135) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 147) (:start . 145)\n (:id . 68))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 152) (:start . 148)\n (:id . 69))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 158)\n (:start . 153) (:id . 70))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 161) (:start . 159)\n (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n (:id . 72))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 173)\n (:start . 166) (:id . 73))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 179)\n (:start . 174) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s6.196) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101936@unknown@formal@none@1@S@The second, 195-aa protein (contig 83099) is the shortest.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 44))\n ((:tag . "JJ") (:stem . "195-aa") (:form . "195-aa") (:end . 18)\n (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 26)\n (:start . 19) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 28) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "contig") (:form . "contig") (:end . 34)\n (:start . 28) (:id . 48))\n ((:tag . "CD") (:stem . "83099") (:form . "83099") (:end . 40) (:start . 35)\n (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 41) (:start . 40)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 44) (:start . 42)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n (:id . 52))\n ((:tag . "NN") (:stem . "shortest") (:form . "shortest") (:end . 57)\n (:start . 49) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 58) (:start . 57)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.197) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101937@unknown@formal@none@1@S@It is only approximately 26% identical to the first protein and more than 90% identical at the DNA level to its duplicate on contig 86231.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 10) (:start . 6)\n (:id . 44))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 24) (:start . 11) (:id . 45))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 28) (:start . 27)\n (:id . 47))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 38)\n (:start . 29) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n (:id . 50))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 51) (:start . 46)\n (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 59)\n (:start . 52) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n (:id . 53))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 68) (:start . 64)\n (:id . 54))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 73) (:start . 69)\n (:id . 55))\n ((:tag . "CD") (:stem . "90") (:form . "90") (:end . 76) (:start . 74)\n (:id . 56))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 77) (:start . 76)\n (:id . 57))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 87)\n (:start . 78) (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 90) (:start . 88)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n (:id . 60))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 98) (:start . 95)\n (:id . 61))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 104) (:start . 99)\n (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 107) (:start . 105)\n (:id . 63))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 111) (:start . 108)\n (:id . 64))\n ((:tag . "NN") (:stem . "duplicate") (:form . "duplicate") (:end . 121)\n (:start . 112) (:id . 65))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 124) (:start . 122)\n (:id . 66))\n ((:tag . "NN") (:stem . "contig") (:form . "contig") (:end . 131)\n (:start . 125) (:id . 67))\n ((:tag . "CD") (:stem . "86231") (:form . "86231") (:end . 137)\n (:start . 132) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s6.198) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101938@unknown@formal@none@1@S@We also found a third protein on contig 768 that contains unique motifs in its N-terminal regions that best match the homologous regions of RAG1.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 15) (:start . 14)\n (:id . 45))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 21) (:start . 16)\n (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 29)\n (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 32) (:start . 30)\n (:id . 48))\n ((:tag . "NN") (:stem . "contig") (:form . "contig") (:end . 39)\n (:start . 33) (:id . 49))\n ((:tag . "CD") (:stem . "768") (:form . "768") (:end . 43) (:start . 40)\n (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 48) (:start . 44)\n (:id . 51))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 57)\n (:start . 49) (:id . 52))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 64)\n (:start . 58) (:id . 53))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 71)\n (:start . 65) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n (:id . 55))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 78) (:start . 75)\n (:id . 56))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 89)\n (:start . 79) (:id . 57))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 97)\n (:start . 90) (:id . 58))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 102) (:start . 98)\n (:id . 59))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 107) (:start . 103)\n (:id . 60))\n ((:tag . "VBP") (:stem . "match") (:form . "match") (:end . 113)\n (:start . 108) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n (:id . 62))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 128)\n (:start . 118) (:id . 63))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 136)\n (:start . 129) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 139) (:start . 137)\n (:id . 65))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 144) (:start . 140)\n (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s6.199) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101940@unknown@formal@none@1@S@By analyzing the lancelet WGS traces, we also found that the lancelet genome encodes five different proteins similar to the N-terminal domain of RAG1 (BLASTP E values in searches against all GenBank proteins were in a range of 10-14–10-7).@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBG") (:stem . "analyze") (:form . "analyzing") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 25)\n (:start . 17) (:id . 45))\n ((:tag . "VBZ") (:stem . "wgs") (:form . "WGS") (:end . 29) (:start . 26)\n (:id . 46))\n ((:tag . "NNS") (:stem . "trace") (:form . "traces") (:end . 36)\n (:start . 30) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 40) (:start . 38)\n (:id . 49))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 45) (:start . 41)\n (:id . 50))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 51) (:start . 46)\n (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 56) (:start . 52)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n (:id . 53))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 69)\n (:start . 61) (:id . 54))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 76)\n (:start . 70) (:id . 55))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 84)\n (:start . 77) (:id . 56))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 89) (:start . 85)\n (:id . 57))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 99)\n (:start . 90) (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 108)\n (:start . 100) (:id . 59))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 116)\n (:start . 109) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 119) (:start . 117)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n (:id . 62))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 134)\n (:start . 124) (:id . 63))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 141)\n (:start . 135) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n (:id . 65))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 149) (:start . 145)\n (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 151) (:start . 150)\n (:id . 67))\n ((:tag . "NNP") (:stem . "BLASTP") (:form . "BLASTP") (:end . 157)\n (:start . 151) (:id . 68))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 159) (:start . 158)\n (:id . 69))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 166)\n (:start . 160) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 169) (:start . 167)\n (:id . 71))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 178)\n (:start . 170) (:id . 72))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 186)\n (:start . 179) (:id . 73))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 190) (:start . 187)\n (:id . 74))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 198)\n (:start . 191) (:id . 75))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 207)\n (:start . 199) (:id . 76))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 212) (:start . 208)\n (:id . 77))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 215) (:start . 213)\n (:id . 78))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 217) (:start . 216)\n (:id . 79))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 223)\n (:start . 218) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 226) (:start . 224)\n (:id . 81))\n ((:tag . "CD") (:stem . "10-14–10-7") (:form . "10-14–10-7") (:end . 237)\n (:start . 227) (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 238) (:start . 237)\n (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 239) (:start . 238)\n (:id . 84)))@@@1@43@((:identifiers (:sid . :s6.201) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101941@unknown@formal@none@1@S@DNA sequences coding for these proteins, P1_BF through P5_BF, were manually assembled from overlapping WGS sequences (data available upon request).@(((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "VBG") (:stem . "cod") (:form . "coding") (:end . 20) (:start . 14)\n (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 24) (:start . 21)\n (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 30) (:start . 25)\n (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 39)\n (:start . 31) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n (:id . 48))\n ((:tag . "NNP") (:stem . "P1_BF") (:form . "P1_BF") (:end . 46) (:start . 41)\n (:id . 49))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 54)\n (:start . 47) (:id . 50))\n ((:tag . "NNP") (:stem . "P5_BF") (:form . "P5_BF") (:end . 60) (:start . 55)\n (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 66) (:start . 62)\n (:id . 53))\n ((:tag . "RB") (:stem . "manually") (:form . "manually") (:end . 75)\n (:start . 67) (:id . 54))\n ((:tag . "VBN") (:stem . "assemble") (:form . "assembled") (:end . 85)\n (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 90) (:start . 86)\n (:id . 56))\n ((:tag . "VBG") (:stem . "overlap") (:form . "overlapping") (:end . 102)\n (:start . 91) (:id . 57))\n ((:tag . "NNP") (:stem . "WGS") (:form . "WGS") (:end . 106) (:start . 103)\n (:id . 58))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 116)\n (:start . 107) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 118) (:start . 117)\n (:id . 60))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 122)\n (:start . 118) (:id . 61))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 132)\n (:start . 123) (:id . 62))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 137) (:start . 133)\n (:id . 63))\n ((:tag . "NN") (:stem . "request") (:form . "request") (:end . 145)\n (:start . 138) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s6.202) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101942@unknown@formal@none@1@S@The proteins detected in the sea urchin and lancelet genome share a ring finger motif as well as two novel motifs matching the N-terminal RAG1 domain (Figure 6) and remotely resembling C-x2-C zinc finger motifs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 21)\n (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 32) (:start . 29)\n (:id . 47))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 39)\n (:start . 33) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n (:id . 49))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 52)\n (:start . 44) (:id . 50))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 59)\n (:start . 53) (:id . 51))\n ((:tag . "VBP") (:stem . "share") (:form . "share") (:end . 65) (:start . 60)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 67) (:start . 66)\n (:id . 53))\n ((:tag . "NN") (:stem . "ring") (:form . "ring") (:end . 72) (:start . 68)\n (:id . 54))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 79)\n (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 85) (:start . 80)\n (:id . 56))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 88) (:start . 86)\n (:id . 57))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 93) (:start . 89)\n (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 96) (:start . 94)\n (:id . 59))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 100) (:start . 97)\n (:id . 60))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 106)\n (:start . 101) (:id . 61))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 113)\n (:start . 107) (:id . 62))\n ((:tag . "VBG") (:stem . "match") (:form . "matching") (:end . 122)\n (:start . 114) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n (:id . 64))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 137)\n (:start . 127) (:id . 65))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 142) (:start . 138)\n (:id . 66))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 149)\n (:start . 143) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 151) (:start . 150)\n (:id . 68))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 157)\n (:start . 151) (:id . 69))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 159) (:start . 158)\n (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 160) (:start . 159)\n (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 164) (:start . 161)\n (:id . 72))\n ((:tag . "RB") (:stem . "remotely") (:form . "remotely") (:end . 173)\n (:start . 165) (:id . 73))\n ((:tag . "VBG") (:stem . "resemble") (:form . "resembling") (:end . 184)\n (:start . 174) (:id . 74))\n ((:tag . "NNP") (:stem . "C-x2-C") (:form . "C-x2-C") (:end . 191)\n (:start . 185) (:id . 75))\n ((:tag . "NN") (:stem . "zinc") (:form . "zinc") (:end . 196) (:start . 192)\n (:id . 76))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 203)\n (:start . 197) (:id . 77))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 210)\n (:start . 204) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n (:id . 79)))@@@1@38@((:identifiers (:sid . :s6.203) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101943@unknown@formal@none@1@S@The new conserved motifs are H-x3-L-x3-C-R-x-C-G and D-x3-I-h-P-x2-F-C-x2-C, and their function remains to be determined.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 17)\n (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 24)\n (:start . 18) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "NNP") (:stem . "H-x3-L-x3-C-R-x-C-G")\n (:form . "H-x3-L-x3-C-R-x-C-G") (:end . 48) (:start . 29) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n (:id . 48))\n ((:tag . "NNP") (:stem . "D-x3-I-h-P-x2-F-C-x2-C")\n (:form . "D-x3-I-h-P-x2-F-C-x2-C") (:end . 75) (:start . 53) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n (:id . 51))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 86)\n (:start . 81) (:id . 52))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 95)\n (:start . 87) (:id . 53))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 103)\n (:start . 96) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 106) (:start . 104)\n (:id . 55))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 109) (:start . 107)\n (:id . 56))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 120)\n (:start . 110) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n (:id . 58)))@@@1@17@((:hcues ((:id . :x6.204.1) (:span 96 120)))\n (:hscopes ((:id . :x6.204.1) (:span 81 120)))\n (:identifiers (:sid . :s6.204) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101944@unknown@formal@none@1@S@It is thought that the ring finger motif of RAG1 functions as a zinc-binding domain, is involved in dimerization [30,35], and acts as an E3 ligase in the ubiquitylation [36].@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "VBN") (:stem . "think") (:form . "thought") (:end . 13)\n (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 46))\n ((:tag . "NN") (:stem . "ring") (:form . "ring") (:end . 27) (:start . 23)\n (:id . 47))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 34)\n (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 40) (:start . 35)\n (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n (:id . 50))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 48) (:start . 44)\n (:id . 51))\n ((:tag . "VBZ") (:stem . "function") (:form . "functions") (:end . 58)\n (:start . 49) (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 61) (:start . 59)\n (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 63) (:start . 62)\n (:id . 54))\n ((:tag . "JJ") (:stem . "zinc-binding") (:form . "zinc-binding") (:end . 76)\n (:start . 64) (:id . 55))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 83)\n (:start . 77) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 87) (:start . 85)\n (:id . 58))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 96)\n (:start . 88) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n (:id . 60))\n ((:tag . "NN") (:stem . "dimerization") (:form . "dimerization") (:end . 112)\n (:start . 100) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 114) (:start . 113)\n (:id . 62))\n ((:tag . "CD") (:stem . "30,35") (:form . "30,35") (:end . 119)\n (:start . 114) (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 120) (:start . 119)\n (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n (:id . 66))\n ((:tag . "VBZ") (:stem . "act") (:form . "acts") (:end . 130) (:start . 126)\n (:id . 67))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 133) (:start . 131)\n (:id . 68))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 136) (:start . 134)\n (:id . 69))\n ((:tag . "NN") (:stem . "e3") (:form . "E3") (:end . 139) (:start . 137)\n (:id . 70))\n ((:tag . "NN") (:stem . "ligase") (:form . "ligase") (:end . 146)\n (:start . 140) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n (:id . 73))\n ((:tag . "NN") (:stem . "ubiquitylation") (:form . "ubiquitylation")\n (:end . 168) (:start . 154) (:id . 74))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 170) (:start . 169)\n (:id . 75))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 172) (:start . 170)\n (:id . 76))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 173) (:start . 172)\n (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n (:id . 78)))@@@1@37@((:hcues ((:id . :x6.205.1) (:span 6 13)))\n (:hscopes ((:id . :x6.205.1) (:span 6 168)))\n (:identifiers (:sid . :s6.205) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101945@unknown@formal@none@1@S@It also likely that the N-terminal RAG1 and RAG1-like proteins share an additional conserved motif W-x-p-h-x(3–6)-C-x2-C that resides between conserved motif 2 and the ring finger (Figure 6).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 14) (:start . 8)\n (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n (:id . 46))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 34)\n (:start . 24) (:id . 47))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 39) (:start . 35)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n (:id . 49))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 53)\n (:start . 44) (:id . 50))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 62)\n (:start . 54) (:id . 51))\n ((:tag . "VBP") (:stem . "share") (:form . "share") (:end . 68) (:start . 63)\n (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 71) (:start . 69)\n (:id . 53))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 82)\n (:start . 72) (:id . 54))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 92)\n (:start . 83) (:id . 55))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 98) (:start . 93)\n (:id . 56))\n ((:tag . "NNP") (:stem . "W-x-p-h-x(3–6)-C-x2-C")\n (:form . "W-x-p-h-x(3–6)-C-x2-C") (:end . 120) (:start . 99) (:id . 57))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 125) (:start . 121)\n (:id . 58))\n ((:tag . "VBZ") (:stem . "reside") (:form . "resides") (:end . 133)\n (:start . 126) (:id . 59))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 141)\n (:start . 134) (:id . 60))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 151)\n (:start . 142) (:id . 61))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 157)\n (:start . 152) (:id . 62))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 159) (:start . 158)\n (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 163) (:start . 160)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 167) (:start . 164)\n (:id . 65))\n ((:tag . "NN") (:stem . "ring") (:form . "ring") (:end . 172) (:start . 168)\n (:id . 66))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 179)\n (:start . 173) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 181) (:start . 180)\n (:id . 68))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 187)\n (:start . 181) (:id . 69))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 189) (:start . 188)\n (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 190) (:start . 189)\n (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n (:id . 72)))@@@1@31@((:hcues ((:id . :x6.206.1) (:span 8 14)))\n (:hscopes ((:id . :x6.206.1) (:span 8 179)))\n (:identifiers (:sid . :s6.206) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101946@unknown@formal@none@1@S@None of the sea urchin and lancelet proteins align to the approximately 100-aa N-terminus of RAG1, which may indicate that this portion is missing from the genome or highly diverged and difficult to detect.@(((:tag . "NN") (:stem . "none") (:form . "None") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n (:id . 44))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 15) (:start . 12)\n (:id . 45))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 22)\n (:start . 16) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n (:id . 47))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 35)\n (:start . 27) (:id . 48))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 44)\n (:start . 36) (:id . 49))\n ((:tag . "VBP") (:stem . "align") (:form . "align") (:end . 50) (:start . 45)\n (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 53) (:start . 51)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n (:id . 52))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 71) (:start . 58) (:id . 53))\n ((:tag . "JJ") (:stem . "100-aa") (:form . "100-aa") (:end . 78)\n (:start . 72) (:id . 54))\n ((:tag . "NN") (:stem . "n-terminus") (:form . "N-terminus") (:end . 89)\n (:start . 79) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n (:id . 56))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 97) (:start . 93)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n (:id . 58))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 104)\n (:start . 99) (:id . 59))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 108) (:start . 105)\n (:id . 60))\n ((:tag . "VB") (:stem . "indicate") (:form . "indicate") (:end . 117)\n (:start . 109) (:id . 61))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 122) (:start . 118)\n (:id . 62))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 127) (:start . 123)\n (:id . 63))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 135)\n (:start . 128) (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 138) (:start . 136)\n (:id . 65))\n ((:tag . "VBG") (:stem . "miss") (:form . "missing") (:end . 146)\n (:start . 139) (:id . 66))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 151) (:start . 147)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n (:id . 68))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 162)\n (:start . 156) (:id . 69))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 165) (:start . 163)\n (:id . 70))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 172)\n (:start . 166) (:id . 71))\n ((:tag . "JJ") (:stem . "diverged") (:form . "diverged") (:end . 181)\n (:start . 173) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 185) (:start . 182)\n (:id . 73))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 195)\n (:start . 186) (:id . 74))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 198) (:start . 196)\n (:id . 75))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 205)\n (:start . 199) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n (:id . 77)))@@@1@36@((:hcues ((:id . :x6.207.1) (:span 163 165))\n ((:id . :x6.207.2) (:span 109 122)) ((:id . :x6.207.3) (:span 105 108)))\n (:hscopes ((:id . :x6.207.1) (:span 139 205))\n ((:id . :x6.207.2) (:span 109 205)) ((:id . :x6.207.3) (:span 105 205)))\n (:identifiers (:sid . :s6.207) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101947@unknown@formal@none@1@S@It is also worth noting that this portion corresponds to a separate exon in some teleosts (see Discussion).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 10) (:start . 6)\n (:id . 44))\n ((:tag . "JJ") (:stem . "worth") (:form . "worth") (:end . 16) (:start . 11)\n (:id . 45))\n ((:tag . "VBG") (:stem . "note") (:form . "noting") (:end . 23) (:start . 17)\n (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 33) (:start . 29)\n (:id . 48))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 41)\n (:start . 34) (:id . 49))\n ((:tag . "VBZ") (:stem . "correspond") (:form . "corresponds") (:end . 53)\n (:start . 42) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 58) (:start . 57)\n (:id . 52))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 67)\n (:start . 59) (:id . 53))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 72) (:start . 68)\n (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 75) (:start . 73)\n (:id . 55))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 80) (:start . 76)\n (:id . 56))\n ((:tag . "NNS") (:stem . "teleost") (:form . "teleosts") (:end . 89)\n (:start . 81) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n (:id . 58))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 94) (:start . 91)\n (:id . 59))\n ((:tag . "NNP") (:stem . "Discussion") (:form . "Discussion") (:end . 105)\n (:start . 95) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.208) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101948@unknown@formal@none@1@S@The ring finger motif itself is also present in several sea urchin proteins unrelated to RAG1 but significantly similar to diverse proteins associated with immune and developmental systems as well as regulation of transcription.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "ring") (:form . "ring") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 15) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 21) (:start . 16)\n (:id . 45))\n ((:tag . "PRP") (:stem . "itself") (:form . "itself") (:end . 28)\n (:start . 22) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 31) (:start . 29)\n (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 36) (:start . 32)\n (:id . 48))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 44)\n (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n (:id . 50))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 55)\n (:start . 48) (:id . 51))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 59) (:start . 56)\n (:id . 52))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 66)\n (:start . 60) (:id . 53))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 75)\n (:start . 67) (:id . 54))\n ((:tag . "JJ") (:stem . "unrelated") (:form . "unrelated") (:end . 85)\n (:start . 76) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n (:id . 56))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 93) (:start . 89)\n (:id . 57))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 97) (:start . 94)\n (:id . 58))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 111) (:start . 98) (:id . 59))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 119)\n (:start . 112) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 122) (:start . 120)\n (:id . 61))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 130)\n (:start . 123) (:id . 62))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 139)\n (:start . 131) (:id . 63))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 150)\n (:start . 140) (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 155) (:start . 151)\n (:id . 65))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 162)\n (:start . 156) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 166) (:start . 163)\n (:id . 67))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n (:end . 180) (:start . 167) (:id . 68))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 188)\n (:start . 181) (:id . 69))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 191) (:start . 189)\n (:id . 70))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 196) (:start . 192)\n (:id . 71))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 199) (:start . 197)\n (:id . 72))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 210)\n (:start . 200) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 213) (:start . 211)\n (:id . 74))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n (:end . 227) (:start . 214) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 228) (:start . 227)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s6.209) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101950@unknown@formal@none@1@S@Even without the finger, the remaining portions of the sea urchin sequences were significantly similar to the corresponding portions of RAG1.@(((:tag . "RB") (:stem . "even") (:form . "Even") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 23)\n (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n (:id . 47))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 38)\n (:start . 29) (:id . 48))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 47)\n (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n (:id . 51))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 58) (:start . 55)\n (:id . 52))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 65)\n (:start . 59) (:id . 53))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 75)\n (:start . 66) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 80) (:start . 76)\n (:id . 55))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 94) (:start . 81) (:id . 56))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 102)\n (:start . 95) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 105) (:start . 103)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n (:id . 59))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 123)\n (:start . 110) (:id . 60))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 132)\n (:start . 124) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 135) (:start . 133)\n (:id . 62))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 140) (:start . 136)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n (:id . 64)))@@@1@23@((:ncues ((:id . :x6.211.1) (:span 5 12)))\n (:nscopes ((:id . :x6.211.1) (:span 5 23)))\n (:identifiers (:sid . :s6.211) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101951@unknown@formal@none@1@S@BLASTP E-values were 9×10-9, 7×10-5, and 10-3 for the P5_SP, P4_SP, and 768_SP sequences, respectively; because both the low-complexity filter and composition-based statistics were applied, the corresponding E-values were estimated very conservatively.@(((:tag . "NNP") (:stem . "BLASTP") (:form . "BLASTP") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-values") (:end . 15)\n (:start . 7) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 20) (:start . 16)\n (:id . 44))\n ((:tag . "CD") (:stem . "9×10-9") (:form . "9×10-9") (:end . 27)\n (:start . 21) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n (:id . 46))\n ((:tag . "CD") (:stem . "7×10-5") (:form . "7×10-5") (:end . 35)\n (:start . 29) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n (:id . 49))\n ((:tag . "CD") (:stem . "10-3") (:form . "10-3") (:end . 45) (:start . 41)\n (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 49) (:start . 46)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n (:id . 52))\n ((:tag . "NNP") (:stem . "P5_SP") (:form . "P5_SP") (:end . 59) (:start . 54)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n (:id . 54))\n ((:tag . "NNP") (:stem . "P4_SP") (:form . "P4_SP") (:end . 66) (:start . 61)\n (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n (:id . 57))\n ((:tag . "NN") (:stem . "768_sp") (:form . "768_SP") (:end . 78)\n (:start . 72) (:id . 58))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 88)\n (:start . 79) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n (:id . 60))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 102)\n (:start . 90) (:id . 61))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 103) (:start . 102)\n (:id . 62))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 111)\n (:start . 104) (:id . 63))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 116) (:start . 112)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n (:id . 65))\n ((:tag . "NN") (:stem . "low-complexity") (:form . "low-complexity")\n (:end . 135) (:start . 121) (:id . 66))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 142)\n (:start . 136) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 146) (:start . 143)\n (:id . 68))\n ((:tag . "JJ") (:stem . "composition-based") (:form . "composition-based")\n (:end . 164) (:start . 147) (:id . 69))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 175)\n (:start . 165) (:id . 70))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 180) (:start . 176)\n (:id . 71))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 188)\n (:start . 181) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 193) (:start . 190)\n (:id . 74))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 207)\n (:start . 194) (:id . 75))\n ((:tag . "NNS") (:stem . "e-value") (:form . "E-values") (:end . 216)\n (:start . 208) (:id . 76))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 221) (:start . 217)\n (:id . 77))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 231)\n (:start . 222) (:id . 78))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 236) (:start . 232)\n (:id . 79))\n ((:tag . "RB") (:stem . "conservatively") (:form . "conservatively")\n (:end . 251) (:start . 237) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 252) (:start . 251)\n (:id . 81)))@@@1@40@((:identifiers (:sid . :s6.212) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101952@unknown@formal@none@1@S@BLASTP searches of the sea urchin sequences against all GenBank proteins, excluding RAG1, detected only the ring finger domain of the sea urchin sequences.@(((:tag . "NNP") (:stem . "BLASTP") (:form . "BLASTP") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 15)\n (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 33)\n (:start . 27) (:id . 47))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 43)\n (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 51)\n (:start . 44) (:id . 49))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 55) (:start . 52)\n (:id . 50))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 63)\n (:start . 56) (:id . 51))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 72)\n (:start . 64) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n (:id . 53))\n ((:tag . "VBG") (:stem . "exclude") (:form . "excluding") (:end . 83)\n (:start . 74) (:id . 54))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 88) (:start . 84)\n (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n (:id . 56))\n ((:tag . "VBD") (:stem . "detect") (:form . "detected") (:end . 98)\n (:start . 90) (:id . 57))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 103) (:start . 99)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n (:id . 59))\n ((:tag . "NN") (:stem . "ring") (:form . "ring") (:end . 112) (:start . 108)\n (:id . 60))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 119)\n (:start . 113) (:id . 61))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 126)\n (:start . 120) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n (:id . 64))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 137) (:start . 134)\n (:id . 65))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 144)\n (:start . 138) (:id . 66))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 154)\n (:start . 145) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n (:id . 68)))@@@1@27@((:ncues ((:id . :x6.213.1) (:span 74 83)))\n (:nscopes ((:id . :x6.213.1) (:span 74 88)))\n (:identifiers (:sid . :s6.213) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101953@unknown@formal@none@1@S@E-values of these matches were much higher than the E-values of similarities to the RAG1 proteins (SP_768: 0.04 versus 7×10-7; SP_86231: 3·10-4 versus 7×10-7; SP_1226: 10-4 versus 2×10-7; P4_SP: 10 versus 2×10-7; P5_SP does not have ring finger and matches RAG1 only, E-value == 9×10-7).@(((:tag . "NNS") (:stem . "e-value") (:form . "E-values") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 17) (:start . 12)\n (:id . 44))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 25)\n (:start . 18) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 30) (:start . 26)\n (:id . 46))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 35) (:start . 31)\n (:id . 47))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 42) (:start . 36)\n (:id . 48))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 47) (:start . 43)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n (:id . 50))\n ((:tag . "NNS") (:stem . "e-value") (:form . "E-values") (:end . 60)\n (:start . 52) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n (:id . 52))\n ((:tag . "NNS") (:stem . "similarity") (:form . "similarities") (:end . 76)\n (:start . 64) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 79) (:start . 77)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n (:id . 55))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 88) (:start . 84)\n (:id . 56))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 97)\n (:start . 89) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 99) (:start . 98)\n (:id . 58))\n ((:tag . "NNP") (:stem . "SP_768") (:form . "SP_768") (:end . 105)\n (:start . 99) (:id . 59))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 106) (:start . 105)\n (:id . 60))\n ((:tag . "CD") (:stem . "0.04") (:form . "0.04") (:end . 111) (:start . 107)\n (:id . 61))\n ((:tag . "CC") (:stem . "versus") (:form . "versus") (:end . 118)\n (:start . 112) (:id . 62))\n ((:tag . "CD") (:stem . "7×10-7") (:form . "7×10-7") (:end . 125)\n (:start . 119) (:id . 63))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 126) (:start . 125)\n (:id . 64))\n ((:tag . "NNP") (:stem . "SP_86231") (:form . "SP_86231") (:end . 135)\n (:start . 127) (:id . 65))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 136) (:start . 135)\n (:id . 66))\n ((:tag . "CD") (:stem . "3·10-4") (:form . "3·10-4") (:end . 143)\n (:start . 137) (:id . 67))\n ((:tag . "CC") (:stem . "versus") (:form . "versus") (:end . 150)\n (:start . 144) (:id . 68))\n ((:tag . "CD") (:stem . "7×10-7") (:form . "7×10-7") (:end . 157)\n (:start . 151) (:id . 69))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 158) (:start . 157)\n (:id . 70))\n ((:tag . "NNP") (:stem . "SP_1226") (:form . "SP_1226") (:end . 166)\n (:start . 159) (:id . 71))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 167) (:start . 166)\n (:id . 72))\n ((:tag . "CD") (:stem . "10-4") (:form . "10-4") (:end . 172) (:start . 168)\n (:id . 73))\n ((:tag . "CC") (:stem . "versus") (:form . "versus") (:end . 179)\n (:start . 173) (:id . 74))\n ((:tag . "CD") (:stem . "2×10-7") (:form . "2×10-7") (:end . 186)\n (:start . 180) (:id . 75))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 187) (:start . 186)\n (:id . 76))\n ((:tag . "NNP") (:stem . "P4_SP") (:form . "P4_SP") (:end . 193)\n (:start . 188) (:id . 77))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 194) (:start . 193)\n (:id . 78))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 197) (:start . 195)\n (:id . 79))\n ((:tag . "CC") (:stem . "versus") (:form . "versus") (:end . 204)\n (:start . 198) (:id . 80))\n ((:tag . "CD") (:stem . "2×10-7") (:form . "2×10-7") (:end . 211)\n (:start . 205) (:id . 81))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 212) (:start . 211)\n (:id . 82))\n ((:tag . "NNP") (:stem . "P5_SP") (:form . "P5_SP") (:end . 218)\n (:start . 213) (:id . 83))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 223) (:start . 219)\n (:id . 84))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 227) (:start . 224)\n (:id . 85))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 232) (:start . 228)\n (:id . 86))\n ((:tag . "NN") (:stem . "ring") (:form . "ring") (:end . 237) (:start . 233)\n (:id . 87))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 244)\n (:start . 238) (:id . 88))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 248) (:start . 245)\n (:id . 89))\n ((:tag . "VBZ") (:stem . "match") (:form . "matches") (:end . 256)\n (:start . 249) (:id . 90))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 261) (:start . 257)\n (:id . 91))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 266) (:start . 262)\n (:id . 92))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 267) (:start . 266)\n (:id . 93))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-value") (:end . 275)\n (:start . 268) (:id . 94))\n ((:tag . "SYM") (:stem . "==") (:form . "==") (:end . 278) (:start . 276)\n (:id . 95))\n ((:tag . "CD") (:stem . "9×10-7") (:form . "9×10-7") (:end . 285)\n (:start . 279) (:id . 96))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 286) (:start . 285)\n (:id . 97))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 287) (:start . 286)\n (:id . 98)))@@@1@57@((:ncues ((:id . :x6.214.1) (:span 224 227)))\n (:nscopes ((:id . :x6.214.1) (:span 224 244)))\n (:identifiers (:sid . :s6.214) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101954@unknown@formal@none@1@S@Based on the same approach, our study found that the starlet sea anemone and hydra genomes also encode several families of the N-terminal RAG1 domain that appear to be separate from the RAG1 core–like proteins (data not shown).@(((:tag . "VBN") (:stem . "base") (:form . "Based") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 8) (:start . 6)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 17) (:start . 13)\n (:id . 45))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 26)\n (:start . 18) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n (:id . 47))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 31) (:start . 28)\n (:id . 48))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 37) (:start . 32)\n (:id . 49))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 43) (:start . 38)\n (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 48) (:start . 44)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n (:id . 52))\n ((:tag . "NN") (:stem . "starlet") (:form . "starlet") (:end . 60)\n (:start . 53) (:id . 53))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 64) (:start . 61)\n (:id . 54))\n ((:tag . "NN") (:stem . "anemone") (:form . "anemone") (:end . 72)\n (:start . 65) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n (:id . 56))\n ((:tag . "NN") (:stem . "hydra") (:form . "hydra") (:end . 82) (:start . 77)\n (:id . 57))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 90)\n (:start . 83) (:id . 58))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 95) (:start . 91)\n (:id . 59))\n ((:tag . "VBP") (:stem . "encode") (:form . "encode") (:end . 102)\n (:start . 96) (:id . 60))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 110)\n (:start . 103) (:id . 61))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 119)\n (:start . 111) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n (:id . 64))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 137)\n (:start . 127) (:id . 65))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 142) (:start . 138)\n (:id . 66))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 149)\n (:start . 143) (:id . 67))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 154) (:start . 150)\n (:id . 68))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 161)\n (:start . 155) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 164) (:start . 162)\n (:id . 70))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 167) (:start . 165)\n (:id . 71))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 176)\n (:start . 168) (:id . 72))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 181) (:start . 177)\n (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 185) (:start . 182)\n (:id . 74))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 190) (:start . 186)\n (:id . 75))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 200)\n (:start . 191) (:id . 76))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 209)\n (:start . 201) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 211) (:start . 210)\n (:id . 78))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 215)\n (:start . 211) (:id . 79))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 219) (:start . 216)\n (:id . 80))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 225)\n (:start . 220) (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 226) (:start . 225)\n (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n (:id . 83)))@@@1@42@((:hcues ((:id . :x6.215.2) (:span 155 161)))\n (:ncues ((:id . :x6.215.1) (:span 216 219)))\n (:hscopes ((:id . :x6.215.2) (:span 150 209)))\n (:nscopes ((:id . :x6.215.1) (:span 216 226)))\n (:identifiers (:sid . :s6.215) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101955@unknown@formal@none@1@S@The only exception was the already mentioned sea anemone RAG1 core–like sequence.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "only") (:form . "only") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "exception") (:form . "exception") (:end . 18)\n (:start . 9) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "RB") (:stem . "already") (:form . "already") (:end . 34)\n (:start . 27) (:id . 47))\n ((:tag . "VBN") (:stem . "mention") (:form . "mentioned") (:end . 44)\n (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 48) (:start . 45)\n (:id . 49))\n ((:tag . "NN") (:stem . "anemone") (:form . "anemone") (:end . 56)\n (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 61) (:start . 57)\n (:id . 51))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 71)\n (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 80)\n (:start . 72) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.216) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101956@unknown@formal@none@1@S@The approximately 90-aa N-terminus of the latter sequence is the ring finger (E < 10-7, multiple BLASTP matches against known ring fingers in GenBank).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 17) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "90-aa") (:form . "90-aa") (:end . 23) (:start . 18)\n (:id . 44))\n ((:tag . "NN") (:stem . "n-terminus") (:form . "N-terminus") (:end . 34)\n (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n (:id . 47))\n ((:tag . "JJ") (:stem . "latter") (:form . "latter") (:end . 48)\n (:start . 42) (:id . 48))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 57)\n (:start . 49) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 60) (:start . 58)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n (:id . 51))\n ((:tag . "NN") (:stem . "ring") (:form . "ring") (:end . 69) (:start . 65)\n (:id . 52))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 76)\n (:start . 70) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n (:id . 54))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 79) (:start . 78)\n (:id . 55))\n ((:tag . "JJR") (:stem . "<") (:form . "<") (:end . 81) (:start . 80)\n (:id . 56))\n ((:tag . "CD") (:stem . "10-7") (:form . "10-7") (:end . 86) (:start . 82)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n (:id . 58))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 96)\n (:start . 88) (:id . 59))\n ((:tag . "NNP") (:stem . "BLASTP") (:form . "BLASTP") (:end . 103)\n (:start . 97) (:id . 60))\n ((:tag . "VBZ") (:stem . "match") (:form . "matches") (:end . 111)\n (:start . 104) (:id . 61))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 119)\n (:start . 112) (:id . 62))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 125)\n (:start . 120) (:id . 63))\n ((:tag . "NN") (:stem . "ring") (:form . "ring") (:end . 130) (:start . 126)\n (:id . 64))\n ((:tag . "NNS") (:stem . "finger") (:form . "fingers") (:end . 138)\n (:start . 131) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 141) (:start . 139)\n (:id . 66))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 149)\n (:start . 142) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 150) (:start . 149)\n (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s6.217) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101957@unknown@formal@none@1@S@Multiple Alignment of the RAG1 N-Terminal Domain and Sea Urchin Protein Sequences@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "alignment") (:form . "Alignment") (:end . 18)\n (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 30) (:start . 26)\n (:id . 46))\n ((:tag . "NNP") (:stem . "N-Terminal") (:form . "N-Terminal") (:end . 41)\n (:start . 31) (:id . 47))\n ((:tag . "NNP") (:stem . "Domain") (:form . "Domain") (:end . 48)\n (:start . 42) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n (:id . 49))\n ((:tag . "NNP") (:stem . "Sea") (:form . "Sea") (:end . 56) (:start . 53)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Urchin") (:form . "Urchin") (:end . 63)\n (:start . 57) (:id . 51))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 71)\n (:start . 64) (:id . 52))\n ((:tag . "NNP") (:stem . "Sequences") (:form . "Sequences") (:end . 81)\n (:start . 72) (:id . 53)))@@@1@12@((:identifiers (:sid . :s6.218) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5101958@unknown@formal@none@1@S@RAG1_HS, RAG1_PD, RAG1_SS, RAG1_RM, and RAG1_LM mark the human (GenBank accession number NP_000439), lungfish (AAS75810), pig (BAC54968), stripe-sided rhabdornis or Rhabdornis mysticalis bird (AAQ76078), and latimeria (AAS75807) proteins, respectively.@(((:tag . "NNP") (:stem . "RAG1_HS") (:form . "RAG1_HS") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NNP") (:stem . "RAG1_PD") (:form . "RAG1_PD") (:end . 16)\n (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "NNP") (:stem . "RAG1_SS") (:form . "RAG1_SS") (:end . 25)\n (:start . 18) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n (:id . 47))\n ((:tag . "NNP") (:stem . "RAG1_RM") (:form . "RAG1_RM") (:end . 34)\n (:start . 27) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n (:id . 50))\n ((:tag . "NNP") (:stem . "RAG1_LM") (:form . "RAG1_LM") (:end . 47)\n (:start . 40) (:id . 51))\n ((:tag . "VBP") (:stem . "mark") (:form . "mark") (:end . 52) (:start . 48)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n (:id . 53))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 62) (:start . 57)\n (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 64) (:start . 63)\n (:id . 55))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 71)\n (:start . 64) (:id . 56))\n ((:tag . "NN") (:stem . "accession") (:form . "accession") (:end . 81)\n (:start . 72) (:id . 57))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 88)\n (:start . 82) (:id . 58))\n ((:tag . "NNP") (:stem . "NP_000439") (:form . "NP_000439") (:end . 98)\n (:start . 89) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n (:id . 61))\n ((:tag . "NN") (:stem . "lungfish") (:form . "lungfish") (:end . 109)\n (:start . 101) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n (:id . 63))\n ((:tag . "NNP") (:stem . "AAS75810") (:form . "AAS75810") (:end . 119)\n (:start . 111) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 120) (:start . 119)\n (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n (:id . 66))\n ((:tag . "NN") (:stem . "pig") (:form . "pig") (:end . 125) (:start . 122)\n (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 127) (:start . 126)\n (:id . 68))\n ((:tag . "NN") (:stem . "bac54968") (:form . "BAC54968") (:end . 135)\n (:start . 127) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n (:id . 71))\n ((:tag . "JJ") (:stem . "stripe-sided") (:form . "stripe-sided") (:end . 150)\n (:start . 138) (:id . 72))\n ((:tag . "NN") (:stem . "rhabdornis") (:form . "rhabdornis") (:end . 161)\n (:start . 151) (:id . 73))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 164) (:start . 162)\n (:id . 74))\n ((:tag . "NNP") (:stem . "Rhabdornis") (:form . "Rhabdornis") (:end . 175)\n (:start . 165) (:id . 75))\n ((:tag . "PRP$") (:stem . "mysticalis") (:form . "mysticalis") (:end . 186)\n (:start . 176) (:id . 76))\n ((:tag . "NN") (:stem . "bird") (:form . "bird") (:end . 191) (:start . 187)\n (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 193) (:start . 192)\n (:id . 78))\n ((:tag . "NNP") (:stem . "AAQ76078") (:form . "AAQ76078") (:end . 201)\n (:start . 193) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 202) (:start . 201)\n (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 203) (:start . 202)\n (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 207) (:start . 204)\n (:id . 82))\n ((:tag . "NNS") (:stem . "latimeria") (:form . "latimeria") (:end . 217)\n (:start . 208) (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 219) (:start . 218)\n (:id . 84))\n ((:tag . "NN") (:stem . "aas75807") (:form . "AAS75807") (:end . 227)\n (:start . 219) (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 228) (:start . 227)\n (:id . 86))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 237)\n (:start . 229) (:id . 87))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 238) (:start . 237)\n (:id . 88))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 251)\n (:start . 239) (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 252) (:start . 251)\n (:id . 90)))@@@1@49@((:identifiers (:sid . :s6.219) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101960@unknown@formal@none@1@S@Protein sequences assembled from the sea urchin and lancelet WGS Trace Archives are denoted as P4-P5_SP and P1-P5_BF, respectively.@(((:tag . "NN") (:stem . "protein") (:form . "Protein") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 17)\n (:start . 8) (:id . 43))\n ((:tag . "VBN") (:stem . "assemble") (:form . "assembled") (:end . 27)\n (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 32) (:start . 28)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n (:id . 46))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 40) (:start . 37)\n (:id . 47))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 47)\n (:start . 41) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n (:id . 49))\n ((:tag . "VB") (:stem . "lancelet") (:form . "lancelet") (:end . 60)\n (:start . 52) (:id . 50))\n ((:tag . "NNP") (:stem . "WGS") (:form . "WGS") (:end . 64) (:start . 61)\n (:id . 51))\n ((:tag . "NNP") (:stem . "Trace") (:form . "Trace") (:end . 70) (:start . 65)\n (:id . 52))\n ((:tag . "NNPS") (:stem . "Archives") (:form . "Archives") (:end . 79)\n (:start . 71) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 83) (:start . 80)\n (:id . 54))\n ((:tag . "VBN") (:stem . "denote") (:form . "denoted") (:end . 91)\n (:start . 84) (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 94) (:start . 92)\n (:id . 56))\n ((:tag . "NNP") (:stem . "P4-P5_SP") (:form . "P4-P5_SP") (:end . 103)\n (:start . 95) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n (:id . 58))\n ((:tag . "NNP") (:stem . "P1-P5_BF") (:form . "P1-P5_BF") (:end . 116)\n (:start . 108) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n (:id . 60))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 130)\n (:start . 118) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.221) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101961@unknown@formal@none@1@S@Three conserved motifs are underlined and numbered.@(((:tag . "CD") (:stem . "three") (:form . "Three") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 15)\n (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 22)\n (:start . 16) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 26) (:start . 23)\n (:id . 45))\n ((:tag . "VBN") (:stem . "underline") (:form . "underlined") (:end . 37)\n (:start . 27) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n (:id . 47))\n ((:tag . "VBN") (:stem . "number") (:form . "numbered") (:end . 50)\n (:start . 42) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 51) (:start . 50)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s6.222) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101962@unknown@formal@none@1@S@The third conserved motif is known as the ring finger.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 19)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 25) (:start . 20)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 34) (:start . 29)\n (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 37) (:start . 35)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n (:id . 49))\n ((:tag . "NN") (:stem . "ring") (:form . "ring") (:end . 46) (:start . 42)\n (:id . 50))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 53)\n (:start . 47) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 54) (:start . 53)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s6.223) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101963@unknown@formal@none@1@S@Distances from the protein N-termini are indicated by numbers.@(((:tag . "NNS") (:stem . "distance") (:form . "Distances") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 14) (:start . 10)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 44))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 26)\n (:start . 19) (:id . 45))\n ((:tag . "NNP") (:stem . "N-termini") (:form . "N-termini") (:end . 36)\n (:start . 27) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 40) (:start . 37)\n (:id . 47))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 50)\n (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 53) (:start . 51)\n (:id . 49))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 61)\n (:start . 54) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 62) (:start . 61)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s6.224) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101964@unknown@formal@none@1@S@Discussion@(((:tag . "NN") (:stem . "discussion") (:form . "Discussion") (:end . 10)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s6.225) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101965@unknown@formal@none@1@S@The significant similarity between the Transib TPases and RAG1 core, the common structure of the Transib TIRs and RSSs, as well as the similar size of TSDs characterizing transpositions of Transib transposons and transpositions catalyzed by RAG1 and RAG2, directly support the 25-year-old hypothesis of a transposon-related origin of the V(D)J machinery.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 26)\n (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 34)\n (:start . 27) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 46)\n (:start . 39) (:id . 47))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 53) (:start . 47)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n (:id . 49))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 62) (:start . 58)\n (:id . 50))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 67) (:start . 63)\n (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n (:id . 53))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 79)\n (:start . 73) (:id . 54))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 89)\n (:start . 80) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n (:id . 57))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 104)\n (:start . 97) (:id . 58))\n ((:tag . "NNPS") (:stem . "TIR") (:form . "TIRs") (:end . 109) (:start . 105)\n (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n (:id . 60))\n ((:tag . "NNPS") (:stem . "RSS") (:form . "RSSs") (:end . 118) (:start . 114)\n (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n (:id . 62))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 122) (:start . 120)\n (:id . 63))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 127) (:start . 123)\n (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 130) (:start . 128)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n (:id . 66))\n ((:tag . 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(:end . 188) (:start . 187)\n (:id . 75)))@@@1@34@((:hcues ((:id . :x6.228.2) (:span 64 70)) ((:id . :x6.228.3) (:span 55 60)))\n (:ncues ((:id . :x6.228.1) (:span 133 144))\n ((:id . :x6.228.4) (:span 19 21)))\n (:hscopes ((:id . :x6.228.2) (:span 64 182))\n ((:id . :x6.228.3) (:span 55 182)))\n (:nscopes ((:id . :x6.228.1) (:span 133 182))\n ((:id . :x6.228.4) (:span 19 50)))\n (:identifiers (:sid . :s6.228) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101968@unknown@formal@none@1@S@These arguments can now be put to rest.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 15)\n (:start . 6) (:id . 43))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 19) (:start . 16)\n (:id . 44))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "VB") (:stem . 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(:end . 209) (:start . 208)\n (:id . 73)))@@@1@32@((:hcues ((:id . :x6.231.1) (:span 55 61)))\n (:hscopes ((:id . :x6.231.1) (:span 55 208)))\n (:identifiers (:sid . :s6.231) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101971@unknown@formal@none@1@S@Afterwards, the RAG1 genes continued to evolve at a slow and steady pace under stabilizing selection, as indicated by the observed conservation of the RAG1 core (79% identity between sharks and mammals).@(((:tag . "RB") (:stem . "afterwards") (:form . "Afterwards") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 26) (:start . 21)\n (:id . 46))\n ((:tag . 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"37") (:end . 152) (:start . 150)\n (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 153) (:start . 152)\n (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 154) (:start . 153)\n (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 158) (:start . 155)\n (:id . 70))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 163) (:start . 159)\n (:id . 71))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 172)\n (:start . 164) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 175) (:start . 173)\n (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n (:id . 74))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 188)\n (:start . 180) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n (:id . 76))\n ((:tag . "NN") (:stem . "starlet") (:form . "starlet") (:end . 197)\n (:start . 190) (:id . 77))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 201) (:start . 198)\n (:id . 78))\n ((:tag . "NN") (:stem . "anemone") (:form . "anemone") (:end . 209)\n (:start . 202) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 210) (:start . 209)\n (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 214) (:start . 211)\n (:id . 81))\n ((:tag . "NN") (:stem . "hydra") (:form . "hydra") (:end . 220)\n (:start . 215) (:id . 82))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 228)\n (:start . 221) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n (:id . 84)))@@@1@43@((:hcues ((:id . :x6.233.1) (:span 57 65)))\n (:hscopes ((:id . :x6.233.1) (:span 0 228)))\n (:identifiers (:sid . :s6.233) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101973@unknown@formal@none@1@S@Based on the presence of stop codons disrupting some of the RAG1-like sequences, it has been suggested [37] that the sea urchin sequences represent remnants of transposable elements.@(((:tag . "VBN") (:stem . "base") (:form . "Based") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 8) (:start . 6)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 21)\n (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n (:id . 46))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 29) (:start . 25)\n (:id . 47))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 36)\n (:start . 30) (:id . 48))\n ((:tag . "VBG") (:stem . "disrupt") (:form . "disrupting") (:end . 47)\n (:start . 37) (:id . 49))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 52) (:start . 48)\n (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n (:id . 52))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 69)\n (:start . 60) (:id . 53))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 79)\n (:start . 70) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n (:id . 55))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 83) (:start . 81)\n (:id . 56))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 87) (:start . 84)\n (:id . 57))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 92) (:start . 88)\n (:id . 58))\n ((:tag . "VBN") (:stem . "suggest") (:form . "suggested") (:end . 102)\n (:start . 93) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 104) (:start . 103)\n (:id . 60))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 106) (:start . 104)\n (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 107) (:start . 106)\n (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 112) (:start . 108)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n (:id . 64))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 120) (:start . 117)\n (:id . 65))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 127)\n (:start . 121) (:id . 66))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 137)\n (:start . 128) (:id . 67))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 147)\n (:start . 138) (:id . 68))\n ((:tag . "NNS") (:stem . "remnant") (:form . "remnants") (:end . 156)\n (:start . 148) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 159) (:start . 157)\n (:id . 70))\n ((:tag . "JJ") (:stem . "transposable") (:form . "transposable") (:end . 172)\n (:start . 160) (:id . 71))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 181)\n (:start . 173) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n (:id . 73)))@@@1@32@((:hcues ((:id . :x6.234.1) (:span 93 102)))\n (:hscopes ((:id . :x6.234.1) (:span 93 181)))\n (:identifiers (:sid . :s6.234) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101974@unknown@formal@none@1@S@Typically, TPase-coding autonomous DNA transposons are present in only a few complete copies per genome.@(((:tag . "RB") (:stem . "typically") (:form . "Typically") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "JJ") (:stem . "tpase-coding") (:form . "TPase-coding") (:end . 23)\n (:start . 11) (:id . 44))\n ((:tag . "JJ") (:stem . "autonomous") (:form . "autonomous") (:end . 34)\n (:start . 24) (:id . 45))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 38) (:start . 35)\n (:id . 46))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 50)\n (:start . 39) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 54) (:start . 51)\n (:id . 48))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 62)\n (:start . 55) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n (:id . 50))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 70) (:start . 66)\n (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 72) (:start . 71)\n (:id . 52))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 76) (:start . 73)\n (:id . 53))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 85)\n (:start . 77) (:id . 54))\n ((:tag . "NNS") (:stem . "copy") (:form . "copies") (:end . 92) (:start . 86)\n (:id . 55))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 96) (:start . 93)\n (:id . 56))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 103)\n (:start . 97) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s6.235) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101975@unknown@formal@none@1@S@At the same time, sequences homologous to their terminal portions, including specific TIRs, are usually abundant due to the proliferation of nonautonomous DNA transposons fueled by the TPase expressed by the corresponding low-copy autonomous elements.@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 16) (:start . 12)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 46))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 27)\n (:start . 18) (:id . 47))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 38)\n (:start . 28) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n (:id . 49))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 47)\n (:start . 42) (:id . 50))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 56)\n (:start . 48) (:id . 51))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 65)\n (:start . 57) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n (:id . 53))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 76)\n (:start . 67) (:id . 54))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 85)\n (:start . 77) (:id . 55))\n ((:tag . "NNS") (:stem . "tir") (:form . "TIRs") (:end . 90) (:start . 86)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 95) (:start . 92)\n (:id . 58))\n ((:tag . "RB") (:stem . "usually") (:form . "usually") (:end . 103)\n (:start . 96) (:id . 59))\n ((:tag . "JJ") (:stem . "abundant") (:form . "abundant") (:end . 112)\n (:start . 104) (:id . 60))\n ((:tag . "IN") (:stem . "due") (:form . "due") (:end . 116) (:start . 113)\n (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 119) (:start . 117)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n (:id . 63))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n (:end . 137) (:start . 124) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 140) (:start . 138)\n (:id . 65))\n ((:tag . "JJ") (:stem . "nonautonomous") (:form . "nonautonomous")\n (:end . 154) (:start . 141) (:id . 66))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 158) (:start . 155)\n (:id . 67))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 170)\n (:start . 159) (:id . 68))\n ((:tag . "VBN") (:stem . "fuel") (:form . "fueled") (:end . 177)\n (:start . 171) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 180) (:start . 178)\n (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 184) (:start . 181)\n (:id . 71))\n ((:tag . "NN") (:stem . "tpase") (:form . "TPase") (:end . 190)\n (:start . 185) (:id . 72))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 200)\n (:start . 191) (:id . 73))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 203) (:start . 201)\n (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 207) (:start . 204)\n (:id . 75))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 221)\n (:start . 208) (:id . 76))\n ((:tag . "JJ") (:stem . "low-copy") (:form . "low-copy") (:end . 230)\n (:start . 222) (:id . 77))\n ((:tag . "JJ") (:stem . "autonomous") (:form . "autonomous") (:end . 241)\n (:start . 231) (:id . 78))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 250)\n (:start . 242) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 251) (:start . 250)\n (:id . 80)))@@@1@39@((:identifiers (:sid . :s6.236) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101976@unknown@formal@none@1@S@Therefore, even if only 30% of the sea urchin genome has been sequenced to date, it is expected that the regions flanking the TPase portions of potential autonomous elements should be similar to numerous nonautonomous elements.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 18) (:start . 16)\n (:id . 45))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 26) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 27) (:start . 26)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 50))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 38) (:start . 35)\n (:id . 51))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 45)\n (:start . 39) (:id . 52))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 52)\n (:start . 46) (:id . 53))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 56) (:start . 53)\n (:id . 54))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 61) (:start . 57)\n (:id . 55))\n ((:tag . "VBN") (:stem . "sequence") (:form . "sequenced") (:end . 71)\n (:start . 62) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 74) (:start . 72)\n (:id . 57))\n ((:tag . "NN") (:stem . "date") (:form . "date") (:end . 79) (:start . 75)\n (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n (:id . 59))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 83) (:start . 81)\n (:id . 60))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 86) (:start . 84)\n (:id . 61))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 95)\n (:start . 87) (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 100) (:start . 96)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n (:id . 64))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 112)\n (:start . 105) (:id . 65))\n ((:tag . "VBG") (:stem . "flank") (:form . "flanking") (:end . 121)\n (:start . 113) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n (:id . 67))\n ((:tag . "NN") (:stem . "tpase") (:form . "TPase") (:end . 131)\n (:start . 126) (:id . 68))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 140)\n (:start . 132) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 143) (:start . 141)\n (:id . 70))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 153)\n (:start . 144) (:id . 71))\n ((:tag . "JJ") (:stem . "autonomous") (:form . "autonomous") (:end . 164)\n (:start . 154) (:id . 72))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 173)\n (:start . 165) (:id . 73))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 180)\n (:start . 174) (:id . 74))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 183) (:start . 181)\n (:id . 75))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 191)\n (:start . 184) (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 194) (:start . 192)\n (:id . 77))\n ((:tag . "JJ") (:stem . "numerous") (:form . "numerous") (:end . 203)\n (:start . 195) (:id . 78))\n ((:tag . "JJ") (:stem . "nonautonomous") (:form . "nonautonomous")\n (:end . 217) (:start . 204) (:id . 79))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 226)\n (:start . 218) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n (:id . 81)))@@@1@40@((:hcues ((:id . :x6.237.1) (:span 174 180))\n ((:id . :x6.237.2) (:span 87 95)))\n (:hscopes ((:id . :x6.237.1) (:span 174 226))\n ((:id . :x6.237.2) (:span 87 226)))\n (:identifiers (:sid . :s6.237) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101977@unknown@formal@none@1@S@So far, we have found no evidence of such similarities.@(((:tag . "RB") (:stem . "so") (:form . "So") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "far") (:form . "far") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 10) (:start . 8)\n (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 15) (:start . 11)\n (:id . 46))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 21) (:start . 16)\n (:id . 47))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 24) (:start . 22)\n (:id . 48))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 33)\n (:start . 25) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n (:id . 50))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 41) (:start . 37)\n (:id . 51))\n ((:tag . "NNS") (:stem . "similarity") (:form . "similarities") (:end . 54)\n (:start . 42) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 55) (:start . 54)\n (:id . 53)))@@@1@12@((:ncues ((:id . :x6.238.1) (:span 22 24)))\n (:nscopes ((:id . :x6.238.1) (:span 22 54)))\n (:identifiers (:sid . :s6.238) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101978@unknown@formal@none@1@S@Detailed analysis of regions flanking the sea urchin RAG1-like DNA coding sequences revealed a variety of different transposable elements inserted in the proximity of the coding sequences (see Figure 5).@(((:tag . "JJ") (:stem . "detailed") (:form . "Detailed") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 17)\n (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 44))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 28)\n (:start . 21) (:id . 45))\n ((:tag . "VBG") (:stem . "flank") (:form . 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"variety") (:end . 102)\n (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n (:id . 57))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 115)\n (:start . 106) (:id . 58))\n ((:tag . "JJ") (:stem . "transposable") (:form . "transposable") (:end . 128)\n (:start . 116) (:id . 59))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 137)\n (:start . 129) (:id . 60))\n ((:tag . "VBN") (:stem . "insert") (:form . "inserted") (:end . 146)\n (:start . 138) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n (:id . 63))\n ((:tag . "NN") (:stem . "proximity") (:form . "proximity") (:end . 163)\n (:start . 154) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 166) (:start . 164)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 170) (:start . 167)\n (:id . 66))\n ((:tag . "VBG") (:stem . "cod") (:form . "coding") (:end . 177)\n (:start . 171) (:id . 67))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 187)\n (:start . 178) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 189) (:start . 188)\n (:id . 69))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 192) (:start . 189)\n (:id . 70))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 199)\n (:start . 193) (:id . 71))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 201) (:start . 200)\n (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 202) (:start . 201)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s6.239) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101980@unknown@formal@none@1@S@We also could not identify the 5-bp TSDs and TIRs characteristic of the Transib superfamily.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 17) (:start . 14)\n (:id . 45))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 26)\n (:start . 18) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n (:id . 47))\n ((:tag . "JJ") (:stem . "5-bp") (:form . "5-bp") (:end . 35) (:start . 31)\n (:id . 48))\n ((:tag . "NNPS") (:stem . "TSD") (:form . "TSDs") (:end . 40) (:start . 36)\n (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n (:id . 50))\n ((:tag . "NNPS") (:stem . "TIR") (:form . "TIRs") (:end . 49) (:start . 45)\n (:id . 51))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n (:end . 64) (:start . 50) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 79)\n (:start . 72) (:id . 55))\n ((:tag . "NN") (:stem . "superfamily") (:form . "superfamily") (:end . 91)\n (:start . 80) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n (:id . 57)))@@@1@16@((:ncues ((:id . :x6.241.1) (:span 14 17)))\n (:nscopes ((:id . :x6.241.1) (:span 14 91)))\n (:identifiers (:sid . :s6.241) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101981@unknown@formal@none@1@S@Still, given that only one third of the sea urchin genome is currently assembled as a set of contigs longer than several thousand nucleotides (the remaining portion is represented by short WGS sequences), we cannot rule out the possibility that the sea urchin RAG1-like proteins are remnants of an unknown branch of Transib transposons.@(((:tag . "RB") (:stem . "still") (:form . "Still") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 12) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 17) (:start . 13)\n (:id . 45))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 22) (:start . 18)\n (:id . 46))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 26) (:start . 23)\n (:id . 47))\n ((:tag . "NN") (:stem . "third") (:form . "third") (:end . 32) (:start . 27)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 50))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 43) (:start . 40)\n (:id . 51))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 50)\n (:start . 44) (:id . 52))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 57)\n (:start . 51) (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 60) (:start . 58)\n (:id . 54))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 70)\n (:start . 61) (:id . 55))\n ((:tag . "VBN") (:stem . "assemble") (:form . "assembled") (:end . 80)\n (:start . 71) (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 83) (:start . 81)\n (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 85) (:start . 84)\n (:id . 58))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 89) (:start . 86)\n (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n (:id . 60))\n ((:tag . "NNS") (:stem . "contig") (:form . "contigs") (:end . 100)\n (:start . 93) (:id . 61))\n ((:tag . "RBR") (:stem . "longer") (:form . "longer") (:end . 107)\n (:start . 101) (:id . 62))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 112) (:start . 108)\n (:id . 63))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 120)\n (:start . 113) (:id . 64))\n ((:tag . "CD") (:stem . "thousand") (:form . "thousand") (:end . 129)\n (:start . 121) (:id . 65))\n ((:tag . "NNS") (:stem . "nucleotide") (:form . 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"sequences") (:end . 202)\n (:start . 193) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 203) (:start . 202)\n (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 204) (:start . 203)\n (:id . 78))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 207) (:start . 205)\n (:id . 79))\n ((:tag . "JJ") (:stem . "cannot") (:form . "cannot") (:end . 214)\n (:start . 208) (:id . 80))\n ((:tag . "VB") (:stem . "rule") (:form . "rule") (:end . 219) (:start . 215)\n (:id . 81))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 223) (:start . 220)\n (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 227) (:start . 224)\n (:id . 83))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 239)\n (:start . 228) (:id . 84))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 244) (:start . 240)\n (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 248) (:start . 245)\n (:id . 86))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 252) (:start . 249)\n (:id . 87))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 259)\n (:start . 253) (:id . 88))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 269)\n (:start . 260) (:id . 89))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 278)\n (:start . 270) (:id . 90))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 282) (:start . 279)\n (:id . 91))\n ((:tag . "NNS") (:stem . "remnant") (:form . "remnants") (:end . 291)\n (:start . 283) (:id . 92))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 294) (:start . 292)\n (:id . 93))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 297) (:start . 295)\n (:id . 94))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 305)\n (:start . 298) (:id . 95))\n ((:tag . "NN") (:stem . "branch") (:form . "branch") (:end . 312)\n (:start . 306) (:id . 96))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 315) (:start . 313)\n (:id . 97))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 323)\n (:start . 316) (:id . 98))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 335)\n (:start . 324) (:id . 99))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 336) (:start . 335)\n (:id . 100)))@@@1@59@((:hcues ((:id . :x6.242.1) (:span 208 239)))\n (:hscopes ((:id . :x6.242.1) (:span 208 335)))\n (:identifiers (:sid . :s6.242) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101982@unknown@formal@none@1@S@Given that the genomes of lancelet, hydra, and starlet sea anemone are currently available only as unassembled WGS traces, the question whether the corresponding RAG1-like sequences are remnants of transposons or genes/pseudogenes must be left open.@(((:tag . "VBN") (:stem . "give") (:form . "Given") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . 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"anemone") (:form . "anemone") (:end . 66)\n (:start . 59) (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 70) (:start . 67)\n (:id . 55))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 80)\n (:start . 71) (:id . 56))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 90)\n (:start . 81) (:id . 57))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 95) (:start . 91)\n (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 98) (:start . 96)\n (:id . 59))\n ((:tag . "JJ") (:stem . "unassembled") (:form . "unassembled") (:end . 110)\n (:start . 99) (:id . 60))\n ((:tag . "NN") (:stem . "wgs") (:form . "WGS") (:end . 114) (:start . 111)\n (:id . 61))\n ((:tag . "NNS") (:stem . "trace") (:form . "traces") (:end . 121)\n (:start . 115) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n (:id . 64))\n ((:tag . "NN") (:stem . "question") (:form . "question") (:end . 135)\n (:start . 127) (:id . 65))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 143)\n (:start . 136) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 147) (:start . 144)\n (:id . 67))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 161)\n (:start . 148) (:id . 68))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 171)\n (:start . 162) (:id . 69))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 181)\n (:start . 172) (:id . 70))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 185) (:start . 182)\n (:id . 71))\n ((:tag . "NNS") (:stem . "remnant") (:form . "remnants") (:end . 194)\n (:start . 186) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 197) (:start . 195)\n (:id . 73))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 209)\n (:start . 198) (:id . 74))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 212) (:start . 210)\n (:id . 75))\n ((:tag . "NNS") (:stem . "genes/pseudogene") (:form . "genes/pseudogenes")\n (:end . 230) (:start . 213) (:id . 76))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 235) (:start . 231)\n (:id . 77))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 238) (:start . 236)\n (:id . 78))\n ((:tag . "VBN") (:stem . "leave") (:form . "left") (:end . 243)\n (:start . 239) (:id . 79))\n ((:tag . "RP") (:stem . "open") (:form . "open") (:end . 248) (:start . 244)\n (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 249) (:start . 248)\n (:id . 81)))@@@1@40@((:hcues ((:id . :x6.243.1) (:span 136 143))\n ((:id . :x6.243.2) (:span 127 135 231 248)))\n (:hscopes ((:id . :x6.243.1) (:span 136 230))\n ((:id . :x6.243.2) (:span 127 248)))\n (:identifiers (:sid . :s6.243) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101983@unknown@formal@none@1@S@The alternative possibility is that the sea urchin RAG1 core–like sequences represent diverse genes and pseudogenes that belong to a rapidly evolving multigene family.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "alternative") (:form . "alternative") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 27)\n (:start . 16) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 30) (:start . 28)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 35) (:start . 31)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 47))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 43) (:start . 40)\n (:id . 48))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 50)\n (:start . 44) (:id . 49))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 55) (:start . 51)\n (:id . 50))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 65)\n (:start . 56) (:id . 51))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 75)\n (:start . 66) (:id . 52))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 85)\n (:start . 76) (:id . 53))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 93)\n (:start . 86) (:id . 54))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 99) (:start . 94)\n (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n (:id . 56))\n ((:tag . "NNS") (:stem . "pseudogene") (:form . "pseudogenes") (:end . 115)\n (:start . 104) (:id . 57))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 120) (:start . 116)\n (:id . 58))\n ((:tag . "VBP") (:stem . "belong") (:form . "belong") (:end . 127)\n (:start . 121) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 130) (:start . 128)\n (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 132) (:start . 131)\n (:id . 61))\n ((:tag . "RB") (:stem . "rapidly") (:form . "rapidly") (:end . 140)\n (:start . 133) (:id . 62))\n ((:tag . "VBG") (:stem . "evolve") (:form . "evolving") (:end . 149)\n (:start . 141) (:id . 63))\n ((:tag . "JJ") (:stem . "multigene") (:form . "multigene") (:end . 159)\n (:start . 150) (:id . 64))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 166)\n (:start . 160) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x6.244.1) (:span 16 27)))\n (:hscopes ((:id . :x6.244.1) (:span 16 166)))\n (:identifiers (:sid . :s6.244) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101984@unknown@formal@none@1@S@This opens the tantalizing possibility that the RAG1 core was recruited from a Transib TPase in a common ancestor of Bilaterians and Cnidarians, and subsequently lost in nematodes, insects, and sea squirts (see Figure 1).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "open") (:form . "opens") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "VBG") (:stem . "tantalize") (:form . "tantalizing") (:end . 26)\n (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 38)\n (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 43) (:start . 39)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n (:id . 48))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 52) (:start . 48)\n (:id . 49))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 57) (:start . 53)\n (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 61) (:start . 58)\n (:id . 51))\n ((:tag . "VBN") (:stem . "recruit") (:form . "recruited") (:end . 71)\n (:start . 62) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 76) (:start . 72)\n (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 78) (:start . 77)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 86)\n (:start . 79) (:id . 55))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 92) (:start . 87)\n (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 95) (:start . 93)\n (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 97) (:start . 96)\n (:id . 58))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 104)\n (:start . 98) (:id . 59))\n ((:tag . "NN") (:stem . "ancestor") (:form . "ancestor") (:end . 113)\n (:start . 105) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n (:id . 61))\n ((:tag . "NNPS") (:stem . "Bilaterian") (:form . "Bilaterians") (:end . 128)\n (:start . 117) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n (:id . 63))\n ((:tag . "NNPS") (:stem . "Cnidarian") (:form . "Cnidarians") (:end . 143)\n (:start . 133) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 148) (:start . 145)\n (:id . 66))\n ((:tag . "RB") (:stem . "subsequently") (:form . "subsequently") (:end . 161)\n (:start . 149) (:id . 67))\n ((:tag . "VBN") (:stem . "lose") (:form . "lost") (:end . 166) (:start . 162)\n (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 169) (:start . 167)\n (:id . 69))\n ((:tag . "NNS") (:stem . "nematode") (:form . "nematodes") (:end . 179)\n (:start . 170) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 180) (:start . 179)\n (:id . 71))\n ((:tag . "NNS") (:stem . "insect") (:form . "insects") (:end . 188)\n (:start . 181) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 193) (:start . 190)\n (:id . 74))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 197) (:start . 194)\n (:id . 75))\n ((:tag . "NNS") (:stem . "squirt") (:form . "squirts") (:end . 205)\n (:start . 198) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 207) (:start . 206)\n (:id . 77))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 210) (:start . 207)\n (:id . 78))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 217)\n (:start . 211) (:id . 79))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 219) (:start . 218)\n (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 220) (:start . 219)\n (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 221) (:start . 220)\n (:id . 82)))@@@1@41@((:hcues ((:id . :x6.245.1) (:span 27 38)))\n (:hscopes ((:id . :x6.245.1) (:span 27 205)))\n (:identifiers (:sid . :s6.245) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101985@unknown@formal@none@1@S@Furthermore, given that the sea urchin, lancelet, hydra, and starlet sea anemone genomes harbor several highly divergent N-terminal–like domains, separate from the RAG1 core–like sequences and known transposable elements, it is very likely that the N-terminal–like domains of RAG1 also form a multigene family that can be traced back to a common ancestor of Deuterostomes (see Figure 1).@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 43))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n (:id . 46))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 31) (:start . 28)\n (:id . 47))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 38)\n (:start . 32) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n (:id . 49))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 48)\n (:start . 40) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n (:id . 51))\n ((:tag . "NN") (:stem . "hydra") (:form . "hydra") (:end . 55) (:start . 50)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n (:id . 54))\n ((:tag . "NN") (:stem . "starlet") (:form . "starlet") (:end . 68)\n (:start . 61) (:id . 55))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 72) (:start . 69)\n (:id . 56))\n ((:tag . "NN") (:stem . "anemone") (:form . "anemone") (:end . 80)\n (:start . 73) (:id . 57))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 88)\n (:start . 81) (:id . 58))\n ((:tag . "VBP") (:stem . "harbor") (:form . "harbor") (:end . 95)\n (:start . 89) (:id . 59))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 103)\n (:start . 96) (:id . 60))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 110)\n (:start . 104) (:id . 61))\n ((:tag . "JJ") (:stem . "divergent") (:form . "divergent") (:end . 120)\n (:start . 111) (:id . 62))\n ((:tag . "JJ") (:stem . "n-terminal–like") (:form . "N-terminal–like")\n (:end . 136) (:start . 121) (:id . 63))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 144)\n (:start . 137) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n (:id . 65))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 154)\n (:start . 146) (:id . 66))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 159) (:start . 155)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 163) (:start . 160)\n (:id . 68))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 168) (:start . 164)\n (:id . 69))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 178)\n (:start . 169) (:id . 70))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 188)\n (:start . 179) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 192) (:start . 189)\n (:id . 72))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 198)\n (:start . 193) (:id . 73))\n ((:tag . "JJ") (:stem . "transposable") (:form . "transposable") (:end . 211)\n (:start . 199) (:id . 74))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 220)\n (:start . 212) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 221) (:start . 220)\n (:id . 76))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 224) (:start . 222)\n (:id . 77))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 227) (:start . 225)\n (:id . 78))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 232) (:start . 228)\n (:id . 79))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 239)\n (:start . 233) (:id . 80))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 244) (:start . 240)\n (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 248) (:start . 245)\n (:id . 82))\n ((:tag . "JJ") (:stem . "n-terminal–like") (:form . "N-terminal–like")\n (:end . 264) (:start . 249) (:id . 83))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 272)\n (:start . 265) (:id . 84))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 275) (:start . 273)\n (:id . 85))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 280) (:start . 276)\n (:id . 86))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 285) (:start . 281)\n (:id . 87))\n ((:tag . "VBP") (:stem . "form") (:form . "form") (:end . 290) (:start . 286)\n (:id . 88))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 292) (:start . 291)\n (:id . 89))\n ((:tag . "JJ") (:stem . "multigene") (:form . "multigene") (:end . 302)\n (:start . 293) (:id . 90))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 309)\n (:start . 303) (:id . 91))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 314) (:start . 310)\n (:id . 92))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 318) (:start . 315)\n (:id . 93))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 321) (:start . 319)\n (:id . 94))\n ((:tag . "VBN") (:stem . "trace") (:form . "traced") (:end . 328)\n (:start . 322) (:id . 95))\n ((:tag . "RB") (:stem . "back") (:form . "back") (:end . 333) (:start . 329)\n (:id . 96))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 336) (:start . 334)\n (:id . 97))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 338) (:start . 337)\n (:id . 98))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 345)\n (:start . 339) (:id . 99))\n ((:tag . "NN") (:stem . "ancestor") (:form . "ancestor") (:end . 354)\n (:start . 346) (:id . 100))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 357) (:start . 355)\n (:id . 101))\n ((:tag . "NNP") (:stem . "Deuterostome") (:form . "Deuterostomes")\n (:end . 371) (:start . 358) (:id . 102))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 373) (:start . 372)\n (:id . 103))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 376) (:start . 373)\n (:id . 104))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 383)\n (:start . 377) (:id . 105))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 385) (:start . 384)\n (:id . 106))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 386) (:start . 385)\n (:id . 107))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 387) (:start . 386)\n (:id . 108)))@@@1@67@((:hcues ((:id . :x6.246.1) (:span 233 239)))\n (:hscopes ((:id . :x6.246.1) (:span 233 371)))\n (:identifiers (:sid . :s6.246) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101986@unknown@formal@none@1@S@If so, then both N-terminal and core domains of RAG1 might have been derived from different genes present in a common ancestor of Deuterostomes.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 44))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 11) (:start . 7)\n (:id . 45))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 16) (:start . 12)\n (:id . 46))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 27)\n (:start . 17) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 31) (:start . 28)\n (:id . 48))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 36) (:start . 32)\n (:id . 49))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 44)\n (:start . 37) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n (:id . 51))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 52) (:start . 48)\n (:id . 52))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 58) (:start . 53)\n (:id . 53))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 63) (:start . 59)\n (:id . 54))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 68) (:start . 64)\n (:id . 55))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 76)\n (:start . 69) (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 81) (:start . 77)\n (:id . 57))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 91)\n (:start . 82) (:id . 58))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 97) (:start . 92)\n (:id . 59))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 105)\n (:start . 98) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 110) (:start . 109)\n (:id . 62))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 117)\n (:start . 111) (:id . 63))\n ((:tag . "NN") (:stem . "ancestor") (:form . "ancestor") (:end . 126)\n (:start . 118) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n (:id . 65))\n ((:tag . "NNP") (:stem . "Deuterostome") (:form . "Deuterostomes")\n (:end . 143) (:start . 130) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n (:id . 67)))@@@1@26@((:hcues ((:id . :x6.247.1) (:span 53 58)))\n (:hscopes ((:id . :x6.247.1) (:span 12 143)))\n (:identifiers (:sid . :s6.247) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101987@unknown@formal@none@1@S@Alternatively, the N-terminal domain of RAG1 might have been derived from a separate, unknown transposon.@(((:tag . "RB") (:stem . "alternatively") (:form . "Alternatively")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 44))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 29)\n (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 36)\n (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n (:id . 47))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 44) (:start . 40)\n (:id . 48))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 50) (:start . 45)\n (:id . 49))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 55) (:start . 51)\n (:id . 50))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 60) (:start . 56)\n (:id . 51))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 68)\n (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 73) (:start . 69)\n (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 75) (:start . 74)\n (:id . 54))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 84)\n (:start . 76) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n (:id . 56))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 93)\n (:start . 86) (:id . 57))\n ((:tag . "NN") (:stem . "transposon") (:form . "transposon") (:end . 104)\n (:start . 94) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n (:id . 59)))@@@1@18@((:hcues ((:id . :x6.248.1) (:span 45 50)))\n (:hscopes ((:id . :x6.248.1) (:span 15 104)))\n (:identifiers (:sid . :s6.248) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101988@unknown@formal@none@1@S@The N-terminal domain of RAG1 has long been viewed as distinct from the core domain due to its lack of direct involvement in the V(D)J recombination reaction.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 21)\n (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n (:id . 45))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 29) (:start . 25)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 33) (:start . 30)\n (:id . 47))\n ((:tag . "RB") (:stem . "long") (:form . "long") (:end . 38) (:start . 34)\n (:id . 48))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 43) (:start . 39)\n (:id . 49))\n ((:tag . "VBN") (:stem . "view") (:form . "viewed") (:end . 50) (:start . 44)\n (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 53) (:start . 51)\n (:id . 51))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 62)\n (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 67) (:start . 63)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n (:id . 54))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 76) (:start . 72)\n (:id . 55))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 83)\n (:start . 77) (:id . 56))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 87) (:start . 84)\n (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 90) (:start . 88)\n (:id . 58))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 94) (:start . 91)\n (:id . 59))\n ((:tag . "NN") (:stem . "lack") (:form . "lack") (:end . 99) (:start . 95)\n (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n (:id . 61))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 109)\n (:start . 103) (:id . 62))\n ((:tag . "NN") (:stem . "involvement") (:form . "involvement") (:end . 121)\n (:start . 110) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 124) (:start . 122)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 128) (:start . 125)\n (:id . 65))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 134)\n (:start . 129) (:id . 66))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 148) (:start . 135) (:id . 67))\n ((:tag . "NN") (:stem . "reaction") (:form . "reaction") (:end . 157)\n (:start . 149) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n (:id . 69)))@@@1@28@((:ncues ((:id . :x6.249.1) (:span 95 99)))\n (:nscopes ((:id . :x6.249.1) (:span 95 157)))\n (:identifiers (:sid . :s6.249) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101990@unknown@formal@none@1@S@The only notable exception is the anemone RAG1 core–like protein sequence, which is capped by the 90-aa ring finger motif.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "only") (:form . "only") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "notable") (:form . "notable") (:end . 16)\n (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "exception") (:form . "exception") (:end . 26)\n (:start . 17) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 47))\n ((:tag . "NN") (:stem . "anemone") (:form . "anemone") (:end . 41)\n (:start . 34) (:id . 48))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 46) (:start . 42)\n (:id . 49))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 56)\n (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 64)\n (:start . 57) (:id . 51))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 73)\n (:start . 65) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 80) (:start . 75)\n (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 83) (:start . 81)\n (:id . 55))\n ((:tag . "VBN") (:stem . "cap") (:form . "capped") (:end . 90) (:start . 84)\n (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 93) (:start . 91)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n (:id . 58))\n ((:tag . "JJ") (:stem . "90-aa") (:form . "90-aa") (:end . 103) (:start . 98)\n (:id . 59))\n ((:tag . "NN") (:stem . "ring") (:form . "ring") (:end . 108) (:start . 104)\n (:id . 60))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 115)\n (:start . 109) (:id . 61))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 121)\n (:start . 116) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.251) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101991@unknown@formal@none@1@S@Taken together with the fact that only the RAG1 core is significantly similar to Transib TPase, the data suggest that the vertebrate RAG1 represents a fusion of once separate proteins.@(((:tag . "VBN") (:stem . "take") (:form . "Taken") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 14)\n (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 28) (:start . 24)\n (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 38) (:start . 34)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n (:id . 49))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 47) (:start . 43)\n (:id . 50))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 52) (:start . 48)\n (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 55) (:start . 53)\n (:id . 52))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 69) (:start . 56) (:id . 53))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 77)\n (:start . 70) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 80) (:start . 78)\n (:id . 55))\n ((:tag . "VB") (:stem . "transib") (:form . "Transib") (:end . 88)\n (:start . 81) (:id . 56))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 94) (:start . 89)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n (:id . 59))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 104)\n (:start . 100) (:id . 60))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 112)\n (:start . 105) (:id . 61))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 117) (:start . 113)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n (:id . 63))\n ((:tag . "NN") (:stem . "vertebrate") (:form . "vertebrate") (:end . 132)\n (:start . 122) (:id . 64))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 137) (:start . 133)\n (:id . 65))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 148)\n (:start . 138) (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 150) (:start . 149)\n (:id . 67))\n ((:tag . "NN") (:stem . "fusion") (:form . "fusion") (:end . 157)\n (:start . 151) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 160) (:start . 158)\n (:id . 69))\n ((:tag . "RB") (:stem . "once") (:form . "once") (:end . 165) (:start . 161)\n (:id . 70))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 174)\n (:start . 166) (:id . 71))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 183)\n (:start . 175) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n (:id . 73)))@@@1@32@((:hcues ((:id . :x6.252.1) (:span 105 112)))\n (:hscopes ((:id . :x6.252.1) (:span 105 183)))\n (:identifiers (:sid . :s6.252) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101992@unknown@formal@none@1@S@This is consistent with the observation that in teleosts, (bony fish) the RAG1 gene is divided into exons by either one or two introns.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 18)\n (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 23) (:start . 19)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n (:id . 46))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 39)\n (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 44) (:start . 40)\n (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "NNS") (:stem . "teleost") (:form . "teleosts") (:end . 56)\n (:start . 48) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 59) (:start . 58)\n (:id . 52))\n ((:tag . "JJ") (:stem . "bony") (:form . "bony") (:end . 63) (:start . 59)\n (:id . 53))\n ((:tag . "NN") (:stem . "fish") (:form . "fish") (:end . 68) (:start . 64)\n (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n (:id . 56))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 78) (:start . 74)\n (:id . 57))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 83) (:start . 79)\n (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 86) (:start . 84)\n (:id . 59))\n ((:tag . "VBN") (:stem . "divide") (:form . "divided") (:end . 94)\n (:start . 87) (:id . 60))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 99) (:start . 95)\n (:id . 61))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 105)\n (:start . 100) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 108) (:start . 106)\n (:id . 63))\n ((:tag . "DT") (:stem . "either") (:form . "either") (:end . 115)\n (:start . 109) (:id . 64))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 119) (:start . 116)\n (:id . 65))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 122) (:start . 120)\n (:id . 66))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 126) (:start . 123)\n (:id . 67))\n ((:tag . "NNS") (:stem . "intron") (:form . "introns") (:end . 134)\n (:start . 127) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n (:id . 69)))@@@1@28@((:hcues ((:id . :x6.253.1) (:span 109 115 120 122)))\n (:hscopes ((:id . :x6.253.1) (:span 109 126)))\n (:identifiers (:sid . :s6.253) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101993@unknown@formal@none@1@S@As a result, the RAG1 core is split into separate exons at the aa position that corresponds to position 460 in the human RAG1gene [29,34,38].@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 11) (:start . 5)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 46))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 21) (:start . 17)\n (:id . 47))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 26) (:start . 22)\n (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n (:id . 49))\n ((:tag . "VBN") (:stem . "split") (:form . "split") (:end . 35) (:start . 30)\n (:id . 50))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 40) (:start . 36)\n (:id . 51))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 49)\n (:start . 41) (:id . 52))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 55) (:start . 50)\n (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 58) (:start . 56)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n (:id . 55))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 65) (:start . 63)\n (:id . 56))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 74)\n (:start . 66) (:id . 57))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 79) (:start . 75)\n (:id . 58))\n ((:tag . "VBZ") (:stem . "correspond") (:form . "corresponds") (:end . 91)\n (:start . 80) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n (:id . 60))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 103)\n (:start . 95) (:id . 61))\n ((:tag . "CD") (:stem . "460") (:form . "460") (:end . 107) (:start . 104)\n (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 110) (:start . 108)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n (:id . 64))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 120)\n (:start . 115) (:id . 65))\n ((:tag . "NNP") (:stem . "RAG1gene") (:form . "RAG1gene") (:end . 129)\n (:start . 121) (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 131) (:start . 130)\n (:id . 67))\n ((:tag . "CD") (:stem . "29,34,38") (:form . "29,34,38") (:end . 139)\n (:start . 131) (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 140) (:start . 139)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s6.254) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101994@unknown@formal@none@1@S@The core-like sequences encoded by the sea urchin WGS sequence contigs 29068 and 12509 correspond to either the second or third RAG1 exon in teleosts (depending on the number of introns), which is remarkably consistent with the fusion model.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "core-like") (:form . "core-like") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 23)\n (:start . 14) (:id . 44))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 31)\n (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 34) (:start . 32)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n (:id . 47))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 42) (:start . 39)\n (:id . 48))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 49)\n (:start . 43) (:id . 49))\n ((:tag . "VBZ") (:stem . "wgs") (:form . "WGS") (:end . 53) (:start . 50)\n (:id . 50))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 62)\n (:start . 54) (:id . 51))\n ((:tag . "NNS") (:stem . "contig") (:form . "contigs") (:end . 70)\n (:start . 63) (:id . 52))\n ((:tag . "CD") (:stem . "29068") (:form . "29068") (:end . 76) (:start . 71)\n (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n (:id . 54))\n ((:tag . "CD") (:stem . "12509") (:form . "12509") (:end . 86) (:start . 81)\n (:id . 55))\n ((:tag . "VBP") (:stem . "correspond") (:form . "correspond") (:end . 97)\n (:start . 87) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n (:id . 57))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 107)\n (:start . 101) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n (:id . 59))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 118)\n (:start . 112) (:id . 60))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 121) (:start . 119)\n (:id . 61))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 127)\n (:start . 122) (:id . 62))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 132) (:start . 128)\n (:id . 63))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 137) (:start . 133)\n (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 140) (:start . 138)\n (:id . 65))\n ((:tag . "NNS") (:stem . "teleost") (:form . "teleosts") (:end . 149)\n (:start . 141) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 151) (:start . 150)\n (:id . 67))\n ((:tag . "VBG") (:stem . "depend") (:form . "depending") (:end . 160)\n (:start . 151) (:id . 68))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 163) (:start . 161)\n (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 167) (:start . 164)\n (:id . 70))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 174)\n (:start . 168) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 177) (:start . 175)\n (:id . 72))\n ((:tag . "NNS") (:stem . "intron") (:form . "introns") (:end . 185)\n (:start . 178) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 186) (:start . 185)\n (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 187) (:start . 186)\n (:id . 75))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 193)\n (:start . 188) (:id . 76))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 196) (:start . 194)\n (:id . 77))\n ((:tag . "RB") (:stem . "remarkably") (:form . "remarkably") (:end . 207)\n (:start . 197) (:id . 78))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 218)\n (:start . 208) (:id . 79))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 223) (:start . 219)\n (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 227) (:start . 224)\n (:id . 81))\n ((:tag . "NN") (:stem . "fusion") (:form . "fusion") (:end . 234)\n (:start . 228) (:id . 82))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 240)\n (:start . 235) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 241) (:start . 240)\n (:id . 84)))@@@1@43@((:hcues ((:id . :x6.255.1) (:span 101 107 119 121)))\n (:hscopes ((:id . :x6.255.1) (:span 101 127)))\n (:identifiers (:sid . :s6.255) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101995@unknown@formal@none@1@S@The same model predicts that the N-terminal domain of RAG1 could also be assembled from two separate domains based on the presence of the second intron in some teleosts, splitting the N-terminal domain into the 102-aa N-terminal subdomain and the rest [34].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "predict") (:form . "predicts") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n (:id . 47))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 43)\n (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 50)\n (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n (:id . 50))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 58) (:start . 54)\n (:id . 51))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 64) (:start . 59)\n (:id . 52))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 69) (:start . 65)\n (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 72) (:start . 70)\n (:id . 54))\n ((:tag . "VBN") (:stem . "assemble") (:form . "assembled") (:end . 82)\n (:start . 73) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 87) (:start . 83)\n (:id . 56))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 91) (:start . 88)\n (:id . 57))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 100)\n (:start . 92) (:id . 58))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 108)\n (:start . 101) (:id . 59))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 114)\n (:start . 109) (:id . 60))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 117) (:start . 115)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n (:id . 62))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 130)\n (:start . 122) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 133) (:start . 131)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n (:id . 65))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 144)\n (:start . 138) (:id . 66))\n ((:tag . "NN") (:stem . "intron") (:form . "intron") (:end . 151)\n (:start . 145) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 154) (:start . 152)\n (:id . 68))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 159) (:start . 155)\n (:id . 69))\n ((:tag . "NNS") (:stem . "teleost") (:form . "teleosts") (:end . 168)\n (:start . 160) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 169) (:start . 168)\n (:id . 71))\n ((:tag . "VBG") (:stem . "split") (:form . "splitting") (:end . 179)\n (:start . 170) (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 183) (:start . 180)\n (:id . 73))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 194)\n (:start . 184) (:id . 74))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 201)\n (:start . 195) (:id . 75))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 206) (:start . 202)\n (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 210) (:start . 207)\n (:id . 77))\n ((:tag . "JJ") (:stem . "102-aa") (:form . "102-aa") (:end . 217)\n (:start . 211) (:id . 78))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 228)\n (:start . 218) (:id . 79))\n ((:tag . "NN") (:stem . "subdomain") (:form . "subdomain") (:end . 238)\n (:start . 229) (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 242) (:start . 239)\n (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 246) (:start . 243)\n (:id . 82))\n ((:tag . "NN") (:stem . "rest") (:form . "rest") (:end . 251) (:start . 247)\n (:id . 83))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 253) (:start . 252)\n (:id . 84))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 255) (:start . 253)\n (:id . 85))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 256) (:start . 255)\n (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 257) (:start . 256)\n (:id . 87)))@@@1@46@((:hcues ((:id . :x6.256.1) (:span 59 64)))\n (:hscopes ((:id . :x6.256.1) (:span 29 251)))\n (:identifiers (:sid . :s6.256) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101996@unknown@formal@none@1@S@As indicated above, this subdomain, corresponding to the first exon in the genes split by two introns, appears to be missing in the sea urchin, lancelet, hydra, and starlet sea anemone N-terminal–like proteins.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 24) (:start . 20)\n (:id . 46))\n ((:tag . "NN") (:stem . "subdomain") (:form . "subdomain") (:end . 34)\n (:start . 25) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n (:id . 48))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 49)\n (:start . 36) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n (:id . 51))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 62) (:start . 57)\n (:id . 52))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 67) (:start . 63)\n (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 70) (:start . 68)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n (:id . 55))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 80) (:start . 75)\n (:id . 56))\n ((:tag . "VBN") (:stem . "split") (:form . "split") (:end . 86) (:start . 81)\n (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 89) (:start . 87)\n (:id . 58))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 93) (:start . 90)\n (:id . 59))\n ((:tag . "NNS") (:stem . "intron") (:form . "introns") (:end . 101)\n (:start . 94) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n (:id . 61))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 110)\n (:start . 103) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 113) (:start . 111)\n (:id . 63))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 116) (:start . 114)\n (:id . 64))\n ((:tag . "VBG") (:stem . "miss") (:form . "missing") (:end . 124)\n (:start . 117) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 127) (:start . 125)\n (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n (:id . 67))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 135) (:start . 132)\n (:id . 68))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 142)\n (:start . 136) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n (:id . 70))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 152)\n (:start . 144) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n (:id . 72))\n ((:tag . "NN") (:stem . "hydra") (:form . "hydra") (:end . 159)\n (:start . 154) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 164) (:start . 161)\n (:id . 75))\n ((:tag . "NN") (:stem . "starlet") (:form . "starlet") (:end . 172)\n (:start . 165) (:id . 76))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 176) (:start . 173)\n (:id . 77))\n ((:tag . "NN") (:stem . "anemone") (:form . "anemone") (:end . 184)\n (:start . 177) (:id . 78))\n ((:tag . "JJ") (:stem . "n-terminal–like") (:form . "N-terminal–like")\n (:end . 200) (:start . 185) (:id . 79))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 209)\n (:start . 201) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 210) (:start . 209)\n (:id . 81)))@@@1@40@((:hcues ((:id . :x6.257.1) (:span 103 110)))\n (:hscopes ((:id . :x6.257.1) (:span 20 209)))\n (:identifiers (:sid . :s6.257) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101997@unknown@formal@none@1@S@It may be encoded by a separate exon that is difficult to detect given its short length and the high level of sequence divergence between these species and vertebrates, or it might have been added in vertebrates.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 9) (:start . 7)\n (:id . 44))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 17)\n (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 20) (:start . 18)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n (:id . 47))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 31)\n (:start . 23) (:id . 48))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 36) (:start . 32)\n (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 41) (:start . 37)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 44) (:start . 42)\n (:id . 51))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 54)\n (:start . 45) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 57) (:start . 55)\n (:id . 53))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 64)\n (:start . 58) (:id . 54))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 70) (:start . 65)\n (:id . 55))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 74) (:start . 71)\n (:id . 56))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 80) (:start . 75)\n (:id . 57))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 87)\n (:start . 81) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n (:id . 60))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 100) (:start . 96)\n (:id . 61))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 106)\n (:start . 101) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 109) (:start . 107)\n (:id . 63))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 118)\n (:start . 110) (:id . 64))\n ((:tag . "NN") (:stem . "divergence") (:form . "divergence") (:end . 129)\n (:start . 119) (:id . 65))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 137)\n (:start . 130) (:id . 66))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 143)\n (:start . 138) (:id . 67))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 151)\n (:start . 144) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 155) (:start . 152)\n (:id . 69))\n ((:tag . "NNS") (:stem . "vertebrate") (:form . "vertebrates") (:end . 167)\n (:start . 156) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 168) (:start . 167)\n (:id . 71))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 171) (:start . 169)\n (:id . 72))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 174) (:start . 172)\n (:id . 73))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 180)\n (:start . 175) (:id . 74))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 185) (:start . 181)\n (:id . 75))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 190) (:start . 186)\n (:id . 76))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 196) (:start . 191)\n (:id . 77))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 199) (:start . 197)\n (:id . 78))\n ((:tag . "NNS") (:stem . "vertebrate") (:form . "vertebrates") (:end . 211)\n (:start . 200) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n (:id . 80)))@@@1@39@((:hcues ((:id . :x6.258.1) (:span 175 180))\n ((:id . :x6.258.3) (:span 169 171)) ((:id . :x6.258.2) (:span 3 6)))\n (:hscopes ((:id . :x6.258.1) (:span 172 211))\n ((:id . :x6.258.3) (:span 0 167)) ((:id . :x6.258.2) (:span 0 211)))\n (:identifiers (:sid . :s6.258) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101998@unknown@formal@none@1@S@Similarly, the RAG1 core–like protein in the sea urchin genome is shorter in its N-terminal part than the core domain in vertebrates and the corresponding Transib TPase.@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 19) (:start . 15)\n (:id . 45))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 29)\n (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 37)\n (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n (:id . 49))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 48) (:start . 45)\n (:id . 50))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 55)\n (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 62)\n (:start . 56) (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 65) (:start . 63)\n (:id . 53))\n ((:tag . "JJR") (:stem . "short") (:form . "shorter") (:end . 73)\n (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n (:id . 55))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 80) (:start . 77)\n (:id . 56))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 91)\n (:start . 81) (:id . 57))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 96) (:start . 92)\n (:id . 58))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 101) (:start . 97)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n (:id . 60))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 110) (:start . 106)\n (:id . 61))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 117)\n (:start . 111) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 120) (:start . 118)\n (:id . 63))\n ((:tag . "NNS") (:stem . "vertebrate") (:form . "vertebrates") (:end . 132)\n (:start . 121) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 136) (:start . 133)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n (:id . 66))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 154)\n (:start . 141) (:id . 67))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 162)\n (:start . 155) (:id . 68))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 168)\n (:start . 163) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s6.259) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102000@unknown@formal@none@1@S@It is currently believed that both RAG1 and RAG2 proteins were originally encoded by the same transposon recruited in a common ancestor of jawed vertebrates [3,12,13,16].@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 15)\n (:start . 6) (:id . 44))\n ((:tag . "VBN") (:stem . "believe") (:form . "believed") (:end . 24)\n (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 29) (:start . 25)\n (:id . 46))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 34) (:start . 30)\n (:id . 47))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 39) (:start . 35)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n (:id . 49))\n ((:tag . "NN") (:stem . "rag2") (:form . "RAG2") (:end . 48) (:start . 44)\n (:id . 50))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 57)\n (:start . 49) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 62) (:start . 58)\n (:id . 52))\n ((:tag . "RB") (:stem . "originally") (:form . "originally") (:end . 73)\n (:start . 63) (:id . 53))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 81)\n (:start . 74) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 84) (:start . 82)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n (:id . 56))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 93) (:start . 89)\n (:id . 57))\n ((:tag . "NN") (:stem . "transposon") (:form . "transposon") (:end . 104)\n (:start . 94) (:id . 58))\n ((:tag . "VBN") (:stem . "recruit") (:form . "recruited") (:end . 114)\n (:start . 105) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 117) (:start . 115)\n (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 119) (:start . 118)\n (:id . 61))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 126)\n (:start . 120) (:id . 62))\n ((:tag . "NN") (:stem . "ancestor") (:form . "ancestor") (:end . 135)\n (:start . 127) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n (:id . 64))\n ((:tag . "VBN") (:stem . "jaw") (:form . "jawed") (:end . 144) (:start . 139)\n (:id . 65))\n ((:tag . "NNS") (:stem . "vertebrate") (:form . "vertebrates") (:end . 156)\n (:start . 145) (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 158) (:start . 157)\n (:id . 67))\n ((:tag . "CD") (:stem . "3,12,13,16") (:form . "3,12,13,16") (:end . 168)\n (:start . 158) (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 169) (:start . 168)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x6.261.1) (:span 16 24)))\n (:hscopes ((:id . :x6.261.1) (:span 16 156)))\n (:identifiers (:sid . :s6.261) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102001@unknown@formal@none@1@S@However, none of the Transib transposons identified so far encode any proteins other than the Transib/RAG TPase.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "none") (:form . "none") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 28)\n (:start . 21) (:id . 47))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 40)\n (:start . 29) (:id . 48))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 51)\n (:start . 41) (:id . 49))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 54) (:start . 52)\n (:id . 50))\n ((:tag . "RB") (:stem . "far") (:form . "far") (:end . 58) (:start . 55)\n (:id . 51))\n ((:tag . "VB") (:stem . "encode") (:form . "encode") (:end . 65)\n (:start . 59) (:id . 52))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 69) (:start . 66)\n (:id . 53))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 78)\n (:start . 70) (:id . 54))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 84) (:start . 79)\n (:id . 55))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 89) (:start . 85)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n (:id . 57))\n ((:tag . "NNP") (:stem . "Transib/RAG") (:form . "Transib/RAG") (:end . 105)\n (:start . 94) (:id . 58))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 111)\n (:start . 106) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n (:id . 60)))@@@1@19@((:ncues ((:id . :x6.262.1) (:span 9 13)))\n (:nscopes ((:id . :x6.262.1) (:span 9 111)))\n (:identifiers (:sid . :s6.262) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102002@unknown@formal@none@1@S@Also, we could not find any RAG2-like sequences in the recently sequenced sea urchin, lancelet, hydra, and sea anemone genomes, which encode RAG1-like sequences.@(((:tag . "RB") (:stem . "also") (:form . "Also") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n (:id . 44))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 14) (:start . 9)\n (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 18) (:start . 15)\n (:id . 46))\n ((:tag . "VB") (:stem . "find") (:form . "find") (:end . 23) (:start . 19)\n (:id . 47))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 27) (:start . 24)\n (:id . 48))\n ((:tag . "JJ") (:stem . "rag2-like") (:form . "RAG2-like") (:end . 37)\n (:start . 28) (:id . 49))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 47)\n (:start . 38) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n (:id . 52))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 63)\n (:start . 55) (:id . 53))\n ((:tag . "VBN") (:stem . "sequence") (:form . "sequenced") (:end . 73)\n (:start . 64) (:id . 54))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 77) (:start . 74)\n (:id . 55))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 84)\n (:start . 78) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n (:id . 57))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 94)\n (:start . 86) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n (:id . 59))\n ((:tag . "NN") (:stem . "hydra") (:form . "hydra") (:end . 101) (:start . 96)\n (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n (:id . 62))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 110) (:start . 107)\n (:id . 63))\n ((:tag . "NN") (:stem . "anemone") (:form . "anemone") (:end . 118)\n (:start . 111) (:id . 64))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 126)\n (:start . 119) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n (:id . 66))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 133)\n (:start . 128) (:id . 67))\n ((:tag . "VBP") (:stem . "encode") (:form . "encode") (:end . 140)\n (:start . 134) (:id . 68))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 150)\n (:start . 141) (:id . 69))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 160)\n (:start . 151) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n (:id . 71)))@@@1@30@((:ncues ((:id . :x6.263.1) (:span 15 18)))\n (:nscopes ((:id . :x6.263.1) (:span 15 160)))\n (:identifiers (:sid . :s6.263) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102003@unknown@formal@none@1@S@Autonomous DNA transposons from the MuDR, Harbinger, and En/Spm superfamilies are each known to encode a second regulatory protein [23,24], whereas some transposons from these superfamilies encode the TPase only.@(((:tag . "JJ") (:stem . "autonomous") (:form . "Autonomous") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 14) (:start . 11)\n (:id . 43))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 26)\n (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 31) (:start . 27)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n (:id . 46))\n ((:tag . "NNP") (:stem . "MuDR") (:form . "MuDR") (:end . 40) (:start . 36)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Harbinger") (:form . "Harbinger") (:end . 51)\n (:start . 42) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n (:id . 51))\n ((:tag . "NNP") (:stem . "En/Spm") (:form . "En/Spm") (:end . 63)\n (:start . 57) (:id . 52))\n ((:tag . "NNS") (:stem . "superfamily") (:form . "superfamilies") (:end . 77)\n (:start . 64) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 81) (:start . 78)\n (:id . 54))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 86) (:start . 82)\n (:id . 55))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 92) (:start . 87)\n (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 95) (:start . 93)\n (:id . 57))\n ((:tag . "VB") (:stem . "encode") (:form . "encode") (:end . 102)\n (:start . 96) (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 104) (:start . 103)\n (:id . 59))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 111)\n (:start . 105) (:id . 60))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 122)\n (:start . 112) (:id . 61))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 130)\n (:start . 123) (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 132) (:start . 131)\n (:id . 63))\n ((:tag . "CD") (:stem . "23,24") (:form . "23,24") (:end . 137)\n (:start . 132) (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 138) (:start . 137)\n (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n (:id . 66))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 147)\n (:start . 140) (:id . 67))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 152) (:start . 148)\n (:id . 68))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 164)\n (:start . 153) (:id . 69))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 169) (:start . 165)\n (:id . 70))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 175)\n (:start . 170) (:id . 71))\n ((:tag . "NNS") (:stem . "superfamily") (:form . "superfamilies")\n (:end . 189) (:start . 176) (:id . 72))\n ((:tag . "VBP") (:stem . "encode") (:form . "encode") (:end . 196)\n (:start . 190) (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 200) (:start . 197)\n (:id . 74))\n ((:tag . "NN") (:stem . "tpase") (:form . "TPase") (:end . 206)\n (:start . 201) (:id . 75))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 211) (:start . 207)\n (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s6.264) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102004@unknown@formal@none@1@S@Therefore, it is in principle possible that an ancient vertebrate Transib that was a direct ancestor of the RAG1 core also encoded a second protein, the direct ancestor of RAG2.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 19) (:start . 17)\n (:id . 46))\n ((:tag . "NN") (:stem . "principle") (:form . "principle") (:end . 29)\n (:start . 20) (:id . 47))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 38)\n (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 43) (:start . 39)\n (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 46) (:start . 44)\n (:id . 50))\n ((:tag . "JJ") (:stem . "ancient") (:form . "ancient") (:end . 54)\n (:start . 47) (:id . 51))\n ((:tag . "NN") (:stem . "vertebrate") (:form . "vertebrate") (:end . 65)\n (:start . 55) (:id . 52))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 73)\n (:start . 66) (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 78) (:start . 74)\n (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 82) (:start . 79)\n (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 84) (:start . 83)\n (:id . 56))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 91)\n (:start . 85) (:id . 57))\n ((:tag . "NN") (:stem . "ancestor") (:form . "ancestor") (:end . 100)\n (:start . 92) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n (:id . 60))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 112) (:start . 108)\n (:id . 61))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 117) (:start . 113)\n (:id . 62))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 122) (:start . 118)\n (:id . 63))\n ((:tag . "VBD") (:stem . "encode") (:form . "encoded") (:end . 130)\n (:start . 123) (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 132) (:start . 131)\n (:id . 65))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 139)\n (:start . 133) (:id . 66))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 147)\n (:start . 140) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n (:id . 69))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 159)\n (:start . 153) (:id . 70))\n ((:tag . "NN") (:stem . "ancestor") (:form . "ancestor") (:end . 168)\n (:start . 160) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 171) (:start . 169)\n (:id . 72))\n ((:tag . "NN") (:stem . "rag2") (:form . "RAG2") (:end . 176) (:start . 172)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n (:id . 74)))@@@1@33@((:hcues ((:id . :x6.265.1) (:span 30 38)))\n (:hscopes ((:id . :x6.265.1) (:span 30 176)))\n (:identifiers (:sid . :s6.265) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102005@unknown@formal@none@1@S@Nevertheless, the apparent lack of RAG2-like proteins in the sequenced portion of the sea urchin, lancelet, hydra, and sea anemone genomes, as well as in Transib transposons suggests that RAG2 was introduced in a separate event in jawless vertebrates.@(((:tag . "RB") (:stem . "nevertheless") (:form . "Nevertheless") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "JJ") (:stem . "apparent") (:form . "apparent") (:end . 26)\n (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "lack") (:form . "lack") (:end . 31) (:start . 27)\n (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n (:id . 47))\n ((:tag . "JJ") (:stem . "rag2-like") (:form . "RAG2-like") (:end . 44)\n (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 53)\n (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n (:id . 51))\n ((:tag . "VBN") (:stem . "sequence") (:form . "sequenced") (:end . 70)\n (:start . 61) (:id . 52))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 78)\n (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n (:id . 55))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 89) (:start . 86)\n (:id . 56))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 96)\n (:start . 90) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n (:id . 58))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 106)\n (:start . 98) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n (:id . 60))\n ((:tag . "NN") (:stem . "hydra") (:form . "hydra") (:end . 113)\n (:start . 108) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n (:id . 63))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 122) (:start . 119)\n (:id . 64))\n ((:tag . "NN") (:stem . "anemone") (:form . "anemone") (:end . 130)\n (:start . 123) (:id . 65))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 138)\n (:start . 131) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n (:id . 67))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 142) (:start . 140)\n (:id . 68))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 147) (:start . 143)\n (:id . 69))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 150) (:start . 148)\n (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 153) (:start . 151)\n (:id . 71))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 161)\n (:start . 154) (:id . 72))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 173)\n (:start . 162) (:id . 73))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 182)\n (:start . 174) (:id . 74))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 187) (:start . 183)\n (:id . 75))\n ((:tag . "NN") (:stem . "rag2") (:form . "RAG2") (:end . 192) (:start . 188)\n (:id . 76))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 196) (:start . 193)\n (:id . 77))\n ((:tag . "VBN") (:stem . "introduce") (:form . "introduced") (:end . 207)\n (:start . 197) (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 210) (:start . 208)\n (:id . 79))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 212) (:start . 211)\n (:id . 80))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 221)\n (:start . 213) (:id . 81))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 227)\n (:start . 222) (:id . 82))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 230) (:start . 228)\n (:id . 83))\n ((:tag . "JJ") (:stem . "jawless") (:form . "jawless") (:end . 238)\n (:start . 231) (:id . 84))\n ((:tag . "NNS") (:stem . "vertebrate") (:form . "vertebrates") (:end . 250)\n (:start . 239) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 251) (:start . 250)\n (:id . 86)))@@@1@45@((:hcues ((:id . :x6.266.1) (:span 174 182))\n ((:id . :x6.266.3) (:span 18 26)))\n (:ncues ((:id . :x6.266.2) (:span 27 31)))\n (:hscopes ((:id . :x6.266.1) (:span 174 250))\n ((:id . :x6.266.3) (:span 18 173)))\n (:nscopes ((:id . :x6.266.2) (:span 27 173)))\n (:identifiers (:sid . :s6.266) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102006@unknown@formal@none@1@S@However, given the low 30% identity between the RAG1 and sea urchin/lancelet/sea squirt RAG1-like proteins, we cannot exclude the possibility that the ancestral RAG2 protein went through a period of strong diversification driven by positive selection, and it can no longer be identified by sequence comparisons but may still be present in invertebrates.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 22) (:start . 19)\n (:id . 46))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 25) (:start . 23)\n (:id . 47))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 26) (:start . 25)\n (:id . 48))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 35)\n (:start . 27) (:id . 49))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 43)\n (:start . 36) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n (:id . 51))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 52) (:start . 48)\n (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n (:id . 53))\n ((:tag . "NN") (:stem . "sea") (:form . 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(:end . 353) (:start . 352)\n (:id . 99)))@@@1@58@((:hcues ((:id . :x6.267.1) (:span 315 318))\n ((:id . :x6.267.3) (:span 111 141)))\n (:ncues ((:id . :x6.267.2) (:span 263 272)))\n (:hscopes ((:id . :x6.267.1) (:span 315 352))\n ((:id . :x6.267.3) (:span 111 352)))\n (:nscopes ((:id . :x6.267.2) (:span 263 310)))\n (:identifiers (:sid . :s6.267) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102007@unknown@formal@none@1@S@In any case, the origin of the V(D)J recombination system in jawless vertebrates appears to be a culmination of earlier evolutionary processes rather than an isolated event associated with insertion of a single transposon.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . 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"to") (:form . "to") (:end . 241) (:start . 239)\n (:id . 96))\n ((:tag . "JJ") (:stem . "insufficient") (:form . "insufficient") (:end . 254)\n (:start . 242) (:id . 97))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 259)\n (:start . 255) (:id . 98))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 260) (:start . 259)\n (:id . 99)))@@@1@58@((:identifiers (:sid . :s6.271) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102011@unknown@formal@none@1@S@Interestingly, only two cysteines of the zinc finger B (ZFB) C2H2 motif in RAG1 (residues 695–761) involved in its binding to RAG2 [30,31] are perfectly conserved in the Transib TPases (motif 7; see Figures 3 and Figure S3).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 43))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "NNS") (:stem . "cysteine") (:form . "cysteines") (:end . 33)\n (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n (:id . 48))\n ((:tag . "NN") (:stem . "zinc") (:form . "zinc") (:end . 45) (:start . 41)\n (:id . 49))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 52)\n (:start . 46) (:id . 50))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 54) (:start . 53)\n (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n (:id . 52))\n ((:tag . "NNP") (:stem . "ZFB") (:form . "ZFB") (:end . 59) (:start . 56)\n (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 60) (:start . 59)\n (:id . 54))\n ((:tag . "NN") (:stem . "c2h2") (:form . "C2H2") (:end . 65) (:start . 61)\n (:id . 55))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 71) (:start . 66)\n (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n (:id . 57))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 79) (:start . 75)\n (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 81) (:start . 80)\n (:id . 59))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 89)\n (:start . 81) (:id . 60))\n ((:tag . "CD") (:stem . "695–761") (:form . "695–761") (:end . 97)\n (:start . 90) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n (:id . 62))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 107)\n (:start . 99) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 110) (:start . 108)\n (:id . 64))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 114) (:start . 111)\n (:id . 65))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 122)\n (:start . 115) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 125) (:start . 123)\n (:id . 67))\n ((:tag . "NN") (:stem . "rag2") (:form . "RAG2") (:end . 130) (:start . 126)\n (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 132) (:start . 131)\n (:id . 69))\n ((:tag . "CD") (:stem . "30,31") (:form . "30,31") (:end . 137)\n (:start . 132) (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 138) (:start . 137)\n (:id . 71))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 142) (:start . 139)\n (:id . 72))\n ((:tag . "RB") (:stem . "perfectly") (:form . "perfectly") (:end . 152)\n (:start . 143) (:id . 73))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 162)\n (:start . 153) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 165) (:start . 163)\n (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 169) (:start . 166)\n (:id . 76))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 177)\n (:start . 170) (:id . 77))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 184)\n (:start . 178) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 186) (:start . 185)\n (:id . 79))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 191)\n (:start . 186) (:id . 80))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 193) (:start . 192)\n (:id . 81))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 194) (:start . 193)\n (:id . 82))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 198) (:start . 195)\n (:id . 83))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 206)\n (:start . 199) (:id . 84))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 208) (:start . 207)\n (:id . 85))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 212) (:start . 209)\n (:id . 86))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 219)\n (:start . 213) (:id . 87))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 222) (:start . 220)\n (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 223) (:start . 222)\n (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 224) (:start . 223)\n (:id . 90)))@@@1@49@((:identifiers (:sid . :s6.272) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102012@unknown@formal@none@1@S@The remaining portion of the ZFB motif was probably lost in TPases of insect Transib transposons, which do not encode RAG2-like proteins.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 21)\n (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "NNP") (:stem . "ZFB") (:form . "ZFB") (:end . 32) (:start . 29)\n (:id . 47))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 38) (:start . 33)\n (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 42) (:start . 39)\n (:id . 49))\n ((:tag . "RB") (:stem . "probably") (:form . "probably") (:end . 51)\n (:start . 43) (:id . 50))\n ((:tag . "VBN") (:stem . "lose") (:form . "lost") (:end . 56) (:start . 52)\n (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n (:id . 52))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 66) (:start . 60)\n (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n (:id . 54))\n ((:tag . "NN") (:stem . "insect") (:form . "insect") (:end . 76)\n (:start . 70) (:id . 55))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 84)\n (:start . 77) (:id . 56))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 96)\n (:start . 85) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n (:id . 58))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 103)\n (:start . 98) (:id . 59))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 106) (:start . 104)\n (:id . 60))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 110) (:start . 107)\n (:id . 61))\n ((:tag . "VB") (:stem . "encode") (:form . "encode") (:end . 117)\n (:start . 111) (:id . 62))\n ((:tag . "JJ") (:stem . "rag2-like") (:form . "RAG2-like") (:end . 127)\n (:start . 118) (:id . 63))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 136)\n (:start . 128) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n (:id . 65)))@@@1@24@((:hcues ((:id . :x6.273.2) (:span 43 51)))\n (:ncues ((:id . :x6.273.1) (:span 107 110)))\n (:hscopes ((:id . :x6.273.2) (:span 0 136)))\n (:nscopes ((:id . :x6.273.1) (:span 107 136)))\n (:identifiers (:sid . :s6.273) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102013@unknown@formal@none@1@S@Notably, two ZFB cysteines are part of the conserved SxxCxxC motif, and mutations of the serine from the same motif cause severe defects in RAG1 transpositions in vitro [32].@(((:tag . "RB") (:stem . "notably") (:form . "Notably") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "NNP") (:stem . "ZFB") (:form . "ZFB") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "NNS") (:stem . "cysteine") (:form . "cysteines") (:end . 26)\n (:start . 17) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 30) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 35) (:start . 31)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n (:id . 50))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 52)\n (:start . 43) (:id . 51))\n ((:tag . "NNP") (:stem . "SxxCxxC") (:form . "SxxCxxC") (:end . 60)\n (:start . 53) (:id . 52))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 66) (:start . 61)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n (:id . 55))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 81)\n (:start . 72) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n (:id . 58))\n ((:tag . "NN") (:stem . "serine") (:form . "serine") (:end . 95)\n (:start . 89) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 100) (:start . 96)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n (:id . 61))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 109) (:start . 105)\n (:id . 62))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 115)\n (:start . 110) (:id . 63))\n ((:tag . "VBP") (:stem . "cause") (:form . "cause") (:end . 121)\n (:start . 116) (:id . 64))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 128)\n (:start . 122) (:id . 65))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 136)\n (:start . 129) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 139) (:start . 137)\n (:id . 67))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 144) (:start . 140)\n (:id . 68))\n ((:tag . "NNS") (:stem . "transposition") (:form . "transpositions")\n (:end . 159) (:start . 145) (:id . 69))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 162) (:start . 160)\n (:id . 70))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 168)\n (:start . 163) (:id . 71))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 170) (:start . 169)\n (:id . 72))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 172) (:start . 170)\n (:id . 73))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 173) (:start . 172)\n (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s6.274) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102014@unknown@formal@none@1@S@Therefore, the presence of serine in this motif is expected to be crucial to Transib transpositions.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "NN") (:stem . "serine") (:form . "serine") (:end . 33)\n (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n (:id . 48))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 41) (:start . 37)\n (:id . 49))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 47) (:start . 42)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 50) (:start . 48)\n (:id . 51))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 59)\n (:start . 51) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 62) (:start . 60)\n (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 65) (:start . 63)\n (:id . 54))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 73)\n (:start . 66) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 76) (:start . 74)\n (:id . 56))\n ((:tag . "VB") (:stem . "transib") (:form . "Transib") (:end . 84)\n (:start . 77) (:id . 57))\n ((:tag . "NNS") (:stem . "transposition") (:form . "transpositions")\n (:end . 99) (:start . 85) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n (:id . 59)))@@@1@18@((:hcues ((:id . :x6.275.1) (:span 51 59)))\n (:hscopes ((:id . :x6.275.1) (:span 11 99)))\n (:identifiers (:sid . :s6.275) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102015@unknown@formal@none@1@S@After submission of our manuscript, additional biochemical evidence favoring evolution of V(D)J recombination from transposable elements was reported [25].@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "submission") (:form . "submission") (:end . 16)\n (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "NN") (:stem . "manuscript") (:form . "manuscript") (:end . 34)\n (:start . 24) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n (:id . 47))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 46)\n (:start . 36) (:id . 48))\n ((:tag . "JJ") (:stem . "biochemical") (:form . "biochemical") (:end . 58)\n (:start . 47) (:id . 49))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 67)\n (:start . 59) (:id . 50))\n ((:tag . "VBG") (:stem . "favor") (:form . "favoring") (:end . 76)\n (:start . 68) (:id . 51))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 86)\n (:start . 77) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n (:id . 53))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 95) (:start . 90)\n (:id . 54))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 109) (:start . 96) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 114) (:start . 110)\n (:id . 56))\n ((:tag . "JJ") (:stem . "transposable") (:form . "transposable") (:end . 127)\n (:start . 115) (:id . 57))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 136)\n (:start . 128) (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 140) (:start . 137)\n (:id . 59))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 149)\n (:start . 141) (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 151) (:start . 150)\n (:id . 61))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 153) (:start . 151)\n (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 154) (:start . 153)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n (:id . 64)))@@@1@23@((:hcues ((:id . :x6.276.1) (:span 68 76)))\n (:hscopes ((:id . :x6.276.1) (:span 68 136)))\n (:identifiers (:sid . :s6.276) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102016@unknown@formal@none@1@S@Analogously to V(D)J recombination, transposition of the fly Hermes transposon, which belongs to the hAT superfamily, is also characterized by a double-strand break via hairpin formation on flanking DNA and 3? OH joining to the target DNA [25].@(((:tag . "RB") (:stem . "analogously") (:form . "Analogously") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n (:id . 43))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 20) (:start . 15)\n (:id . 44))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 34) (:start . 21) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n (:id . 46))\n ((:tag . "NN") (:stem . "transposition") (:form . "transposition")\n (:end . 49) (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n (:id . 49))\n ((:tag . "JJ") (:stem . "fly") (:form . "fly") (:end . 60) (:start . 57)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Hermes") (:form . "Hermes") (:end . 67)\n (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "transposon") (:form . "transposon") (:end . 78)\n (:start . 68) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 85) (:start . 80)\n (:id . 54))\n ((:tag . "VBZ") (:stem . "belong") (:form . "belongs") (:end . 93)\n (:start . 86) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 96) (:start . 94)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n (:id . 57))\n ((:tag . "NN") (:stem . "hat") (:form . "hAT") (:end . 104) (:start . 101)\n (:id . 58))\n ((:tag . "NN") (:stem . "superfamily") (:form . "superfamily") (:end . 116)\n (:start . 105) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n (:id . 60))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 120) (:start . 118)\n (:id . 61))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 125) (:start . 121)\n (:id . 62))\n ((:tag . "VBN") (:stem . "characterize") (:form . "characterized")\n (:end . 139) (:start . 126) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 142) (:start . 140)\n (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 144) (:start . 143)\n (:id . 65))\n ((:tag . "JJ") (:stem . "double-strand") (:form . "double-strand")\n (:end . 158) (:start . 145) (:id . 66))\n ((:tag . "NN") (:stem . "break") (:form . "break") (:end . 164)\n (:start . 159) (:id . 67))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 168) (:start . 165)\n (:id . 68))\n ((:tag . "NN") (:stem . "hairpin") (:form . "hairpin") (:end . 176)\n (:start . 169) (:id . 69))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 186)\n (:start . 177) (:id . 70))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 189) (:start . 187)\n (:id . 71))\n ((:tag . "VBG") (:stem . "flank") (:form . "flanking") (:end . 198)\n (:start . 190) (:id . 72))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 202) (:start . 199)\n (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 206) (:start . 203)\n (:id . 74))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 208) (:start . 207)\n (:id . 75))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 209) (:start . 208)\n (:id . 76))\n ((:tag . "NN") (:stem . "oh") (:form . "OH") (:end . 212) (:start . 210)\n (:id . 77))\n ((:tag . 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(:end . 244) (:start . 243)\n (:id . 86)))@@@1@45@((:identifiers (:sid . :s6.277) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102017@unknown@formal@none@1@S@However, although the observed biochemical relationship between the hAT TPase and V(D)J recombination is a step forward in our understanding of transposition reaction, several arguments strongly suggest that V(D)J machinery evolved from a Transib rather than from hAT transposon.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 17)\n (:start . 9) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n (:id . 45))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 30)\n (:start . 22) (:id . 46))\n ((:tag . "JJ") (:stem . 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(:end . 279) (:start . 278)\n (:id . 83)))@@@1@42@((:hcues ((:id . :x6.278.2) (:span 195 202)))\n (:ncues ((:id . :x6.278.1) (:span 247 258)))\n (:hscopes ((:id . :x6.278.2) (:span 195 278)))\n (:nscopes ((:id . :x6.278.1) (:span 247 278)))\n (:identifiers (:sid . :s6.278) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102018@unknown@formal@none@1@S@First, as we mentioned previously, there is no significant sequence identity between hAT TPases and RAG1, even if one employs a PSI-BLAST search with most relaxed parameters (i.e., E < 10, no filters, no composition-based statistics).@(((:tag . "RB") (:stem . "first") (:form . "First") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 9) (:start . 7)\n (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . 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"<") (:end . 184) (:start . 183)\n (:id . 76))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 187) (:start . 185)\n (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 188) (:start . 187)\n (:id . 78))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 191) (:start . 189)\n (:id . 79))\n ((:tag . "NNS") (:stem . "filter") (:form . "filters") (:end . 199)\n (:start . 192) (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 200) (:start . 199)\n (:id . 81))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 203) (:start . 201)\n (:id . 82))\n ((:tag . "JJ") (:stem . "composition-based") (:form . "composition-based")\n (:end . 221) (:start . 204) (:id . 83))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 232)\n (:start . 222) (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 233) (:start . 232)\n (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n (:id . 86)))@@@1@45@((:ncues ((:id . :x6.279.1) (:span 201 203))\n ((:id . :x6.279.2) (:span 189 191)))\n (:nscopes ((:id . :x6.279.1) (:span 201 232))\n ((:id . :x6.279.2) (:span 189 199)))\n (:identifiers (:sid . :s6.279) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102020@unknown@formal@none@1@S@Third, unlike in the case of Transib transposons, TIRs of hAT transposons are different from RSS both in terms of DNA sequence similarities and their conservation patterns (Figure S7).@(((:tag . "RB") (:stem . "third") (:form . "Third") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "unlike") (:form . "unlike") (:end . 13) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . 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"and") (:end . 143) (:start . 140)\n (:id . 67))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 149)\n (:start . 144) (:id . 68))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 162)\n (:start . 150) (:id . 69))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 171)\n (:start . 163) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 173) (:start . 172)\n (:id . 71))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 179)\n (:start . 173) (:id . 72))\n ((:tag . "NNP") (:stem . "S7") (:form . "S7") (:end . 182) (:start . 180)\n (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 183) (:start . 182)\n (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s6.281) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102021@unknown@formal@none@1@S@Fourth, hAT- and RAG1/2-mediated transpositions differ dramatically in terms of the GC content of their target sites: Unlike Transib transposons and RAG1 transpositions occurring in GC-rich DNA, hAT transposons tend to be integrated into AT-rich regions (Table S2).@(((:tag . "NN") (:stem . "fourth") (:form . "Fourth") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "hat-") (:form . "hAT-") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "JJ") (:stem . "rag1/2-mediated") (:form . "RAG1/2-mediated")\n (:end . 32) (:start . 17) (:id . 46))\n ((:tag . "NNS") (:stem . 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"during") (:end . 164)\n (:start . 158) (:id . 67))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 170)\n (:start . 165) (:id . 68))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 184) (:start . 171) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 188) (:start . 185)\n (:id . 70))\n ((:tag . "NN") (:stem . "hat") (:form . "hAT") (:end . 192) (:start . 189)\n (:id . 71))\n ((:tag . "NN") (:stem . "transposition") (:form . "transposition")\n (:end . 206) (:start . 193) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n (:id . 73)))@@@1@32@((:hcues ((:id . :x6.284.1) (:span 5 11)))\n (:hscopes ((:id . :x6.284.1) (:span 5 144)))\n (:identifiers (:sid . :s6.284) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102024@unknown@formal@none@1@S@Materials and Methods@(((:tag . "NNPS") (:stem . "Material") (:form . 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(:end . 26) (:start . 25)\n (:id . 46)))@@@1@5@((:identifiers (:sid . :s6.286) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5102026@unknown@formal@none@1@S@Assembled D. pseudoobscura sequences were downloaded from the Human Genome Sequencing Center at Baylor College of Medicine through the Web site at http://hgsc.bcm.tmc.edu/projects/drosophila/ on 2 March 2004.@(((:tag . "NNP") (:stem . "Assembled") (:form . "Assembled") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 12) (:start . 10)\n (:id . 43))\n ((:tag . "NN") (:stem . "pseudoobscura") (:form . "pseudoobscura")\n (:end . 26) (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 36)\n (:start . 27) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 41) (:start . 37)\n (:id . 46))\n ((:tag . "VBN") (:stem . "downloade") (:form . 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(:end . 151) (:start . 150)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s6.288) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102028@unknown@formal@none@1@S@Assembled D. melanogaster sequences were downloaded from the Berkeley Drosophila Genome Project at http://www.fruitfly.org/sequence/download.html on 17 February 2004.@(((:tag . "NNP") (:stem . "Assembled") (:form . "Assembled") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 12) (:start . 10)\n (:id . 43))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 25)\n (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 35)\n (:start . 26) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 40) (:start . 36)\n (:id . 46))\n ((:tag . "VBN") (:stem . "downloade") (:form . "downloaded") (:end . 51)\n (:start . 41) (:id . 47))\n ((:tag . 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".") (:stem . ".") (:form . ".") (:end . 263) (:start . 262)\n (:id . 85)))@@@1@44@((:identifiers (:sid . :s6.291) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102031@unknown@formal@none@1@S@We downloaded these sequences from the GenBank Trace Archive at the National Center for Biotechnology Information (NCBI; ftp://ftp.ncbi.nih.gov/pub/TraceDB/strongylocentrotus_purpuratus/) on 17 November 2004.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "downloade") (:form . "downloaded") (:end . 13)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 19) (:start . 14)\n (:id . 44))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 29)\n (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 34) (:start . 30)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . 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"Information") (:end . 113)\n (:start . 102) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n (:id . 58))\n ((:tag . "NNP") (:stem . "NCBI") (:form . "NCBI") (:end . 119) (:start . 115)\n (:id . 59))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 120) (:start . 119)\n (:id . 60))\n ((:tag . "CD")\n (:stem\n . "ftp://ftp.ncbi.nih.gov/pub/TraceDB/strongylocentrotus_purpuratus/")\n (:form\n . "ftp://ftp.ncbi.nih.gov/pub/TraceDB/strongylocentrotus_purpuratus/")\n (:end . 186) (:start . 121) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 187) (:start . 186)\n (:id . 62))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 190) (:start . 188)\n (:id . 63))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 193) (:start . 191)\n (:id . 64))\n ((:tag . "NNP") (:stem . "November") (:form . "November") (:end . 202)\n (:start . 194) (:id . 65))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 207) (:start . 203)\n (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s6.292) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102032@unknown@formal@none@1@S@Also, we downloaded an approximately 5-Gb set of unassembled traces that cover almost completely the 600-Mb genome of Florida lancelet (ftp://ftp.ncbi.nih.gov/pub/TraceDB/branchiostoma_floridae/; 3 December 2004).@(((:tag . "RB") (:stem . "also") (:form . "Also") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n (:id . 44))\n ((:tag . "VBD") (:stem . "downloade") (:form . "downloaded") (:end . 19)\n (:start . 9) (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 22) (:start . 20)\n (:id . 46))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n (:end . 36) (:start . 23) (:id . 47))\n ((:tag . "JJ") (:stem . "5-gb") (:form . "5-Gb") (:end . 41) (:start . 37)\n (:id . 48))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 45) (:start . 42)\n (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n (:id . 50))\n ((:tag . "JJ") (:stem . "unassembled") (:form . "unassembled") (:end . 60)\n (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "trace") (:form . "traces") (:end . 67)\n (:start . 61) (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 72) (:start . 68)\n (:id . 53))\n ((:tag . "VBP") (:stem . "cover") (:form . "cover") (:end . 78) (:start . 73)\n (:id . 54))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 85)\n (:start . 79) (:id . 55))\n ((:tag . "RB") (:stem . "completely") (:form . "completely") (:end . 96)\n (:start . 86) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . 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"3") (:end . 197) (:start . 196)\n (:id . 66))\n ((:tag . "NNP") (:stem . "December") (:form . "December") (:end . 206)\n (:start . 198) (:id . 67))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 211) (:start . 207)\n (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 212) (:start . 211)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 213) (:start . 212)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s6.293) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102033@unknown@formal@none@1@S@These sequences were produced and deposited in the GenBank Trace Archive by Department of Energy Joint Genomic Institute (http://www.jgi.doe.gov/).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 15)\n (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 20) (:start . 16)\n (:id . 44))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 29)\n (:start . 21) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n (:id . 46))\n ((:tag . "VBN") (:stem . "deposit") (:form . "deposited") (:end . 43)\n (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n (:id . 49))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 58)\n (:start . 51) (:id . 50))\n ((:tag . "NNP") (:stem . "Trace") (:form . "Trace") (:end . 64) (:start . 59)\n (:id . 51))\n ((:tag . "NNP") (:stem . "Archive") (:form . "Archive") (:end . 72)\n (:start . 65) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 75) (:start . 73)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Department") (:form . "Department") (:end . 86)\n (:start . 76) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Energy") (:form . "Energy") (:end . 96)\n (:start . 90) (:id . 56))\n ((:tag . "NNP") (:stem . "Joint") (:form . "Joint") (:end . 102)\n (:start . 97) (:id . 57))\n ((:tag . "NNP") (:stem . "Genomic") (:form . "Genomic") (:end . 110)\n (:start . 103) (:id . 58))\n ((:tag . "NNP") (:stem . "Institute") (:form . "Institute") (:end . 120)\n (:start . 111) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 122) (:start . 121)\n (:id . 60))\n ((:tag . "NNP") (:stem . "http://www.jgi.doe.gov/")\n (:form . "http://www.jgi.doe.gov/") (:end . 145) (:start . 122) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.294) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102034@unknown@formal@none@1@S@All other DNA and protein sequences were accessed from GenBank (NCBI) through the server at http://www.ncbi.nih.gov/Genbank/ and from Ensembl (EMBL-EBI and Sanger Institute) via the server at http://www.ensembl.org.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 17) (:start . 14)\n (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 25)\n (:start . 18) (:id . 46))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 35)\n (:start . 26) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 40) (:start . 36)\n (:id . 48))\n ((:tag . "VBN") (:stem . "access") (:form . "accessed") (:end . 49)\n (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 54) (:start . 50)\n (:id . 50))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 62)\n (:start . 55) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 64) (:start . 63)\n (:id . 52))\n ((:tag . "NNP") (:stem . "NCBI") (:form . "NCBI") (:end . 68) (:start . 64)\n (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n (:id . 54))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 77)\n (:start . 70) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n (:id . 56))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 88)\n (:start . 82) (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 91) (:start . 89)\n (:id . 58))\n ((:tag . "NNP") (:stem . "http://www.ncbi.nih.gov/Genbank/")\n (:form . "http://www.ncbi.nih.gov/Genbank/") (:end . 124) (:start . 92)\n (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 133) (:start . 129)\n (:id . 61))\n ((:tag . "NNP") (:stem . "Ensembl") (:form . "Ensembl") (:end . 141)\n (:start . 134) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n (:id . 63))\n ((:tag . "NNP") (:stem . "EMBL-EBI") (:form . "EMBL-EBI") (:end . 151)\n (:start . 143) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 155) (:start . 152)\n (:id . 65))\n ((:tag . "NNP") (:stem . "Sanger") (:form . "Sanger") (:end . 162)\n (:start . 156) (:id . 66))\n ((:tag . "NNP") (:stem . "Institute") (:form . "Institute") (:end . 172)\n (:start . 163) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 173) (:start . 172)\n (:id . 68))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 177) (:start . 174)\n (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 181) (:start . 178)\n (:id . 70))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 188)\n (:start . 182) (:id . 71))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 191) (:start . 189)\n (:id . 72))\n ((:tag . "VBG") (:stem . "http://www.ensembl.org")\n (:form . "http://www.ensembl.org") (:end . 214) (:start . 192) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s6.295) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102035@unknown@formal@none@1@S@Sequences of the Transib1 through Transib4 and Transib1_AG through Transib3_AG transposons [17] were obtained from the D. melanogaster (drorep.ref) and A. gambiae (angrep.ref) sections of Repbase Update [39] at Genetic Information Research Institute (http://www.girinst.org).@(((:tag . "NNS") (:stem . "sequence") (:form . "Sequences") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "NN") (:stem . "transib1") (:form . "Transib1") (:end . 25)\n (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 33)\n (:start . 26) (:id . 46))\n ((:tag . 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"obtained") (:end . 109)\n (:start . 101) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 114) (:start . 110)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n (:id . 59))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 121) (:start . 119)\n (:id . 60))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 134)\n (:start . 122) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 136) (:start . 135)\n (:id . 62))\n ((:tag . "NN") (:stem . "drorep.ref") (:form . "drorep.ref") (:end . 146)\n (:start . 136) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 151) (:start . 148)\n (:id . 65))\n ((:tag . "NNP") (:stem . "A.") (:form . "A.") (:end . 154) (:start . 152)\n (:id . 66))\n ((:tag . "NN") (:stem . "gambiae") (:form . "gambiae") (:end . 162)\n (:start . 155) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 164) (:start . 163)\n (:id . 68))\n ((:tag . "NN") (:stem . "angrep.ref") (:form . "angrep.ref") (:end . 174)\n (:start . 164) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 175) (:start . 174)\n (:id . 70))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 184)\n (:start . 176) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 187) (:start . 185)\n (:id . 72))\n ((:tag . "NNP") (:stem . "Repbase") (:form . "Repbase") (:end . 195)\n (:start . 188) (:id . 73))\n ((:tag . "NNP") (:stem . "Update") (:form . "Update") (:end . 202)\n (:start . 196) (:id . 74))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 204) (:start . 203)\n (:id . 75))\n ((:tag . "CD") (:stem . "39") (:form . "39") (:end . 206) (:start . 204)\n (:id . 76))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 207) (:start . 206)\n (:id . 77))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 210) (:start . 208)\n (:id . 78))\n ((:tag . "JJ") (:stem . "genetic") (:form . "Genetic") (:end . 218)\n (:start . 211) (:id . 79))\n ((:tag . "NNP") (:stem . "Information") (:form . "Information") (:end . 230)\n (:start . 219) (:id . 80))\n ((:tag . "NNP") (:stem . "Research") (:form . "Research") (:end . 239)\n (:start . 231) (:id . 81))\n ((:tag . "NNP") (:stem . "Institute") (:form . "Institute") (:end . 249)\n (:start . 240) (:id . 82))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 251) (:start . 250)\n (:id . 83))\n ((:tag . "NN") (:stem . "http://www.girinst.org")\n (:form . "http://www.girinst.org") (:end . 273) (:start . 251) (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 274) (:start . 273)\n (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 275) (:start . 274)\n (:id . 86)))@@@1@45@((:identifiers (:sid . :s6.296) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102036@unknown@formal@none@1@S@Sequence analysis.@(((:tag . "NN") (:stem . "sequence") (:form . "Sequence") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 17)\n (:start . 9) (:id . 43))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 18) (:start . 17)\n (:id . 44)))@@@1@3@((:identifiers (:sid . :s6.297) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5102037@unknown@formal@none@1@S@Computer-assisted identification and reconstruction of the Transib transposons was done as described previously [17,40–42].@(((:tag . "JJ") (:stem . "computer-assisted") (:form . "Computer-assisted")\n (:end . 17) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . 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"upon") (:end . 225) (:start . 221)\n (:id . 72))\n ((:tag . "NN") (:stem . "request") (:form . "request") (:end . 233)\n (:start . 226) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 234) (:start . 233)\n (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 238) (:start . 235)\n (:id . 75))\n ((:tag . "NNP") (:stem . "WU-BLASTN") (:form . "WU-BLASTN") (:end . 248)\n (:start . 239) (:id . 76))\n ((:tag . "CD") (:stem . "2.0") (:form . "2.0") (:end . 252) (:start . 249)\n (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 254) (:start . 253)\n (:id . 78))\n ((:tag . "NN") (:stem . "http://blast.wustl.edu")\n (:form . "http://blast.wustl.edu") (:end . 276) (:start . 254) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 277) (:start . 276)\n (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 278) (:start . 277)\n (:id . 81)))@@@1@40@((:identifiers (:sid . :s6.299) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102040@unknown@formal@none@1@S@(We included in the analysis incomplete relics of the Transib2–5_AA TPases represented by single DNA copies.)@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 3) (:start . 1)\n (:id . 43))\n ((:tag . "VBD") (:stem . "include") (:form . "included") (:end . 12)\n (:start . 4) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 46))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 28)\n (:start . 20) (:id . 47))\n ((:tag . "JJ") (:stem . "incomplete") (:form . "incomplete") (:end . 39)\n (:start . 29) (:id . 48))\n ((:tag . 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(:end . 108) (:start . 107)\n (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 109) (:start . 108)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.301) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102041@unknown@formal@none@1@S@Prediction of putative exons and introns encoded by the Transib consensus sequences was done with FGENESH [33] (at http://www.softberry.com).@(((:tag . "NN") (:stem . "prediction") (:form . "Prediction") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 43))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 22)\n (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 28) (:start . 23)\n (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n (:id . 46))\n ((:tag . "NNS") (:stem . "intron") (:form . 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(:end . 141) (:start . 140)\n (:id . 65)))@@@1@24@((:hcues ((:id . :x6.302.1) (:span 14 22)))\n (:hscopes ((:id . :x6.302.1) (:span 14 83)))\n (:identifiers (:sid . :s6.302) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102042@unknown@formal@none@1@S@Multiple alignments of distantly related RAG1 and Transib TPase protein sequences were created by T-Coffee [40].@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 19)\n (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n (:id . 44))\n ((:tag . "RB") (:stem . "distantly") (:form . "distantly") (:end . 32)\n (:start . 23) (:id . 45))\n ((:tag . "JJ") (:stem . "related") (:form . "related") (:end . 40)\n (:start . 33) (:id . 46))\n ((:tag . "NNP") (:stem . "RAG1") (:form . 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"CD") (:stem . "40") (:form . "40") (:end . 110) (:start . 108)\n (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 111) (:start . 110)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.303) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102043@unknown@formal@none@1@S@Shading and minor manual refinements of the aligned sequences were done using Genedoc [43].@(((:tag . "VBG") (:stem . "shade") (:form . "Shading") (:end . 7) (:start . 0)\n (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n (:id . 43))\n ((:tag . "JJ") (:stem . "minor") (:form . "minor") (:end . 17) (:start . 12)\n (:id . 44))\n ((:tag . "JJ") (:stem . "manual") (:form . "manual") (:end . 24)\n (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "refinement") (:form . 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"assembled") (:end . 83)\n (:start . 74) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 88) (:start . 84)\n (:id . 55))\n ((:tag . "NNS") (:stem . "trace") (:form . "traces") (:end . 95)\n (:start . 89) (:id . 56))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 101) (:start . 96)\n (:id . 57))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 104) (:start . 102)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n (:id . 59))\n ((:tag . "NNP") (:stem . "Baylor") (:form . "Baylor") (:end . 115)\n (:start . 109) (:id . 60))\n ((:tag . "NNP") (:stem . "BAC-Fisher") (:form . "BAC-Fisher") (:end . 126)\n (:start . 116) (:id . 61))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 133)\n (:start . 127) (:id . 62))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 136) (:start . 134)\n (:id . 63))\n ((:tag . "NNP") (:stem . "http://www.hgsc.bcm.tmc.edu/BAC-Fisher/")\n (:form . "http://www.hgsc.bcm.tmc.edu/BAC-Fisher/") (:end . 176)\n (:start . 137) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 178) (:start . 177)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 181) (:start . 178)\n (:id . 66))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 189)\n (:start . 182) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 192) (:start . 190)\n (:id . 68))\n ((:tag . "NN") (:stem . "assembly") (:form . "assembly") (:end . 201)\n (:start . 193) (:id . 69))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 206) (:start . 202)\n (:id . 70))\n ((:tag . "VBN") (:stem . "verify") (:form . "verified") (:end . 215)\n (:start . 207) (:id . 71))\n ((:tag . "RB") (:stem . "manually") (:form . "manually") (:end . 224)\n (:start . 216) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 225) (:start . 224)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 226) (:start . 225)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s6.306) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102046@unknown@formal@none@1@S@All GenBank proteins were downloaded from ftp://ftp.ncbi.nih.gov/blast/DB/fasta/nr (February 2004) and were combined into a single set with the identified Transib TPases.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 20)\n (:start . 12) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 25) (:start . 21)\n (:id . 45))\n ((:tag . "VBN") (:stem . "downloade") (:form . "downloaded") (:end . 36)\n (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 41) (:start . 37)\n (:id . 47))\n ((:tag . "NN") (:stem . "ftp://ftp.ncbi.nih.gov/blast/DB/fasta/nr")\n (:form . "ftp://ftp.ncbi.nih.gov/blast/DB/fasta/nr") (:end . 82)\n (:start . 42) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n (:id . 49))\n ((:tag . "NNP") (:stem . "February") (:form . "February") (:end . 92)\n (:start . 84) (:id . 50))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 97) (:start . 93)\n (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 107) (:start . 103)\n (:id . 54))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 116)\n (:start . 108) (:id . 55))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 121) (:start . 117)\n (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 123) (:start . 122)\n (:id . 57))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 130)\n (:start . 124) (:id . 58))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 134) (:start . 131)\n (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 139) (:start . 135)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n (:id . 61))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 154)\n (:start . 144) (:id . 62))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 162)\n (:start . 155) (:id . 63))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 169)\n (:start . 163) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s6.307) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102047@unknown@formal@none@1@S@No Transib TPases had been deposited or annotated previously in GenBank, except for two short hypothetical proteins predicted automatically during annotation of the D. melanogaster genome: 151-aa gi:30923617 and 123-aa gi:30923765.@(((:tag . "DT") (:stem . "no") (:form . "No") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 17) (:start . 11)\n (:id . 44))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 21) (:start . 18)\n (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 26) (:start . 22)\n (:id . 46))\n ((:tag . "VBN") (:stem . "deposit") (:form . "deposited") (:end . 36)\n (:start . 27) (:id . 47))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 39) (:start . 37)\n (:id . 48))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 49)\n (:start . 40) (:id . 49))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 60)\n (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n (:id . 51))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 71)\n (:start . 64) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n (:id . 53))\n ((:tag . "IN") (:stem . "except") (:form . "except") (:end . 79)\n (:start . 73) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 83) (:start . 80)\n (:id . 55))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 87) (:start . 84)\n (:id . 56))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 93) (:start . 88)\n (:id . 57))\n ((:tag . "JJ") (:stem . "hypothetical") (:form . "hypothetical") (:end . 106)\n (:start . 94) (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 115)\n (:start . 107) (:id . 59))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 125)\n (:start . 116) (:id . 60))\n ((:tag . "RB") (:stem . "automatically") (:form . "automatically")\n (:end . 139) (:start . 126) (:id . 61))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 146)\n (:start . 140) (:id . 62))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 157)\n (:start . 147) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 160) (:start . 158)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 164) (:start . 161)\n (:id . 65))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 167) (:start . 165)\n (:id . 66))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 180)\n (:start . 168) (:id . 67))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 187)\n (:start . 181) (:id . 68))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 188) (:start . 187)\n (:id . 69))\n ((:tag . "JJ") (:stem . "151-aa") (:form . "151-aa") (:end . 195)\n (:start . 189) (:id . 70))\n ((:tag . "CD") (:stem . "gi:30923617") (:form . "gi:30923617") (:end . 207)\n (:start . 196) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 211) (:start . 208)\n (:id . 72))\n ((:tag . "JJ") (:stem . "123-aa") (:form . "123-aa") (:end . 218)\n (:start . 212) (:id . 73))\n ((:tag . "CD") (:stem . "gi:30923765") (:form . "gi:30923765") (:end . 230)\n (:start . 219) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 231) (:start . 230)\n (:id . 75)))@@@1@34@((:ncues ((:id . :x6.308.1) (:span 0 2)))\n (:nscopes ((:id . :x6.308.1) (:span 0 71)))\n (:identifiers (:sid . :s6.308) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102048@unknown@formal@none@1@S@These proteins are apparent fragments of Transib TPases encoded by relics of Transib transposons, including Transib5_DM.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 14)\n (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 18) (:start . 15)\n (:id . 44))\n ((:tag . "JJ") (:stem . "apparent") (:form . "apparent") (:end . 27)\n (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "fragment") (:form . "fragments") (:end . 37)\n (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 48)\n (:start . 41) (:id . 48))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 55) (:start . 49)\n (:id . 49))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 63)\n (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 66) (:start . 64)\n (:id . 51))\n ((:tag . "NNS") (:stem . "relic") (:form . "relics") (:end . 73)\n (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 84)\n (:start . 77) (:id . 54))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 96)\n (:start . 85) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n (:id . 56))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 107)\n (:start . 98) (:id . 57))\n ((:tag . "NNP") (:stem . "Transib5_DM") (:form . "Transib5_DM") (:end . 119)\n (:start . 108) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s6.309) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102050@unknown@formal@none@1@S@The PSI-BLAST program [18,45] is much more sensitive than a regular BLAST search due to the use of PSSM) PSI-BLAST first performs a standard BLASTP search of a protein query against a protein database and constructs a multiple alignment of matches exceeding a certain E-value threshold (called Ei value for the inclusion of sequences into PSI-BLAST iterations).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 21)\n (:start . 14) (:id . 44))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 23) (:start . 22)\n (:id . 45))\n ((:tag . "CD") (:stem . "18,45") (:form . "18,45") (:end . 28) (:start . 23)\n (:id . 46))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 29) (:start . 28)\n (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 32) (:start . 30)\n (:id . 48))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 37) (:start . 33)\n (:id . 49))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 42) (:start . 38)\n (:id . 50))\n ((:tag . "JJ") (:stem . "sensitive") (:form . "sensitive") (:end . 52)\n (:start . 43) (:id . 51))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 57) (:start . 53)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 59) (:start . 58)\n (:id . 53))\n ((:tag . "JJ") (:stem . "regular") (:form . "regular") (:end . 67)\n (:start . 60) (:id . 54))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 73) (:start . 68)\n (:id . 55))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 80)\n (:start . 74) (:id . 56))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 84) (:start . 81)\n (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 87) (:start . 85)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n (:id . 59))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 95) (:start . 92)\n (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n (:id . 61))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 103) (:start . 99)\n (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n (:id . 63))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 114)\n (:start . 105) (:id . 64))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 120)\n (:start . 115) (:id . 65))\n ((:tag . "VBZ") (:stem . "perform") (:form . "performs") (:end . 129)\n (:start . 121) (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 131) (:start . 130)\n (:id . 67))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 140)\n (:start . 132) (:id . 68))\n ((:tag . "NNP") (:stem . "BLASTP") (:form . "BLASTP") (:end . 147)\n (:start . 141) (:id . 69))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 154)\n (:start . 148) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 157) (:start . 155)\n (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 159) (:start . 158)\n (:id . 72))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 167)\n (:start . 160) (:id . 73))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 173)\n (:start . 168) (:id . 74))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 181)\n (:start . 174) (:id . 75))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 183) (:start . 182)\n (:id . 76))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 191)\n (:start . 184) (:id . 77))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 200)\n (:start . 192) (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 204) (:start . 201)\n (:id . 79))\n ((:tag . "VBZ") (:stem . "construct") (:form . "constructs") (:end . 215)\n (:start . 205) (:id . 80))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 217) (:start . 216)\n (:id . 81))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 226)\n (:start . 218) (:id . 82))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 236)\n (:start . 227) (:id . 83))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 239) (:start . 237)\n (:id . 84))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 247)\n (:start . 240) (:id . 85))\n ((:tag . "VBG") (:stem . "exceed") (:form . "exceeding") (:end . 257)\n (:start . 248) (:id . 86))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 259) (:start . 258)\n (:id . 87))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 267)\n (:start . 260) (:id . 88))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-value") (:end . 275)\n (:start . 268) (:id . 89))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 285)\n (:start . 276) (:id . 90))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 287) (:start . 286)\n (:id . 91))\n ((:tag . "VBN") (:stem . "call") (:form . "called") (:end . 293)\n (:start . 287) (:id . 92))\n ((:tag . "NNP") (:stem . "Ei") (:form . "Ei") (:end . 296) (:start . 294)\n (:id . 93))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 302)\n (:start . 297) (:id . 94))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 306) (:start . 303)\n (:id . 95))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 310) (:start . 307)\n (:id . 96))\n ((:tag . "NN") (:stem . "inclusion") (:form . "inclusion") (:end . 320)\n (:start . 311) (:id . 97))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 323) (:start . 321)\n (:id . 98))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 333)\n (:start . 324) (:id . 99))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 338) (:start . 334)\n (:id . 100))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 348)\n (:start . 339) (:id . 101))\n ((:tag . "NNS") (:stem . "iteration") (:form . "iterations") (:end . 359)\n (:start . 349) (:id . 102))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 360) (:start . 359)\n (:id . 103))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 361) (:start . 360)\n (:id . 104)))@@@1@63@((:identifiers (:sid . :s6.311) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102051@unknown@formal@none@1@S@From this alignment, a PSSM is constructed.@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 19)\n (:start . 10) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n (:id . 46))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 27) (:start . 23)\n (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 30) (:start . 28)\n (:id . 48))\n ((:tag . "VBN") (:stem . "construct") (:form . "constructed") (:end . 42)\n (:start . 31) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 43) (:start . 42)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s6.312) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102052@unknown@formal@none@1@S@The PSSM is a weight matrix indicating the relative occurrence of each of the 20 aa at each position in the alignment.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n (:id . 45))\n ((:tag . "NN") (:stem . "weight") (:form . "weight") (:end . 20)\n (:start . 14) (:id . 46))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 27)\n (:start . 21) (:id . 47))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 38)\n (:start . 28) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n (:id . 49))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 51)\n (:start . 43) (:id . 50))\n ((:tag . "NN") (:stem . "occurrence") (:form . "occurrence") (:end . 62)\n (:start . 52) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n (:id . 52))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 70) (:start . 66)\n (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n (:id . 55))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 80) (:start . 78)\n (:id . 56))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 83) (:start . 81)\n (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 86) (:start . 84)\n (:id . 58))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 91) (:start . 87)\n (:id . 59))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 100)\n (:start . 92) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n (:id . 62))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 117)\n (:start . 108) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s6.313) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102053@unknown@formal@none@1@S@This new PSSM is used as the score matrix for a new BLAST search in a second iteration.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "pssm") (:form . "PSSM") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 21) (:start . 17)\n (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 24) (:start . 22)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n (:id . 48))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 34) (:start . 29)\n (:id . 49))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 41)\n (:start . 35) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 45) (:start . 42)\n (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 47) (:start . 46)\n (:id . 52))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 51) (:start . 48)\n (:id . 53))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 57) (:start . 52)\n (:id . 54))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 64)\n (:start . 58) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 69) (:start . 68)\n (:id . 57))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 76)\n (:start . 70) (:id . 58))\n ((:tag . "NN") (:stem . "iteration") (:form . "iteration") (:end . 86)\n (:start . 77) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.314) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102054@unknown@formal@none@1@S@The process is repeated for a specific number of iterations or until convergence, when no additional proteins are added on successive iterations.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "VBN") (:stem . "repeat") (:form . "repeated") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 27) (:start . 24)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n (:id . 47))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 38)\n (:start . 30) (:id . 48))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 45)\n (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n (:id . 50))\n ((:tag . "NNS") (:stem . "iteration") (:form . "iterations") (:end . 59)\n (:start . 49) (:id . 51))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 62) (:start . 60)\n (:id . 52))\n ((:tag . "IN") (:stem . "until") (:form . "until") (:end . 68) (:start . 63)\n (:id . 53))\n ((:tag . "NN") (:stem . "convergence") (:form . "convergence") (:end . 80)\n (:start . 69) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n (:id . 55))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 86) (:start . 82)\n (:id . 56))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 89) (:start . 87)\n (:id . 57))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 100)\n (:start . 90) (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 109)\n (:start . 101) (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 113) (:start . 110)\n (:id . 60))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 119) (:start . 114)\n (:id . 61))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 122) (:start . 120)\n (:id . 62))\n ((:tag . "JJ") (:stem . "successive") (:form . "successive") (:end . 133)\n (:start . 123) (:id . 63))\n ((:tag . "NNS") (:stem . "iteration") (:form . "iterations") (:end . 144)\n (:start . 134) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n (:id . 65)))@@@1@24@((:ncues ((:id . :x6.315.1) (:span 87 89)))\n (:nscopes ((:id . :x6.315.1) (:span 87 144)))\n (:identifiers (:sid . :s6.315) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102055@unknown@formal@none@1@S@The use of a PSSM in place of a fixed generic substitution matrix such as BLOSUM62 results in a much more sensitive BLAST search [18,45].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 12) (:start . 11)\n (:id . 45))\n ((:tag . "NN") (:stem . "pssm") (:form . "PSSM") (:end . 17) (:start . 13)\n (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 20) (:start . 18)\n (:id . 47))\n ((:tag . "NN") (:stem . "place") (:form . "place") (:end . 26) (:start . 21)\n (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 31) (:start . 30)\n (:id . 50))\n ((:tag . "JJ") (:stem . "fixed") (:form . "fixed") (:end . 37) (:start . 32)\n (:id . 51))\n ((:tag . "JJ") (:stem . "generic") (:form . "generic") (:end . 45)\n (:start . 38) (:id . 52))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 58)\n (:start . 46) (:id . 53))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 65)\n (:start . 59) (:id . 54))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 70) (:start . 66)\n (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 73) (:start . 71)\n (:id . 56))\n ((:tag . "NN") (:stem . "blosum62") (:form . "BLOSUM62") (:end . 82)\n (:start . 74) (:id . 57))\n ((:tag . "VBZ") (:stem . "result") (:form . "results") (:end . 90)\n (:start . 83) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 93) (:start . 91)\n (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 95) (:start . 94)\n (:id . 60))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 100) (:start . 96)\n (:id . 61))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 105) (:start . 101)\n (:id . 62))\n ((:tag . "JJ") (:stem . "sensitive") (:form . "sensitive") (:end . 115)\n (:start . 106) (:id . 63))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 121)\n (:start . 116) (:id . 64))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 128)\n (:start . 122) (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 130) (:start . 129)\n (:id . 66))\n ((:tag . "CD") (:stem . "18,45") (:form . "18,45") (:end . 135)\n (:start . 130) (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 136) (:start . 135)\n (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s6.316) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102056@unknown@formal@none@1@S@Important practical aspects of using PSI-BLAST were recently described [46].@(((:tag . "JJ") (:stem . "important") (:form . "Important") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "practical") (:form . "practical") (:end . 19)\n (:start . 10) (:id . 43))\n ((:tag . "NNS") (:stem . "aspect") (:form . "aspects") (:end . 27)\n (:start . 20) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 36) (:start . 31)\n (:id . 46))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 46)\n (:start . 37) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 51) (:start . 47)\n (:id . 48))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 60)\n (:start . 52) (:id . 49))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 70)\n (:start . 61) (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 72) (:start . 71)\n (:id . 51))\n ((:tag . "CD") (:stem . "46") (:form . "46") (:end . 74) (:start . 72)\n (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 75) (:start . 74)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.317) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102057@unknown@formal@none@1@S@To ensure that a conservation profile for the Transib TPases and RAG1 proteins was not produced by a systematic error, we employed a procedure of “step-wise” PSI-BLAST iterations.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "ensure") (:form . "ensure") (:end . 9) (:start . 3)\n (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 29)\n (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 37)\n (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 41) (:start . 38)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n (:id . 49))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 53)\n (:start . 46) (:id . 50))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 60) (:start . 54)\n (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 64) (:start . 61)\n (:id . 52))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 69) (:start . 65)\n (:id . 53))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 78)\n (:start . 70) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 82) (:start . 79)\n (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 86) (:start . 83)\n (:id . 56))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 95)\n (:start . 87) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 98) (:start . 96)\n (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 100) (:start . 99)\n (:id . 59))\n ((:tag . "JJ") (:stem . "systematic") (:form . "systematic") (:end . 111)\n (:start . 101) (:id . 60))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 117)\n (:start . 112) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n (:id . 62))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 121) (:start . 119)\n (:id . 63))\n ((:tag . "VBD") (:stem . "employ") (:form . "employed") (:end . 130)\n (:start . 122) (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 132) (:start . 131)\n (:id . 65))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 142)\n (:start . 133) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 145) (:start . 143)\n (:id . 67))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 147) (:start . 146)\n (:id . 68))\n ((:tag . "JJ") (:stem . "step-wise") (:form . "step-wise") (:end . 156)\n (:start . 147) (:id . 69))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 157) (:start . 156)\n (:id . 70))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 167)\n (:start . 158) (:id . 71))\n ((:tag . "NNS") (:stem . "iteration") (:form . "iterations") (:end . 178)\n (:start . 168) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n (:id . 73)))@@@1@32@((:ncues ((:id . :x6.318.1) (:span 83 86)))\n (:nscopes ((:id . :x6.318.1) (:span 15 117)))\n (:identifiers (:sid . :s6.318) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102058@unknown@formal@none@1@S@In this procedure we studied dependence of Ei values on the number of the Transib TPases combined with the GenBank proteins.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 17)\n (:start . 8) (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 20) (:start . 18)\n (:id . 45))\n ((:tag . "VBD") (:stem . "study") (:form . "studied") (:end . 28)\n (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "dependence") (:form . "dependence") (:end . 39)\n (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Ei") (:form . "Ei") (:end . 45) (:start . 43)\n (:id . 49))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 52)\n (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 55) (:start . 53)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n (:id . 52))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 66)\n (:start . 60) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 81)\n (:start . 74) (:id . 56))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 88) (:start . 82)\n (:id . 57))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 97)\n (:start . 89) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 102) (:start . 98)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n (:id . 60))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 114)\n (:start . 107) (:id . 61))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 123)\n (:start . 115) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.319) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102060@unknown@formal@none@1@S@Significant convergence of RAG1 and Transib TPases was observed to be independent of the particular type of substitution matrix (the same result was observed for both BLOSUM62 and PAM70 matrixes).@(((:tag . "JJ") (:stem . "significant") (:form . "Significant") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "convergence") (:form . "convergence") (:end . 23)\n (:start . 12) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 44))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 31) (:start . 27)\n (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 43)\n (:start . 36) (:id . 47))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 50) (:start . 44)\n (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 54) (:start . 51)\n (:id . 49))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 63)\n (:start . 55) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 69) (:start . 67)\n (:id . 52))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 81)\n (:start . 70) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n (:id . 55))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 99)\n (:start . 89) (:id . 56))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 104) (:start . 100)\n (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n (:id . 58))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 120)\n (:start . 108) (:id . 59))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 127)\n (:start . 121) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 129) (:start . 128)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n (:id . 62))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 137) (:start . 133)\n (:id . 63))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 144)\n (:start . 138) (:id . 64))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 148) (:start . 145)\n (:id . 65))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 157)\n (:start . 149) (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 161) (:start . 158)\n (:id . 67))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 166) (:start . 162)\n (:id . 68))\n ((:tag . "NN") (:stem . "blosum62") (:form . "BLOSUM62") (:end . 175)\n (:start . 167) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 179) (:start . 176)\n (:id . 70))\n ((:tag . "NN") (:stem . "pam70") (:form . "PAM70") (:end . 185)\n (:start . 180) (:id . 71))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrixes") (:end . 194)\n (:start . 186) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 195) (:start . 194)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s6.321) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102061@unknown@formal@none@1@S@To avoid detection of false similarities caused by simple repeats and coiled coils, the PSI-BLAST search was performed using stringent conditions with the SEG [47] and COILS [48] filters masking all low-complexity regions and coiled coils, respectively; composition-based statistics [45] were also employed.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "avoid") (:form . "avoid") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "detection") (:form . "detection") (:end . 18)\n (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 27) (:start . 22)\n (:id . 46))\n ((:tag . "NNS") (:stem . "similarity") (:form . "similarities") (:end . 40)\n (:start . 28) (:id . 47))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 47)\n (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 50) (:start . 48)\n (:id . 49))\n ((:tag . "JJ") (:stem . "simple") (:form . "simple") (:end . 57)\n (:start . 51) (:id . 50))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 65)\n (:start . 58) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n (:id . 52))\n ((:tag . "VBD") (:stem . "coil") (:form . "coiled") (:end . 76) (:start . 70)\n (:id . 53))\n ((:tag . "NNS") (:stem . "coil") (:form . "coils") (:end . 82) (:start . 77)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n (:id . 56))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 97)\n (:start . 88) (:id . 57))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 104)\n (:start . 98) (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 108) (:start . 105)\n (:id . 59))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 118)\n (:start . 109) (:id . 60))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 124) (:start . 119)\n (:id . 61))\n ((:tag . "JJ") (:stem . "stringent") (:form . "stringent") (:end . 134)\n (:start . 125) (:id . 62))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 145)\n (:start . 135) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 150) (:start . 146)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n (:id . 65))\n ((:tag . "NNP") (:stem . "SEG") (:form . "SEG") (:end . 158) (:start . 155)\n (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 160) (:start . 159)\n (:id . 67))\n ((:tag . "CD") (:stem . "47") (:form . "47") (:end . 162) (:start . 160)\n (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 163) (:start . 162)\n (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 167) (:start . 164)\n (:id . 70))\n ((:tag . "NN") (:stem . "coils") (:form . "COILS") (:end . 173)\n (:start . 168) (:id . 71))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 175) (:start . 174)\n (:id . 72))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 177) (:start . 175)\n (:id . 73))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 178) (:start . 177)\n (:id . 74))\n ((:tag . "NNS") (:stem . "filter") (:form . "filters") (:end . 186)\n (:start . 179) (:id . 75))\n ((:tag . "VBG") (:stem . "mask") (:form . "masking") (:end . 194)\n (:start . 187) (:id . 76))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 198) (:start . 195)\n (:id . 77))\n ((:tag . "JJ") (:stem . "low-complexity") (:form . "low-complexity")\n (:end . 213) (:start . 199) (:id . 78))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 221)\n (:start . 214) (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 225) (:start . 222)\n (:id . 80))\n ((:tag . "VBD") (:stem . "coil") (:form . "coiled") (:end . 232)\n (:start . 226) (:id . 81))\n ((:tag . "NNS") (:stem . "coil") (:form . "coils") (:end . 238)\n (:start . 233) (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 239) (:start . 238)\n (:id . 83))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 252)\n (:start . 240) (:id . 84))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 253) (:start . 252)\n (:id . 85))\n ((:tag . "JJ") (:stem . "composition-based") (:form . "composition-based")\n (:end . 271) (:start . 254) (:id . 86))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 282)\n (:start . 272) (:id . 87))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 284) (:start . 283)\n (:id . 88))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 286) (:start . 284)\n (:id . 89))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 287) (:start . 286)\n (:id . 90))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 292) (:start . 288)\n (:id . 91))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 297) (:start . 293)\n (:id . 92))\n ((:tag . "VBN") (:stem . "employ") (:form . "employed") (:end . 306)\n (:start . 298) (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 307) (:start . 306)\n (:id . 94)))@@@1@53@((:identifiers (:sid . :s6.322) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102062@unknown@formal@none@1@S@The probability P1 that the 5? terminus of a transposon from a particular Transib family would match by chance an RSS at its most conserved positions (positions 1-3 in the RSS heptamer, and positions 5 and 6 in the RSS nonamer) was estimated based on the following formula: P1 = fC × fA × fC × fA × fA, where fC (0.2) and fA (0.3) are frequencies of C and A in a set of 38-bp 5? termini of Transib transposons from 21 families (see Figure 4).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "p1") (:form . "P1") (:end . 18) (:start . 16)\n (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n (:id . 46))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 29) (:start . 28)\n (:id . 47))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 30) (:start . 29)\n (:id . 48))\n ((:tag . "NN") (:stem . "terminus") (:form . "terminus") (:end . 39)\n (:start . 31) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n (:id . 51))\n ((:tag . "NN") (:stem . "transposon") (:form . "transposon") (:end . 55)\n (:start . 45) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 60) (:start . 56)\n (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 62) (:start . 61)\n (:id . 54))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 73)\n (:start . 63) (:id . 55))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 81)\n (:start . 74) (:id . 56))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 88)\n (:start . 82) (:id . 57))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 94) (:start . 89)\n (:id . 58))\n ((:tag . "VB") (:stem . "match") (:form . "match") (:end . 100) (:start . 95)\n (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 103) (:start . 101)\n (:id . 60))\n ((:tag . "NN") (:stem . "chance") (:form . "chance") (:end . 110)\n (:start . 104) (:id . 61))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 113) (:start . 111)\n (:id . 62))\n ((:tag . "NN") (:stem . "rss") (:form . "RSS") (:end . 117) (:start . 114)\n (:id . 63))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 120) (:start . 118)\n (:id . 64))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 124) (:start . 121)\n (:id . 65))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 129) (:start . 125)\n (:id . 66))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 139)\n (:start . 130) (:id . 67))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 149)\n (:start . 140) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 151) (:start . 150)\n (:id . 69))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 160)\n (:start . 151) (:id . 70))\n ((:tag . "CD") (:stem . "1-3") (:form . "1-3") (:end . 164) (:start . 161)\n (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 167) (:start . 165)\n (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 171) (:start . 168)\n (:id . 73))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSS") (:end . 175) (:start . 172)\n (:id . 74))\n ((:tag . "NN") (:stem . "heptamer") (:form . "heptamer") (:end . 184)\n (:start . 176) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 185) (:start . 184)\n (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 189) (:start . 186)\n (:id . 77))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 199)\n (:start . 190) (:id . 78))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 201) (:start . 200)\n (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 205) (:start . 202)\n (:id . 80))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 207) (:start . 206)\n (:id . 81))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 210) (:start . 208)\n (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 214) (:start . 211)\n (:id . 83))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSS") (:end . 218) (:start . 215)\n (:id . 84))\n ((:tag . "NN") (:stem . "nonamer") (:form . "nonamer") (:end . 226)\n (:start . 219) (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 227) (:start . 226)\n (:id . 86))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 231) (:start . 228)\n (:id . 87))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 241)\n (:start . 232) (:id . 88))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 247)\n (:start . 242) (:id . 89))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 250) (:start . 248)\n (:id . 90))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 254) (:start . 251)\n (:id . 91))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 264)\n (:start . 255) (:id . 92))\n ((:tag . "NN") (:stem . "formula") (:form . "formula") (:end . 272)\n (:start . 265) (:id . 93))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 273) (:start . 272)\n (:id . 94))\n ((:tag . "NNP") (:stem . "P1") (:form . "P1") (:end . 276) (:start . 274)\n (:id . 95))\n ((:tag . "JJ") (:stem . "=") (:form . "=") (:end . 278) (:start . 277)\n (:id . 96))\n ((:tag . "NN") (:stem . "fc") (:form . "fC") (:end . 281) (:start . 279)\n (:id . 97))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 283) (:start . 282)\n (:id . 98))\n ((:tag . "NN") (:stem . "fa") (:form . "fA") (:end . 286) (:start . 284)\n (:id . 99))\n ((:tag . "NNP") (:stem . "×") (:form . "×") (:end . 288) (:start . 287)\n (:id . 100))\n ((:tag . "NN") (:stem . "fc") (:form . "fC") (:end . 291) (:start . 289)\n (:id . 101))\n ((:tag . "NNP") (:stem . "×") (:form . "×") (:end . 293) (:start . 292)\n (:id . 102))\n ((:tag . "NNP") (:stem . "fA") (:form . "fA") (:end . 296) (:start . 294)\n (:id . 103))\n ((:tag . "NNP") (:stem . "×") (:form . "×") (:end . 298) (:start . 297)\n (:id . 104))\n ((:tag . "NNP") (:stem . "fA") (:form . "fA") (:end . 301) (:start . 299)\n (:id . 105))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 302) (:start . 301)\n (:id . 106))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 308)\n (:start . 303) (:id . 107))\n ((:tag . "NN") (:stem . "fc") (:form . "fC") (:end . 311) (:start . 309)\n (:id . 108))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 313) (:start . 312)\n (:id . 109))\n ((:tag . "CD") (:stem . "0.2") (:form . "0.2") (:end . 316) (:start . 313)\n (:id . 110))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 317) (:start . 316)\n (:id . 111))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 321) (:start . 318)\n (:id . 112))\n ((:tag . "NNP") (:stem . "fA") (:form . "fA") (:end . 324) (:start . 322)\n (:id . 113))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 326) (:start . 325)\n (:id . 114))\n ((:tag . "CD") (:stem . "0.3") (:form . "0.3") (:end . 329) (:start . 326)\n (:id . 115))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 330) (:start . 329)\n (:id . 116))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 334) (:start . 331)\n (:id . 117))\n ((:tag . "NNS") (:stem . "frequency") (:form . "frequencies") (:end . 346)\n (:start . 335) (:id . 118))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 349) (:start . 347)\n (:id . 119))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 351) (:start . 350)\n (:id . 120))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 355) (:start . 352)\n (:id . 121))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 357) (:start . 356)\n (:id . 122))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 360) (:start . 358)\n (:id . 123))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 362) (:start . 361)\n (:id . 124))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 366) (:start . 363)\n (:id . 125))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 369) (:start . 367)\n (:id . 126))\n ((:tag . "JJ") (:stem . "38-bp") (:form . "38-bp") (:end . 375)\n (:start . 370) (:id . 127))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 377) (:start . 376)\n (:id . 128))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 378) (:start . 377)\n (:id . 129))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 386)\n (:start . 379) (:id . 130))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 389) (:start . 387)\n (:id . 131))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 397)\n (:start . 390) (:id . 132))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 409)\n (:start . 398) (:id . 133))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 414) (:start . 410)\n (:id . 134))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 417) (:start . 415)\n (:id . 135))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 426)\n (:start . 418) (:id . 136))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 428) (:start . 427)\n (:id . 137))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 431) (:start . 428)\n (:id . 138))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 438)\n (:start . 432) (:id . 139))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 440) (:start . 439)\n (:id . 140))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 441) (:start . 440)\n (:id . 141))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 442) (:start . 441)\n (:id . 142)))@@@1@101@((:identifiers (:sid . :s6.323) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102063@unknown@formal@none@1@S@The value of P1 is 0.001, indicating a significant similarity between Transib TIRs and RSS.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n (:id . 44))\n ((:tag . "NNP") (:stem . "P1") (:form . "P1") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n (:id . 46))\n ((:tag . "CD") (:stem . "0.001") (:form . "0.001") (:end . 24) (:start . 19)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n (:id . 48))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 36)\n (:start . 26) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n (:id . 50))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 50)\n (:start . 39) (:id . 51))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 61)\n (:start . 51) (:id . 52))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 69)\n (:start . 62) (:id . 53))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 77)\n (:start . 70) (:id . 54))\n ((:tag . "NNPS") (:stem . "TIR") (:form . "TIRs") (:end . 82) (:start . 78)\n (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n (:id . 56))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSS") (:end . 90) (:start . 87)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s6.324) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102064@unknown@formal@none@1@S@Indeed, given that these five positions conserved in RSS are conserved in all TIRs from 21 families of Transib transposons, and the average identity between these 38-bp TIRs is only 49%, the chance of randomly matching these positions in TIRs from all 21 families is extremely small.@(((:tag . "RB") (:stem . "indeed") (:form . "Indeed") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n (:id . 45))\n ((:tag . "DT") (:stem . 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(:end . 54) (:start . 53)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s6.336) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102076@unknown@formal@none@1@S@Amino acids are shaded on the basis of their physiochemical properties according to the color scheme implemented in Genedoc [43]: Black shading marks hydrophobic residues, blue indicates charged (white font), positively charged (red font), and negatively charged (green font); red indicates proline (blue font) and glycine (green font); gray indicates aliphatic (red font) and aromatic (blue font); green indicates polar (black font) and amphoteric (red font); yellow indicates tiny (blue font) and small (green font).@(((:tag . "NN") (:stem . "amino") (:form . "Amino") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . 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(:form . ".") (:end . 518) (:start . 517)\n (:id . 149)))@@@1@108@((:identifiers (:sid . :s6.337) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102077@unknown@formal@none@1@S@The species abbreviations are as follows: SP, sea urchin; DP, D. pseudoobscura fruit fly; AG, African malaria mosquito; AA, yellow fever mosquito.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "species") (:form . "species") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "abbreviation") (:form . "abbreviations")\n (:end . 25) (:start . 12) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 32) (:start . 30)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 40)\n (:start . 33) (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . 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"fever") (:form . "fever") (:end . 136)\n (:start . 131) (:id . 70))\n ((:tag . "NN") (:stem . "mosquito") (:form . "mosquito") (:end . 145)\n (:start . 137) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n (:id . 72)))@@@1@31@((:identifiers (:sid . :s6.338) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102078@unknown@formal@none@1@S@Transib1 through Transib5 are from the D. melanogaster fruit fly genome.@(((:tag . "NN") (:stem . "transib1") (:form . "Transib1") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 16)\n (:start . 9) (:id . 43))\n ((:tag . "NN") (:stem . "transib5") (:form . "Transib5") (:end . 25)\n (:start . 17) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 34) (:start . 30)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n (:id . 47))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 41) (:start . 39)\n (:id . 48))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 54)\n (:start . 42) (:id . 49))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 60) (:start . 55)\n (:id . 50))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 64) (:start . 61)\n (:id . 51))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 71)\n (:start . 65) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s6.339) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102080@unknown@formal@none@1@S@The shading scheme is the same as in Figure S2.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBG") (:stem . "shade") (:form . "shading") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 18)\n (:start . 12) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 46))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 30) (:start . 26)\n (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 33) (:start . 31)\n (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n (:id . 49))\n ((:tag . "NN") (:stem . "figure") (:form . "Figure") (:end . 43)\n (:start . 37) (:id . 50))\n ((:tag . "NN") (:stem . "s2") (:form . "S2") (:end . 46) (:start . 44)\n (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 47) (:start . 46)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s6.341) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102081@unknown@formal@none@1@S@The catalytic DDE triad is marked by black rectangles.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "catalytic") (:form . "catalytic") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "dde") (:form . "DDE") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "triad") (:form . "triad") (:end . 23) (:start . 18)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 33) (:start . 27)\n (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 36) (:start . 34)\n (:id . 48))\n ((:tag . "JJ") (:stem . "black") (:form . "black") (:end . 42) (:start . 37)\n (:id . 49))\n ((:tag . "NNS") (:stem . "rectangle") (:form . "rectangles") (:end . 53)\n (:start . 43) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 54) (:start . 53)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s6.342) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102082@unknown@formal@none@1@S@RAG1 aa whose replacements resulted in previously detected defects of V(D)J recombination [31] are marked by color rectangles indicated below the alignment blocks; red indicates DNA binding defect; green indicates nicking defect; cyan indicates hairpin defect; blue indicates joining mutants; yellow indicates catalytic mutants; gray indicates joining/transposition.@(((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "NNS") (:stem . "replacement") (:form . "replacements") (:end . 26)\n (:start . 14) (:id . 45))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 35)\n (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n (:id . 47))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 49)\n (:start . 39) (:id . 48))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 58)\n (:start . 50) (:id . 49))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 66)\n (:start . 59) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n (:id . 51))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 75) (:start . 70)\n (:id . 52))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 89) (:start . 76) (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 91) (:start . 90)\n (:id . 54))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 93) (:start . 91)\n (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 94) (:start . 93)\n (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 98) (:start . 95)\n (:id . 57))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 105)\n (:start . 99) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 108) (:start . 106)\n (:id . 59))\n ((:tag . "NN") (:stem . "color") (:form . "color") (:end . 114)\n (:start . 109) (:id . 60))\n ((:tag . "NNS") (:stem . "rectangle") (:form . "rectangles") (:end . 125)\n (:start . 115) (:id . 61))\n ((:tag . "VBD") (:stem . "indicate") (:form . "indicated") (:end . 135)\n (:start . 126) (:id . 62))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 141)\n (:start . 136) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n (:id . 64))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 155)\n (:start . 146) (:id . 65))\n ((:tag . "NNS") (:stem . "block") (:form . "blocks") (:end . 162)\n (:start . 156) (:id . 66))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 163) (:start . 162)\n (:id . 67))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 167) (:start . 164)\n (:id . 68))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 177)\n (:start . 168) (:id . 69))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 181) (:start . 178)\n (:id . 70))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 189)\n (:start . 182) (:id . 71))\n ((:tag . "NN") (:stem . "defect") (:form . "defect") (:end . 196)\n (:start . 190) (:id . 72))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 197) (:start . 196)\n (:id . 73))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 203)\n (:start . 198) (:id . 74))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 213)\n (:start . 204) (:id . 75))\n ((:tag . "NN") (:stem . "nicking") (:form . "nicking") (:end . 221)\n (:start . 214) (:id . 76))\n ((:tag . "NN") (:stem . "defect") (:form . "defect") (:end . 228)\n (:start . 222) (:id . 77))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 229) (:start . 228)\n (:id . 78))\n ((:tag . "NN") (:stem . "cyan") (:form . "cyan") (:end . 234) (:start . 230)\n (:id . 79))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 244)\n (:start . 235) (:id . 80))\n ((:tag . "NN") (:stem . "hairpin") (:form . "hairpin") (:end . 252)\n (:start . 245) (:id . 81))\n ((:tag . "NN") (:stem . "defect") (:form . "defect") (:end . 259)\n (:start . 253) (:id . 82))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 260) (:start . 259)\n (:id . 83))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 265) (:start . 261)\n (:id . 84))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 275)\n (:start . 266) (:id . 85))\n ((:tag . "VBG") (:stem . "join") (:form . "joining") (:end . 283)\n (:start . 276) (:id . 86))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 291)\n (:start . 284) (:id . 87))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 292) (:start . 291)\n (:id . 88))\n ((:tag . "NN") (:stem . "yellow") (:form . "yellow") (:end . 299)\n (:start . 293) (:id . 89))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 309)\n (:start . 300) (:id . 90))\n ((:tag . "JJ") (:stem . "catalytic") (:form . "catalytic") (:end . 319)\n (:start . 310) (:id . 91))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 327)\n (:start . 320) (:id . 92))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 328) (:start . 327)\n (:id . 93))\n ((:tag . "NN") (:stem . "gray") (:form . "gray") (:end . 333) (:start . 329)\n (:id . 94))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 343)\n (:start . 334) (:id . 95))\n ((:tag . "NN") (:stem . "joining/transposition")\n (:form . "joining/transposition") (:end . 365) (:start . 344) (:id . 96))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 366) (:start . 365)\n (:id . 97)))@@@1@56@((:identifiers (:sid . :s6.343) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102083@unknown@formal@none@1@S@Presence and absence of corresponding residues in the Transib TPases are indicated by + and -, respectively.@(((:tag . "NNP") (:stem . "Presence") (:form . "Presence") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 12) (:start . 9)\n (:id . 43))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 20)\n (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 45))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 37)\n (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 46)\n (:start . 38) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n (:id . 49))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 61)\n (:start . 54) (:id . 50))\n ((:tag . "NNPS") (:stem . "TPas") (:form . "TPases") (:end . 68)\n (:start . 62) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 72) (:start . 69)\n (:id . 52))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 82)\n (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 85) (:start . 83)\n (:id . 54))\n ((:tag . "SYM") (:stem . "+") (:form . "+") (:end . 87) (:start . 86)\n (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n (:id . 56))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 93) (:start . 92)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n (:id . 58))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 107)\n (:start . 95) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n (:id . 60)))@@@1@19@((:ncues ((:id . :x6.344.1) (:span 13 20)))\n (:nscopes ((:id . :x6.344.1) (:span 13 68)))\n (:identifiers (:sid . :s6.344) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102084@unknown@formal@none@1@S@Conserved motifs are marked by lines numbered from 1 to 10.@(((:tag . "VBN") (:stem . "conserve") (:form . "Conserved") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 16)\n (:start . 10) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 20) (:start . 17)\n (:id . 44))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 27) (:start . 21)\n (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 36) (:start . 31)\n (:id . 47))\n ((:tag . "VBN") (:stem . "number") (:form . "numbered") (:end . 45)\n (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 50) (:start . 46)\n (:id . 49))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 52) (:start . 51)\n (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 55) (:start . 53)\n (:id . 51))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 58) (:start . 56)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 59) (:start . 58)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s6.345) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102085@unknown@formal@none@1@S@The species abbreviations are as follows: DP, D. pseudoobscura fruit fly; AG, African malaria mosquito; AA, yellow fever mosquito; GG, chicken; HS, human; XL, frog; CL, bull shark; FR, fugu fish.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "species") (:form . "species") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "abbreviation") (:form . "abbreviations")\n (:end . 25) (:start . 12) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 32) (:start . 30)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 40)\n (:start . 33) (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 41) (:start . 40)\n (:id . 48))\n ((:tag . "NNP") (:stem . "DP") (:form . "DP") (:end . 44) (:start . 42)\n (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n (:id . 50))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 48) (:start . 46)\n (:id . 51))\n ((:tag . "NN") (:stem . "pseudoobscura") (:form . "pseudoobscura")\n (:end . 62) (:start . 49) (:id . 52))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 68) (:start . 63)\n (:id . 53))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 72) (:start . 69)\n (:id . 54))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 73) (:start . 72)\n (:id . 55))\n ((:tag . "NNP") (:stem . "AG") (:form . "AG") (:end . 76) (:start . 74)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n (:id . 57))\n ((:tag . "JJ") (:stem . "african") (:form . "African") (:end . 85)\n (:start . 78) (:id . 58))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 93)\n (:start . 86) (:id . 59))\n ((:tag . "NN") (:stem . "mosquito") (:form . "mosquito") (:end . 102)\n (:start . 94) (:id . 60))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 103) (:start . 102)\n (:id . 61))\n ((:tag . "NN") (:stem . "aa") (:form . "AA") (:end . 106) (:start . 104)\n (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n (:id . 63))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 114)\n (:start . 108) (:id . 64))\n ((:tag . "NN") (:stem . "fever") (:form . "fever") (:end . 120)\n (:start . 115) (:id . 65))\n ((:tag . "NN") (:stem . "mosquito") (:form . "mosquito") (:end . 129)\n (:start . 121) (:id . 66))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 130) (:start . 129)\n (:id . 67))\n ((:tag . "NNP") (:stem . "GG") (:form . "GG") (:end . 133) (:start . 131)\n (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n (:id . 69))\n ((:tag . "NN") (:stem . "chicken") (:form . "chicken") (:end . 142)\n (:start . 135) (:id . 70))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 143) (:start . 142)\n (:id . 71))\n ((:tag . "NNP") (:stem . "HS") (:form . "HS") (:end . 146) (:start . 144)\n (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n (:id . 73))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 153)\n (:start . 148) (:id . 74))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 154) (:start . 153)\n (:id . 75))\n ((:tag . "NNP") (:stem . "XL") (:form . "XL") (:end . 157) (:start . 155)\n (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n (:id . 77))\n ((:tag . "NN") (:stem . "frog") (:form . "frog") (:end . 163) (:start . 159)\n (:id . 78))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 164) (:start . 163)\n (:id . 79))\n ((:tag . "NNP") (:stem . "CL") (:form . "CL") (:end . 167) (:start . 165)\n (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 168) (:start . 167)\n (:id . 81))\n ((:tag . "NN") (:stem . "bull") (:form . "bull") (:end . 173) (:start . 169)\n (:id . 82))\n ((:tag . "NN") (:stem . "shark") (:form . "shark") (:end . 179)\n (:start . 174) (:id . 83))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 180) (:start . 179)\n (:id . 84))\n ((:tag . "NNP") (:stem . "FR") (:form . "FR") (:end . 183) (:start . 181)\n (:id . 85))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n (:id . 86))\n ((:tag . "NN") (:stem . "fugu") (:form . "fugu") (:end . 189) (:start . 185)\n (:id . 87))\n ((:tag . "NN") (:stem . "fish") (:form . "fish") (:end . 194) (:start . 190)\n (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n (:id . 89)))@@@1@48@((:identifiers (:sid . :s6.346) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102086@unknown@formal@none@1@S@TSDs in Transposons from Different Transib Families@(((:tag . "NNP") (:stem . "TSD") (:form . "TSDs") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "NNPS") (:stem . "Transposon") (:form . "Transposons") (:end . 19)\n (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 24) (:start . 20)\n (:id . 45))\n ((:tag . "JJ") (:stem . "different") (:form . "Different") (:end . 34)\n (:start . 25) (:id . 46))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 42)\n (:start . 35) (:id . 47))\n ((:tag . "NNS") (:stem . "family") (:form . "Families") (:end . 51)\n (:start . 43) (:id . 48)))@@@1@7@((:identifiers (:sid . :s6.347) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5102087@unknown@formal@none@1@S@For each family, DNA copies of transposons are aligned to the corresponding consensus sequence.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 15) (:start . 9)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 20) (:start . 17)\n (:id . 46))\n ((:tag . "NNS") (:stem . "copy") (:form . "copies") (:end . 27) (:start . 21)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 48))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 42)\n (:start . 31) (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 46) (:start . 43)\n (:id . 50))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 54)\n (:start . 47) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 57) (:start . 55)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n (:id . 53))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 75)\n (:start . 62) (:id . 54))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 85)\n (:start . 76) (:id . 55))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 94)\n (:start . 86) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s6.348) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102088@unknown@formal@none@1@S@The consensus sequence is shown in the top line.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 22)\n (:start . 14) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n (:id . 45))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 31) (:start . 26)\n (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n (:id . 48))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 42) (:start . 39)\n (:id . 49))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 47) (:start . 43)\n (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 48) (:start . 47)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s6.349) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102090@unknown@formal@none@1@S@Internal portions of transposons are not shown and are marked by xxx.@(((:tag . "JJ") (:stem . "internal") (:form . "Internal") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 17)\n (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 44))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 32)\n (:start . 21) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 36) (:start . 33)\n (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 40) (:start . 37)\n (:id . 47))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 46) (:start . 41)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 54) (:start . 51)\n (:id . 50))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 61) (:start . 55)\n (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 64) (:start . 62)\n (:id . 52))\n ((:tag . "NN") (:stem . "xxx") (:form . "xxx") (:end . 68) (:start . 65)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n (:id . 54)))@@@1@13@((:ncues ((:id . :x6.351.1) (:span 37 40)))\n (:nscopes ((:id . :x6.351.1) (:span 0 46)))\n (:identifiers (:sid . :s6.351) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102091@unknown@formal@none@1@S@TSDs are highlighted.@(((:tag . "NNS") (:stem . "tsd") (:form . "TSDs") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "VBN") (:stem . "highlight") (:form . "highlighted") (:end . 20)\n (:start . 9) (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 21) (:start . 20)\n (:id . 45)))@@@1@4@((:identifiers (:sid . :s6.352) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102092@unknown@formal@none@1@S@Coordinates of the reported elements are shown in the first two columns (sequence name, beginning to end).@(((:tag . "NNS") (:stem . "coordinate") (:form . "Coordinates") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 44))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 27)\n (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 36)\n (:start . 28) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 40) (:start . 37)\n (:id . 47))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 46) (:start . 41)\n (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n (:id . 50))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 59) (:start . 54)\n (:id . 51))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 63) (:start . 60)\n (:id . 52))\n ((:tag . "NNS") (:stem . "column") (:form . "columns") (:end . 71)\n (:start . 64) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n (:id . 54))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 81)\n (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "name") (:form . "name") (:end . 86) (:start . 82)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n (:id . 57))\n ((:tag . "VBG") (:stem . "begin") (:form . "beginning") (:end . 97)\n (:start . 88) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n (:id . 59))\n ((:tag . "VB") (:stem . "end") (:form . "end") (:end . 104) (:start . 101)\n (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.353) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102093@unknown@formal@none@1@S@(A) TransibN1_AG family from mosquito.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "TransibN1_AG") (:form . "TransibN1_AG") (:end . 16)\n (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 23)\n (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 28) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "mosquito") (:form . "mosquito") (:end . 37)\n (:start . 29) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 38) (:start . 37)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s6.354) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102094@unknown@formal@none@1@S@(B) TransibN2_AG family from mosquito.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "TransibN2_AG") (:form . "TransibN2_AG") (:end . 16)\n (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 23)\n (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 28) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "mosquito") (:form . "mosquito") (:end . 37)\n (:start . 29) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 38) (:start . 37)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s6.355) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102095@unknown@formal@none@1@S@(C) TransibN3_AG family from mosquito.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "TransibN3_AG") (:form . "TransibN3_AG") (:end . 16)\n (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 23)\n (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 28) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "mosquito") (:form . "mosquito") (:end . 37)\n (:start . 29) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 38) (:start . 37)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s6.356) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102096@unknown@formal@none@1@S@(D) TransibN1_DP family from fruit fly.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "TransibN1_DP") (:form . "TransibN1_DP") (:end . 16)\n (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 23)\n (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 28) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 34) (:start . 29)\n (:id . 48))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 38) (:start . 35)\n (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 39) (:start . 38)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s6.357) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102097@unknown@formal@none@1@S@(E) Hopper family from fruit fly.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "hopper") (:form . "Hopper") (:end . 10) (:start . 4)\n (:id . 45))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 17)\n (:start . 11) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 22) (:start . 18)\n (:id . 47))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 28) (:start . 23)\n (:id . 48))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 32) (:start . 29)\n (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 33) (:start . 32)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s6.358) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102098@unknown@formal@none@1@S@(F) TransibN1_DM family from fruit fly.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "F") (:form . "F") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "TransibN1_DM") (:form . "TransibN1_DM") (:end . 16)\n (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 23)\n (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 28) (:start . 24)\n (:id . 47))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 34) (:start . 29)\n (:id . 48))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 38) (:start . 35)\n (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 39) (:start . 38)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s6.359) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102100@unknown@formal@none@1@S@Multiple Alignment of the RAG1 Core and RAG1 Core–Like Proteins Encoded by the Sea Urchin and Lancelet Genomes@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "alignment") (:form . "Alignment") (:end . 18)\n (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 30) (:start . 26)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Core") (:form . "Core") (:end . 35) (:start . 31)\n (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 44) (:start . 40)\n (:id . 49))\n ((:tag . "NNP") (:stem . "Core–Like") (:form . "Core–Like") (:end . 54)\n (:start . 45) (:id . 50))\n ((:tag . "NNPS") (:stem . "Protein") (:form . "Proteins") (:end . 63)\n (:start . 55) (:id . 51))\n ((:tag . "VBN") (:stem . "encode") (:form . "Encoded") (:end . 71)\n (:start . 64) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 74) (:start . 72)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Sea") (:form . "Sea") (:end . 82) (:start . 79)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Urchin") (:form . "Urchin") (:end . 89)\n (:start . 83) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n (:id . 57))\n ((:tag . "NNP") (:stem . "Lancelet") (:form . "Lancelet") (:end . 102)\n (:start . 94) (:id . 58))\n ((:tag . "NNPS") (:stem . "Genome") (:form . "Genomes") (:end . 110)\n (:start . 103) (:id . 59)))@@@1@18@((:identifiers (:sid . :s6.361) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5102101@unknown@formal@none@1@S@The shading scheme is the same as in Figure S2 and S3.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBG") (:stem . "shade") (:form . "shading") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 18)\n (:start . 12) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 46))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 30) (:start . 26)\n (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 33) (:start . 31)\n (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n (:id . 49))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 43)\n (:start . 37) (:id . 50))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 46) (:start . 44)\n (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n (:id . 52))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 53) (:start . 51)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 54) (:start . 53)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.362) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102102@unknown@formal@none@1@S@The species abbreviations are as follows: SP, sea urchin; BF, lancelet; HS, human; CL, bull shark; GG, chicken; XL, frog; FR, fugu fish.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "species") (:form . "species") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "abbreviation") (:form . "abbreviations")\n (:end . 25) (:start . 12) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 32) (:start . 30)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 40)\n (:start . 33) (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 41) (:start . 40)\n (:id . 48))\n ((:tag . "NNP") (:stem . "SP") (:form . "SP") (:end . 44) (:start . 42)\n (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n (:id . 50))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 49) (:start . 46)\n (:id . 51))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 56)\n (:start . 50) (:id . 52))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 57) (:start . 56)\n (:id . 53))\n ((:tag . "NNP") (:stem . "BF") (:form . "BF") (:end . 60) (:start . 58)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n (:id . 55))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 70)\n (:start . 62) (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 71) (:start . 70)\n (:id . 57))\n ((:tag . "NNP") (:stem . "HS") (:form . "HS") (:end . 74) (:start . 72)\n (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n (:id . 59))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 81) (:start . 76)\n (:id . 60))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 82) (:start . 81)\n (:id . 61))\n ((:tag . "NNP") (:stem . "CL") (:form . "CL") (:end . 85) (:start . 83)\n (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n (:id . 63))\n ((:tag . "NN") (:stem . "bull") (:form . "bull") (:end . 91) (:start . 87)\n (:id . 64))\n ((:tag . "NN") (:stem . "shark") (:form . "shark") (:end . 97) (:start . 92)\n (:id . 65))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 98) (:start . 97)\n (:id . 66))\n ((:tag . "NNP") (:stem . "GG") (:form . "GG") (:end . 101) (:start . 99)\n (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n (:id . 68))\n ((:tag . "NN") (:stem . "chicken") (:form . "chicken") (:end . 110)\n (:start . 103) (:id . 69))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 111) (:start . 110)\n (:id . 70))\n ((:tag . "NNP") (:stem . "XL") (:form . "XL") (:end . 114) (:start . 112)\n (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n (:id . 72))\n ((:tag . "NN") (:stem . "frog") (:form . "frog") (:end . 120) (:start . 116)\n (:id . 73))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 121) (:start . 120)\n (:id . 74))\n ((:tag . "NNP") (:stem . "FR") (:form . "FR") (:end . 124) (:start . 122)\n (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n (:id . 76))\n ((:tag . "NN") (:stem . "fugu") (:form . "fugu") (:end . 130) (:start . 126)\n (:id . 77))\n ((:tag . "NN") (:stem . "fish") (:form . "fish") (:end . 135) (:start . 131)\n (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n (:id . 79)))@@@1@38@((:identifiers (:sid . :s6.363) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102103@unknown@formal@none@1@S@The lancelet RAG1L_BF protein is encoded by several overlapping WGS trace sequences (for example, GenBank Trace Archive identification numbers 543943730, 538583629).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "rag1l_bf") (:form . "RAG1L_BF") (:end . 21)\n (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 29)\n (:start . 22) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 32) (:start . 30)\n (:id . 46))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 40)\n (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 43) (:start . 41)\n (:id . 48))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 51)\n (:start . 44) (:id . 49))\n ((:tag . "VBG") (:stem . "overlap") (:form . "overlapping") (:end . 63)\n (:start . 52) (:id . 50))\n ((:tag . "NN") (:stem . "wgs") (:form . "WGS") (:end . 67) (:start . 64)\n (:id . 51))\n ((:tag . "NN") (:stem . "trace") (:form . "trace") (:end . 73) (:start . 68)\n (:id . 52))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 83)\n (:start . 74) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 88) (:start . 85)\n (:id . 55))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 96)\n (:start . 89) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n (:id . 57))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 105)\n (:start . 98) (:id . 58))\n ((:tag . "NNP") (:stem . "Trace") (:form . "Trace") (:end . 111)\n (:start . 106) (:id . 59))\n ((:tag . "NNP") (:stem . "Archive") (:form . "Archive") (:end . 119)\n (:start . 112) (:id . 60))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n (:end . 134) (:start . 120) (:id . 61))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 142)\n (:start . 135) (:id . 62))\n ((:tag . "CD") (:stem . "543943730") (:form . "543943730") (:end . 152)\n (:start . 143) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n (:id . 64))\n ((:tag . "CD") (:stem . "538583629") (:form . "538583629") (:end . 163)\n (:start . 154) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 164) (:start . 163)\n (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s6.364) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102104@unknown@formal@none@1@S@RAG1-Like Protein SP_29068 in the Sea Urchin Contig 29068@(((:tag . "NNP") (:stem . "RAG1-Like") (:form . "RAG1-Like") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 17)\n (:start . 10) (:id . 43))\n ((:tag . "NN") (:stem . "sp_29068") (:form . "SP_29068") (:end . 26)\n (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Sea") (:form . "Sea") (:end . 37) (:start . 34)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Urchin") (:form . "Urchin") (:end . 44)\n (:start . 38) (:id . 48))\n ((:tag . "NNP") (:stem . "Contig") (:form . "Contig") (:end . 51)\n (:start . 45) (:id . 49))\n ((:tag . "CD") (:stem . "29068") (:form . "29068") (:end . 57) (:start . 52)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s6.365) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5102105@unknown@formal@none@1@S@(A) Exon/intron structure of the SP_29068 gene is reported based on the FGENESH prediction.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Exon/intron") (:form . "Exon/intron") (:end . 15)\n (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 25)\n (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n (:id . 48))\n ((:tag . "NN") (:stem . "sp_29068") (:form . "SP_29068") (:end . 41)\n (:start . 33) (:id . 49))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 46) (:start . 42)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 49) (:start . 47)\n (:id . 51))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 58)\n (:start . 50) (:id . 52))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 64) (:start . 59)\n (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 67) (:start . 65)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n (:id . 55))\n ((:tag . "NN") (:stem . "fgenesh") (:form . "FGENESH") (:end . 79)\n (:start . 72) (:id . 56))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 90)\n (:start . 80) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s6.366) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102106@unknown@formal@none@1@S@(B) Alignment of the predicted protein and human RAG1 (29% identity, E = 10-43.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Alignment") (:form . "Alignment") (:end . 13)\n (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 47))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 30)\n (:start . 21) (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 38)\n (:start . 31) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n (:id . 50))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 48) (:start . 43)\n (:id . 51))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 53) (:start . 49)\n (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n (:id . 53))\n ((:tag . "CD") (:stem . "29") (:form . "29") (:end . 57) (:start . 55)\n (:id . 54))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 58) (:start . 57)\n (:id . 55))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 67)\n (:start . 59) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n (:id . 57))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 70) (:start . 69)\n (:id . 58))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 72) (:start . 71)\n (:id . 59))\n ((:tag . "CD") (:stem . "10-43") (:form . "10-43") (:end . 78) (:start . 73)\n (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.367) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102107@unknown@formal@none@1@S@The intron in SP_29068 is inserted between residues shaded in green and red.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "intron") (:form . "intron") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "sp_29068") (:form . "SP_29068") (:end . 22)\n (:start . 14) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n (:id . 46))\n ((:tag . "VBN") (:stem . "insert") (:form . "inserted") (:end . 34)\n (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 42)\n (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 51)\n (:start . 43) (:id . 49))\n ((:tag . "VBN") (:stem . "shade") (:form . "shaded") (:end . 58)\n (:start . 52) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n (:id . 51))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 67) (:start . 62)\n (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n (:id . 53))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 75) (:start . 72)\n (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s6.368) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102108@unknown@formal@none@1@S@Gly460 that harbors the intron in the teleost RAG1 is shaded in black.@(((:tag . "NNP") (:stem . "Gly460") (:form . "Gly460") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 11) (:start . 7)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "harbor") (:form . "harbors") (:end . 19)\n (:start . 12) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "NN") (:stem . "intron") (:form . "intron") (:end . 30)\n (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n (:id . 48))\n ((:tag . "NN") (:stem . "teleost") (:form . "teleost") (:end . 45)\n (:start . 38) (:id . 49))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 50) (:start . 46)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 53) (:start . 51)\n (:id . 51))\n ((:tag . "VBN") (:stem . "shade") (:form . "shaded") (:end . 60)\n (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n (:id . 53))\n ((:tag . "NN") (:stem . "black") (:form . "black") (:end . 69) (:start . 64)\n (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s6.369) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102110@unknown@formal@none@1@S@Non-gapped alignment of consensus sequences of 5? termini of transposons from 22 different families is shown beneath the RSS23 consensus sequence, composed of the RSS heptamer and nonamer.@(((:tag . "JJ") (:stem . "non-gapped") (:form . "Non-gapped") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 20)\n (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n (:id . 44))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 33)\n (:start . 24) (:id . 45))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 43)\n (:start . 34) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n (:id . 47))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 48) (:start . 47)\n (:id . 48))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 49) (:start . 48)\n (:id . 49))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 57)\n (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n (:id . 51))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 72)\n (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 77) (:start . 73)\n (:id . 53))\n ((:tag . "CD") (:stem . "22") (:form . "22") (:end . 80) (:start . 78)\n (:id . 54))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 90)\n (:start . 81) (:id . 55))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 99)\n (:start . 91) (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 102) (:start . 100)\n (:id . 57))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 108)\n (:start . 103) (:id . 58))\n ((:tag . "IN") (:stem . "beneath") (:form . "beneath") (:end . 116)\n (:start . 109) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n (:id . 60))\n ((:tag . "NN") (:stem . "rss23") (:form . "RSS23") (:end . 126)\n (:start . 121) (:id . 61))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 136)\n (:start . 127) (:id . 62))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 145)\n (:start . 137) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n (:id . 64))\n ((:tag . "VBN") (:stem . "compose") (:form . "composed") (:end . 155)\n (:start . 147) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 158) (:start . 156)\n (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 162) (:start . 159)\n (:id . 67))\n ((:tag . "NN") (:stem . "rss") (:form . "RSS") (:end . 166) (:start . 163)\n (:id . 68))\n ((:tag . "NN") (:stem . "heptamer") (:form . "heptamer") (:end . 175)\n (:start . 167) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 179) (:start . 176)\n (:id . 70))\n ((:tag . "NN") (:stem . "nonamer") (:form . "nonamer") (:end . 187)\n (:start . 180) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n (:id . 72)))@@@1@31@((:identifiers (:sid . :s6.371) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102111@unknown@formal@none@1@S@The most conserved nucleotides in the heptamer and nonamer, which are necessary for efficient V(D)J recombination, are highlighted.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 18)\n (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "nucleotide") (:form . "nucleotides") (:end . 30)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n (:id . 47))\n ((:tag . "NN") (:stem . "heptamer") (:form . "heptamer") (:end . 46)\n (:start . 38) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n (:id . 49))\n ((:tag . "NN") (:stem . "nonamer") (:form . "nonamer") (:end . 58)\n (:start . 51) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 65) (:start . 60)\n (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 69) (:start . 66)\n (:id . 53))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 79)\n (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 83) (:start . 80)\n (:id . 55))\n ((:tag . "JJ") (:stem . "efficient") (:form . "efficient") (:end . 93)\n (:start . 84) (:id . 56))\n ((:tag . "NNP") (:stem . "V(D)J") (:form . "V(D)J") (:end . 99) (:start . 94)\n (:id . 57))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n (:end . 113) (:start . 100) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 118) (:start . 115)\n (:id . 60))\n ((:tag . "VBN") (:stem . "highlight") (:form . "highlighted") (:end . 130)\n (:start . 119) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.372) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102112@unknown@formal@none@1@S@Among the necessary RSS nucleotides, only one, marked by a + corresponds to a nucleotide that is 100% conserved in hAT transposons.@(((:tag . "IN") (:stem . "among") (:form . "Among") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 19)\n (:start . 10) (:id . 44))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSS") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "NNS") (:stem . "nucleotide") (:form . "nucleotides") (:end . 35)\n (:start . 24) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n (:id . 47))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 41) (:start . 37)\n (:id . 48))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 45) (:start . 42)\n (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n (:id . 50))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 53) (:start . 47)\n (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 56) (:start . 54)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 58) (:start . 57)\n (:id . 53))\n ((:tag . "SYM") (:stem . "+") (:form . "+") (:end . 60) (:start . 59)\n (:id . 54))\n ((:tag . "VBZ") (:stem . "correspond") (:form . "corresponds") (:end . 72)\n (:start . 61) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 75) (:start . 73)\n (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 77) (:start . 76)\n (:id . 57))\n ((:tag . "NN") (:stem . "nucleotide") (:form . "nucleotide") (:end . 88)\n (:start . 78) (:id . 58))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 93) (:start . 89)\n (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 96) (:start . 94)\n (:id . 60))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 100) (:start . 97)\n (:id . 61))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 101) (:start . 100)\n (:id . 62))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 111)\n (:start . 102) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n (:id . 64))\n ((:tag . "NN") (:stem . "hat") (:form . "hAT") (:end . 118) (:start . 115)\n (:id . 65))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 130)\n (:start . 119) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s6.373) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102113@unknown@formal@none@1@S@The critical third nucleotide of the hAT 5? termini is always G, as opposed to C in the RSS heptamer.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "critical") (:form . "critical") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "NN") (:stem . "nucleotide") (:form . "nucleotide") (:end . 29)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n (:id . 47))\n ((:tag . "NN") (:stem . "hat") (:form . "hAT") (:end . 40) (:start . 37)\n (:id . 48))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 42) (:start . 41)\n (:id . 49))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 43) (:start . 42)\n (:id . 50))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 51)\n (:start . 44) (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 54) (:start . 52)\n (:id . 52))\n ((:tag . "RB") (:stem . "always") (:form . "always") (:end . 61)\n (:start . 55) (:id . 53))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 63) (:start . 62)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 67) (:start . 65)\n (:id . 56))\n ((:tag . "VBN") (:stem . "oppose") (:form . "opposed") (:end . 75)\n (:start . 68) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n (:id . 58))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 80) (:start . 79)\n (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 83) (:start . 81)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n (:id . 61))\n ((:tag . "NNP") (:stem . "RSS") (:form . "RSS") (:end . 91) (:start . 88)\n (:id . 62))\n ((:tag . "NN") (:stem . "heptamer") (:form . "heptamer") (:end . 100)\n (:start . 92) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s6.374) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102114@unknown@formal@none@1@S@It is also clear from the alignment that the hAT termini do not have any second conserved block, which is expected to be preserved if RSSs have evolved from hAT termini.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 10) (:start . 6)\n (:id . 44))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 16) (:start . 11)\n (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 21) (:start . 17)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 47))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 35)\n (:start . 26) (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 40) (:start . 36)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n (:id . 50))\n ((:tag . "NN") (:stem . "hat") (:form . "hAT") (:end . 48) (:start . 45)\n (:id . 51))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 56)\n (:start . 49) (:id . 52))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 59) (:start . 57)\n (:id . 53))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 63) (:start . 60)\n (:id . 54))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 68) (:start . 64)\n (:id . 55))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 72) (:start . 69)\n (:id . 56))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 79)\n (:start . 73) (:id . 57))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 89)\n (:start . 80) (:id . 58))\n ((:tag . "NN") (:stem . "block") (:form . "block") (:end . 95) (:start . 90)\n (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n (:id . 60))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 102)\n (:start . 97) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 105) (:start . 103)\n (:id . 62))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 114)\n (:start . 106) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 117) (:start . 115)\n (:id . 64))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 120) (:start . 118)\n (:id . 65))\n ((:tag . "VBN") (:stem . "preserve") (:form . "preserved") (:end . 130)\n (:start . 121) (:id . 66))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 133) (:start . 131)\n (:id . 67))\n ((:tag . "NNS") (:stem . "rss") (:form . "RSSs") (:end . 138) (:start . 134)\n (:id . 68))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 143) (:start . 139)\n (:id . 69))\n ((:tag . "VBN") (:stem . "evolve") (:form . "evolved") (:end . 151)\n (:start . 144) (:id . 70))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 156) (:start . 152)\n (:id . 71))\n ((:tag . "NN") (:stem . "hat") (:form . "hAT") (:end . 160) (:start . 157)\n (:id . 72))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 168)\n (:start . 161) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n (:id . 74)))@@@1@33@((:hcues ((:id . :x6.375.1) (:span 106 114)))\n (:ncues ((:id . :x6.375.2) (:span 60 63)))\n (:hscopes ((:id . :x6.375.1) (:span 97 168)))\n (:nscopes ((:id . :x6.375.2) (:span 60 95)))\n (:identifiers (:sid . :s6.375) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102115@unknown@formal@none@1@S@Hobo (GenBank number X04705), Homer (AF110403), Hermes (L34807), Ac9 (K01904), Tam3_AM (X55078), TAG1 (L12220), Pegasus (U47019) are active hAT transposons from fruit fly, Queensland fruit fly, house fly, maize, snapdragon, thale-cress, and African malaria mosquito, respectively.@(((:tag . "NNP") (:stem . "Hobo") (:form . "Hobo") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 13)\n (:start . 6) (:id . 44))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 20)\n (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "x04705") (:form . "X04705") (:end . 27)\n (:start . 21) (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 28) (:start . 27)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Homer") (:form . "Homer") (:end . 35) (:start . 30)\n (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n (:id . 50))\n ((:tag . "NNP") (:stem . "AF110403") (:form . "AF110403") (:end . 45)\n (:start . 37) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 46) (:start . 45)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Herme") (:form . "Hermes") (:end . 54)\n (:start . 48) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n (:id . 55))\n ((:tag . "NNP") (:stem . "L34807") (:form . "L34807") (:end . 62)\n (:start . 56) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Ac9") (:form . "Ac9") (:end . 68) (:start . 65)\n (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n (:id . 60))\n ((:tag . "NNP") (:stem . "K01904") (:form . "K01904") (:end . 76)\n (:start . 70) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n (:id . 63))\n ((:tag . "NNP") (:stem . "Tam3_AM") (:form . "Tam3_AM") (:end . 86)\n (:start . 79) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 88) (:start . 87)\n (:id . 65))\n ((:tag . "NNP") (:stem . "X55078") (:form . "X55078") (:end . 94)\n (:start . 88) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 95) (:start . 94)\n (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n (:id . 68))\n ((:tag . "NNP") (:stem . "TAG1") (:form . "TAG1") (:end . 101) (:start . 97)\n (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n (:id . 70))\n ((:tag . "NNP") (:stem . "L12220") (:form . "L12220") (:end . 109)\n (:start . 103) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n (:id . 73))\n ((:tag . "NNP") (:stem . "Pegasus") (:form . "Pegasus") (:end . 119)\n (:start . 112) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n (:id . 75))\n ((:tag . "NN") (:stem . "u47019") (:form . "U47019") (:end . 127)\n (:start . 121) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 128) (:start . 127)\n (:id . 77))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 132) (:start . 129)\n (:id . 78))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 139)\n (:start . 133) (:id . 79))\n ((:tag . "NN") (:stem . "hat") (:form . "hAT") (:end . 143) (:start . 140)\n (:id . 80))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 155)\n (:start . 144) (:id . 81))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 160) (:start . 156)\n (:id . 82))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 166)\n (:start . 161) (:id . 83))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 170) (:start . 167)\n (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n (:id . 85))\n ((:tag . "NNP") (:stem . "Queensland") (:form . "Queensland") (:end . 182)\n (:start . 172) (:id . 86))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 188)\n (:start . 183) (:id . 87))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 192) (:start . 189)\n (:id . 88))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 193) (:start . 192)\n (:id . 89))\n ((:tag . "NN") (:stem . "house") (:form . "house") (:end . 199)\n (:start . 194) (:id . 90))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 203) (:start . 200)\n (:id . 91))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 204) (:start . 203)\n (:id . 92))\n ((:tag . "NN") (:stem . "maize") (:form . "maize") (:end . 210)\n (:start . 205) (:id . 93))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 211) (:start . 210)\n (:id . 94))\n ((:tag . "NN") (:stem . "snapdragon") (:form . "snapdragon") (:end . 222)\n (:start . 212) (:id . 95))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 223) (:start . 222)\n (:id . 96))\n ((:tag . "NN") (:stem . "thale-cress") (:form . "thale-cress") (:end . 235)\n (:start . 224) (:id . 97))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 236) (:start . 235)\n (:id . 98))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 240) (:start . 237)\n (:id . 99))\n ((:tag . "JJ") (:stem . "african") (:form . "African") (:end . 248)\n (:start . 241) (:id . 100))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 256)\n (:start . 249) (:id . 101))\n ((:tag . "NN") (:stem . "mosquito") (:form . "mosquito") (:end . 265)\n (:start . 257) (:id . 102))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 266) (:start . 265)\n (:id . 103))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 279)\n (:start . 267) (:id . 104))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 280) (:start . 279)\n (:id . 105)))@@@1@64@((:identifiers (:sid . :s6.376) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102116@unknown@formal@none@1@S@HOPPER_BD is from oriental fruit fly (GenBank AF486809).@(((:tag . "NNP") (:stem . "HOPPER_BD") (:form . "HOPPER_BD") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n (:id . 43))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 17) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "oriental") (:form . "oriental") (:end . 26)\n (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 32) (:start . 27)\n (:id . 46))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 36) (:start . 33)\n (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 38) (:start . 37)\n (:id . 48))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 45)\n (:start . 38) (:id . 49))\n ((:tag . "NNP") (:stem . "AF486809") (:form . "AF486809") (:end . 54)\n (:start . 46) (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s6.377) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102117@unknown@formal@none@1@S@The consensus sequences of hAT-1N_DP and hAT-1N_DP (nonautonomous transposons from fruit fly, D. pseudoobscura); HAT1N_DR, hAT-2n1_DR, and hAT-N19_DR (nonautonomous transposons from zebrafish); CHARLIE1A and CHESHIRE (human); hAT-N1_SP (sea urchin); ATHAT1, ATHAT7, and ATHAT10 (thale-cress); PegasusA, HATN4_AG, and hAT-2N_AG (African malaria mosquito) were reported in Repbase Update.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 23)\n (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 45))\n ((:tag . 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"TPase") (:end . 370)\n (:start . 365) (:id . 106))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 380)\n (:start . 371) (:id . 107))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 384) (:start . 381)\n (:id . 108))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 389) (:start . 385)\n (:id . 109))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 397)\n (:start . 390) (:id . 110))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 400) (:start . 398)\n (:id . 111))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 404) (:start . 401)\n (:id . 112))\n ((:tag . "NN") (:stem . "dbest") (:form . "dbEST") (:end . 410)\n (:start . 405) (:id . 113))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 418)\n (:start . 411) (:id . 114))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 421) (:start . 419)\n (:id . 115))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 429)\n (:start . 422) (:id . 116))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 430) (:start . 429)\n (:id . 117))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 431) (:start . 430)\n (:id . 118)))@@@1@77@((:hcues ((:id . :x6.382.1) (:span 139 145)))\n (:hscopes ((:id . :x6.382.1) (:span 139 170)))\n (:identifiers (:sid . :s6.382) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102122@unknown@formal@none@1@S@Analogously, matches to the Transib TPase detected in the AC011430 HTGs and AADC01054609 WGS GenBank sequences, which were annotated as portions of the human genome, were discarded as products of contamination (these sequences contain 100% identical copies of the non-long terminal repeat (LTR) retrotransposon G2_DM [17] from D. melanogaster).@(((:tag . "RB") (:stem . "analogously") (:form . "Analogously") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . 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"Content") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Target") (:form . "Target") (:end . 20)\n (:start . 14) (:id . 45))\n ((:tag . "NNPS") (:stem . "Site") (:form . "Sites") (:end . 26) (:start . 21)\n (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 30) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "hat") (:form . "hAT") (:end . 34) (:start . 31)\n (:id . 48))\n ((:tag . "NNS") (:stem . "transposon") (:form . "Transposons") (:end . 46)\n (:start . 35) (:id . 49)))@@@1@8@((:identifiers (:sid . :s6.384) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011 5102124@unknown@formal@none@1@S@The table shows that hAT transposons are inserted preferentially into GC-rich sites.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . 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"sites") (:end . 83) (:start . 78)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.385) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102125@unknown@formal@none@1@S@Each of the 35-bp insertion sites corresponds to two 14-bp and 13-bp DNA fragments flanking a genomic hAT element at its 5? and 3? termini; one of the 8-bp TSDs (flanking the 3? terminus of a transposon) was excluded in each case.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n (:id . 44))\n ((:tag . "JJ") (:stem . "35-bp") (:form . "35-bp") (:end . 17) (:start . 12)\n (:id . 45))\n ((:tag . "NN") (:stem . "insertion") (:form . 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"NNS") (:stem . "terminus") (:form . "termini") (:end . 138)\n (:start . 131) (:id . 68))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 139) (:start . 138)\n (:id . 69))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 143) (:start . 140)\n (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 146) (:start . 144)\n (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 150) (:start . 147)\n (:id . 72))\n ((:tag . "JJ") (:stem . "8-bp") (:form . "8-bp") (:end . 155) (:start . 151)\n (:id . 73))\n ((:tag . "NNS") (:stem . "tsd") (:form . "TSDs") (:end . 160) (:start . 156)\n (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 162) (:start . 161)\n (:id . 75))\n ((:tag . "VBG") (:stem . "flank") (:form . "flanking") (:end . 170)\n (:start . 162) (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 174) (:start . 171)\n (:id . 77))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 176) (:start . 175)\n (:id . 78))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 177) (:start . 176)\n (:id . 79))\n ((:tag . "NN") (:stem . "terminus") (:form . "terminus") (:end . 186)\n (:start . 178) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 189) (:start . 187)\n (:id . 81))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 191) (:start . 190)\n (:id . 82))\n ((:tag . "NN") (:stem . "transposon") (:form . "transposon") (:end . 202)\n (:start . 192) (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 203) (:start . 202)\n (:id . 84))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 207) (:start . 204)\n (:id . 85))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 216)\n (:start . 208) (:id . 86))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 219) (:start . 217)\n (:id . 87))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 224) (:start . 220)\n (:id . 88))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 229) (:start . 225)\n (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 230) (:start . 229)\n (:id . 90)))@@@1@49@((:identifiers (:sid . :s6.386) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102126@unknown@formal@none@1@S@Analogously, the 15-bp insertion sites were composed of two 4-bp and 3-bp flanking fragments.@(((:tag . "RB") (:stem . "analogously") (:form . "Analogously") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "15-bp") (:form . "15-bp") (:end . 22) (:start . 17)\n (:id . 45))\n ((:tag . "NN") (:stem . "insertion") (:form . "insertion") (:end . 32)\n (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "site") (:form . 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(:end . 265) (:start . 264)\n (:id . 88)))@@@1@47@((:identifiers (:sid . :s7.14) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102143@unknown@formal@none@1@S@Without intervention, the affected individuals die from opportunistic infections within the first few months of life.@(((:tag . "IN") (:stem . "without") (:form . "Without") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "intervention") (:form . "intervention") (:end . 20)\n (:start . 8) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "JJ") (:stem . "affected") (:form . "affected") (:end . 34)\n (:start . 26) (:id . 46))\n ((:tag . "NNS") (:stem . "individual") (:form . "individuals") (:end . 46)\n (:start . 35) (:id . 47))\n ((:tag . "VBP") (:stem . "die") (:form . 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"life") (:end . 116) (:start . 112)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n (:id . 59)))@@@1@18@((:ncues ((:id . :x7.15.1) (:span 0 7)))\n (:nscopes ((:id . :x7.15.1) (:span 0 20)))\n (:identifiers (:sid . :s7.15) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102144@unknown@formal@none@1@S@ADA occurs as a soluble monomer in all human cells, but also exists as “ecto-ADA,” bound to the membrane glycoprotein CD26/dipeptidyl peptidase IV, and it has been suggested that this form of ADA regulates extracellular adenosine levels [3].@(((:tag . "NNP") (:stem . "ADA") (:form . "ADA") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . 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"]") (:end . 240) (:start . 239)\n (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 241) (:start . 240)\n (:id . 87)))@@@1@46@((:hcues ((:id . :x7.16.1) (:span 164 173)))\n (:hscopes ((:id . :x7.16.1) (:span 164 236)))\n (:identifiers (:sid . :s7.16) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102145@unknown@formal@none@1@S@ADA deficiency is accompanied by greatly elevated levels of the ADA substrates adenosine and deoxyadenosine, both of which are biologically active purines that can have a deep impact on cellular physiology.@(((:tag . "NNP") (:stem . "ADA") (:form . "ADA") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "deficiency") (:form . "deficiency") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 17) (:start . 15)\n (:id . 44))\n ((:tag . "VBN") (:stem . "accompany") (:form . 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(:end . 206) (:start . 205)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s7.17) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102146@unknown@formal@none@1@S@Adenosine is not just a metabolite; it is also a signaling molecule that regulates numerous cellular functions by binding to G protein-coupled adenosine receptors (A1, A2a, A2b, and A3 in mammals) that can regulate intracellular cyclic adenosine monophosphate [4].@(((:tag . "NNP") (:stem . "Adenosine") (:form . "Adenosine") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n (:id . 43))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "RB") (:stem . "just") (:form . "just") (:end . 21) (:start . 17)\n (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n (:id . 46))\n ((:tag . "NN") (:stem . "metabolite") (:form . 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(:end . 264) (:start . 263)\n (:id . 89)))@@@1@48@((:identifiers (:sid . :s7.18) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102147@unknown@formal@none@1@S@Deoxyadenosine is a cytotoxic metabolite released by various cell populations that undergo programmed cell death; it can kill cells through a mechanism that includes disturbances in deoxynucleotide metabolism [5].@(((:tag . "NNP") (:stem . "Deoxyadenosine") (:form . "Deoxyadenosine")\n (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 17) (:start . 15)\n (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 19) (:start . 18)\n (:id . 44))\n ((:tag . "JJ") (:stem . "cytotoxic") (:form . "cytotoxic") (:end . 29)\n (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "metabolite") (:form . "metabolite") (:end . 40)\n (:start . 30) (:id . 46))\n ((:tag . "VBN") (:stem . "release") (:form . 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(:end . 213) (:start . 212)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s7.19) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102148@unknown@formal@none@1@S@Extracellular adenosine is now considered an important stress hormone that is released in excessive amounts in the vicinity of immune cells during both systemic and cellular stress [6].@(((:tag . "JJ") (:stem . "extracellular") (:form . "Extracellular")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "adenosine") (:form . "adenosine") (:end . 23)\n (:start . 14) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n (:id . 44))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 30) (:start . 27)\n (:id . 45))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 41)\n (:start . 31) (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 44) (:start . 42)\n (:id . 47))\n ((:tag . 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(:end . 59) (:start . 58)\n (:id . 52)))@@@1@11@((:ncues ((:id . :x7.24.1) (:span 7 10)))\n (:nscopes ((:id . :x7.24.1) (:span 7 58)))\n (:identifiers (:sid . :s7.24) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102153@unknown@formal@none@1@S@Recently, the cat eye syndrome critical region protein 1 (CECR1) gene was identified and shown to encode a protein representing a subfamily of proteins related to but distinct from classical ADAs [9].@(((:tag . "RB") (:stem . "recently") (:form . "Recently") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "NN") (:stem . "cat") (:form . "cat") (:end . 17) (:start . 14)\n (:id . 45))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "NN") (:stem . "syndrome") (:form . "syndrome") (:end . 30)\n (:start . 22) (:id . 47))\n ((:tag . "JJ") (:stem . "critical") (:form . "critical") (:end . 39)\n (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 46)\n (:start . 40) (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 54)\n (:start . 47) (:id . 50))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 56) (:start . 55)\n (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n (:id . 52))\n ((:tag . "NN") (:stem . "cecr1") (:form . "CECR1") (:end . 63) (:start . 58)\n (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 64) (:start . 63)\n (:id . 54))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 69) (:start . 65)\n (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 73) (:start . 70)\n (:id . 56))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 84)\n (:start . 74) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n (:id . 58))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 94) (:start . 89)\n (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 97) (:start . 95)\n (:id . 60))\n ((:tag . "VB") (:stem . "encode") (:form . "encode") (:end . 104)\n (:start . 98) (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 106) (:start . 105)\n (:id . 62))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 114)\n (:start . 107) (:id . 63))\n ((:tag . "VBG") (:stem . "represent") (:form . "representing") (:end . 127)\n (:start . 115) (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 129) (:start . 128)\n (:id . 65))\n ((:tag . "NN") (:stem . "subfamily") (:form . "subfamily") (:end . 139)\n (:start . 130) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n (:id . 67))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 151)\n (:start . 143) (:id . 68))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 159)\n (:start . 152) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 162) (:start . 160)\n (:id . 70))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 166) (:start . 163)\n (:id . 71))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 175)\n (:start . 167) (:id . 72))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 180) (:start . 176)\n (:id . 73))\n ((:tag . "JJ") (:stem . "classical") (:form . "classical") (:end . 190)\n (:start . 181) (:id . 74))\n ((:tag . "NNS") (:stem . "ada") (:form . "ADAs") (:end . 195) (:start . 191)\n (:id . 75))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 197) (:start . 196)\n (:id . 76))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 198) (:start . 197)\n (:id . 77))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 199) (:start . 198)\n (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n (:id . 79)))@@@1@38@((:identifiers (:sid . :s7.25) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102154@unknown@formal@none@1@S@The duplication of a small region of chromosome 22 containing this gene is associated with “cat eye syndrome,” a disorder characterized by hypoplastic kidneys, congenital heart malformation, and anomalous pulmonary venous connections.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "duplication") (:form . "duplication") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n (:id . 45))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 26) (:start . 21)\n (:id . 46))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 33)\n (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n (:id . 48))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 47)\n (:start . 37) (:id . 49))\n ((:tag . "CD") (:stem . "22") (:form . "22") (:end . 50) (:start . 48)\n (:id . 50))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 61)\n (:start . 51) (:id . 51))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 66) (:start . 62)\n (:id . 52))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 71) (:start . 67)\n (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 74) (:start . 72)\n (:id . 54))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 85)\n (:start . 75) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 90) (:start . 86)\n (:id . 56))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 92) (:start . 91)\n (:id . 57))\n ((:tag . "NN") (:stem . "cat") (:form . "cat") (:end . 95) (:start . 92)\n (:id . 58))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 99) (:start . 96)\n (:id . 59))\n ((:tag . "NN") (:stem . "syndrome") (:form . "syndrome") (:end . 108)\n (:start . 100) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n (:id . 61))\n ((:tag . "VBD") (:stem . "”") (:form . "”") (:end . 110) (:start . 109)\n (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 112) (:start . 111)\n (:id . 63))\n ((:tag . "NN") (:stem . "disorder") (:form . "disorder") (:end . 121)\n (:start . 113) (:id . 64))\n ((:tag . "VBN") (:stem . "characterize") (:form . "characterized")\n (:end . 135) (:start . 122) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 138) (:start . 136)\n (:id . 66))\n ((:tag . "JJ") (:stem . "hypoplastic") (:form . "hypoplastic") (:end . 150)\n (:start . 139) (:id . 67))\n ((:tag . "NNS") (:stem . "kidney") (:form . "kidneys") (:end . 158)\n (:start . 151) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 159) (:start . 158)\n (:id . 69))\n ((:tag . "JJ") (:stem . "congenital") (:form . "congenital") (:end . 170)\n (:start . 160) (:id . 70))\n ((:tag . "NN") (:stem . "heart") (:form . "heart") (:end . 176)\n (:start . 171) (:id . 71))\n ((:tag . "NN") (:stem . "malformation") (:form . "malformation") (:end . 189)\n (:start . 177) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 190) (:start . 189)\n (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 194) (:start . 191)\n (:id . 74))\n ((:tag . "JJ") (:stem . "anomalous") (:form . "anomalous") (:end . 204)\n (:start . 195) (:id . 75))\n ((:tag . "JJ") (:stem . "pulmonary") (:form . "pulmonary") (:end . 214)\n (:start . 205) (:id . 76))\n ((:tag . "JJ") (:stem . "venous") (:form . "venous") (:end . 221)\n (:start . 215) (:id . 77))\n ((:tag . "NNS") (:stem . "connection") (:form . "connections") (:end . 233)\n (:start . 222) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n (:id . 79)))@@@1@38@((:identifiers (:sid . :s7.26) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102155@unknown@formal@none@1@S@The founding member of this subfamily is encoded by insect-derived growth factor(IDGF) [10], and homologs have been described in various organisms [11–14].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBG") (:stem . "found") (:form . "founding") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "member") (:form . "member") (:end . 19)\n (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 27) (:start . 23)\n (:id . 46))\n ((:tag . "NN") (:stem . "subfamily") (:form . "subfamily") (:end . 37)\n (:start . 28) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 40) (:start . 38)\n (:id . 48))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 48)\n (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 51) (:start . 49)\n (:id . 50))\n ((:tag . "JJ") (:stem . "insect-derived") (:form . "insect-derived")\n (:end . 66) (:start . 52) (:id . 51))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 73)\n (:start . 67) (:id . 52))\n ((:tag . "NNS") (:stem . "factor(IDGF)") (:form . "factor(IDGF)") (:end . 86)\n (:start . 74) (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 88) (:start . 87)\n (:id . 54))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 90) (:start . 88)\n (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 91) (:start . 90)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n (:id . 58))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 105)\n (:start . 97) (:id . 59))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 110) (:start . 106)\n (:id . 60))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 115) (:start . 111)\n (:id . 61))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 125)\n (:start . 116) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 128) (:start . 126)\n (:id . 63))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 136)\n (:start . 129) (:id . 64))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 146)\n (:start . 137) (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 148) (:start . 147)\n (:id . 66))\n ((:tag . "CD") (:stem . "11–14") (:form . "11–14") (:end . 153)\n (:start . 148) (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 154) (:start . 153)\n (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s7.27) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102156@unknown@formal@none@1@S@We have previously found six Drosophila genes with sequence similarity to the CECR1 subfamily [15].@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 18)\n (:start . 8) (:id . 44))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 24) (:start . 19)\n (:id . 45))\n ((:tag . "CD") (:stem . "six") (:form . "six") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 39)\n (:start . 29) (:id . 47))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 45) (:start . 40)\n (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 50) (:start . 46)\n (:id . 49))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 59)\n (:start . 51) (:id . 50))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 70)\n (:start . 60) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n (:id . 53))\n ((:tag . "NN") (:stem . "cecr1") (:form . "CECR1") (:end . 83) (:start . 78)\n (:id . 54))\n ((:tag . "NN") (:stem . "subfamily") (:form . "subfamily") (:end . 93)\n (:start . 84) (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 95) (:start . 94)\n (:id . 56))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 97) (:start . 95)\n (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 98) (:start . 97)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.28) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102157@unknown@formal@none@1@S@Their products are mitogenic on Drosophila cells, and at least two of them (ADGF-A and ADGF-D) exhibit strong ADA activity, which is necessary for their mitogenic function.@(((:tag . "PRP$") (:stem . "their") (:form . "Their") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "product") (:form . "products") (:end . 14)\n (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 18) (:start . 15)\n (:id . 44))\n ((:tag . "JJ") (:stem . "mitogenic") (:form . "mitogenic") (:end . 28)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 31) (:start . 29)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 42)\n (:start . 32) (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 48) (:start . 43)\n (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 56) (:start . 54)\n (:id . 51))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 62) (:start . 57)\n (:id . 52))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 66) (:start . 63)\n (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n (:id . 54))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 74) (:start . 70)\n (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 76) (:start . 75)\n (:id . 56))\n ((:tag . "NNP") (:stem . "ADGF-A") (:form . "ADGF-A") (:end . 82)\n (:start . 76) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n (:id . 58))\n ((:tag . "NNP") (:stem . "ADGF-D") (:form . "ADGF-D") (:end . 93)\n (:start . 87) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 94) (:start . 93)\n (:id . 60))\n ((:tag . "VBP") (:stem . "exhibit") (:form . "exhibit") (:end . 102)\n (:start . 95) (:id . 61))\n ((:tag . "JJ") (:stem . "strong") (:form . "strong") (:end . 109)\n (:start . 103) (:id . 62))\n ((:tag . "NNP") (:stem . "ADA") (:form . "ADA") (:end . 113) (:start . 110)\n (:id . 63))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 122)\n (:start . 114) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n (:id . 65))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 129)\n (:start . 124) (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 132) (:start . 130)\n (:id . 67))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 142)\n (:start . 133) (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 146) (:start . 143)\n (:id . 69))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 152)\n (:start . 147) (:id . 70))\n ((:tag . "JJ") (:stem . "mitogenic") (:form . "mitogenic") (:end . 162)\n (:start . 153) (:id . 71))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 171)\n (:start . 163) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s7.29) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102158@unknown@formal@none@1@S@We therefore named them adenosine deaminase-related growth factors (ADGFs).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . "VBD") (:stem . "name") (:form . "named") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 23) (:start . 19)\n (:id . 45))\n ((:tag . "JJ") (:stem . "adenosine") (:form . "adenosine") (:end . 33)\n (:start . 24) (:id . 46))\n ((:tag . "JJ") (:stem . "deaminase-related") (:form . "deaminase-related")\n (:end . 51) (:start . 34) (:id . 47))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 58)\n (:start . 52) (:id . 48))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 66)\n (:start . 59) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n (:id . 50))\n ((:tag . "NNP") (:stem . "ADGF") (:form . "ADGFs") (:end . 73) (:start . 68)\n (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 74) (:start . 73)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s7.30) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102160@unknown@formal@none@1@S@Drosophila also contains a gene, termed Ada, with sequence similarity to human ADA, but as we have previously shown the product of this gene is most likely not an active ADA [16].@(((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . 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"ADA") (:end . 173) (:start . 170)\n (:id . 75))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 175) (:start . 174)\n (:id . 76))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 177) (:start . 175)\n (:id . 77))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 178) (:start . 177)\n (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n (:id . 79)))@@@1@38@((:hcues ((:id . :x7.32.2) (:span 149 155)))\n (:ncues ((:id . :x7.32.1) (:span 156 159)))\n (:hscopes ((:id . :x7.32.2) (:span 149 173)))\n (:nscopes ((:id . :x7.32.1) (:span 156 173)))\n (:identifiers (:sid . :s7.32) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102161@unknown@formal@none@1@S@In this report we show that a null mutation in Drosophila ADGF-A gene leads to dramatically increased levels of adenosine and deoxyadenosine in the larval hemolymph.@(((:tag . "IN") (:stem . "in") (:form . 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(:end . 123) (:start . 122)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s7.34) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102163@unknown@formal@none@1@S@We present a detailed analysis of the hematopoietic defects associated with the adgf-a mutation, show a genetic interaction of this mutation with signaling through the Drosophila adenosine receptor (AdoR, encoded by the gene CG9753) and with regulation of premetamorphic changes by ecdysone, as well as a genetic interaction of ADGF-A with a major innate immunity regulator—the Toll signaling pathway.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "present") (:form . "present") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "JJ") (:stem . "detailed") (:form . 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"disc") (:form . "discs") (:end . 91) (:start . 86)\n (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n (:id . 58))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 101) (:start . 96)\n (:id . 59))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 108)\n (:start . 102) (:id . 60))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 115)\n (:start . 109) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n (:id . 62)))@@@1@21@((:ncues ((:id . :x7.43.1) (:span 37 42)))\n (:nscopes ((:id . :x7.43.1) (:span 0 67)))\n (:identifiers (:sid . :s7.43) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102172@unknown@formal@none@1@S@Less than 30% of homozygotes eventually pupate.@(((:tag . "RBR") (:stem . "less") (:form . "Less") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "than") (:form . 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"(") (:end . 73) (:start . 72)\n (:id . 57))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 79)\n (:start . 73) (:id . 58))\n ((:tag . "NN") (:stem . "1d") (:form . "1D") (:end . 82) (:start . 80)\n (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s7.46) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102175@unknown@formal@none@1@S@Less than 2% of mutant pupae develop normally and eventually emerge as adults without any obvious abnormalities besides the abdominal curvature; some of them are sterile.@(((:tag . "RBR") (:stem . "less") (:form . "Less") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . "CD") (:stem . "2") (:form . 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"NNS") (:stem . "adult") (:form . "adults") (:end . 77)\n (:start . 71) (:id . 55))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 85)\n (:start . 78) (:id . 56))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 89) (:start . 86)\n (:id . 57))\n ((:tag . "JJ") (:stem . "obvious") (:form . "obvious") (:end . 97)\n (:start . 90) (:id . 58))\n ((:tag . "NNS") (:stem . "abnormality") (:form . "abnormalities")\n (:end . 111) (:start . 98) (:id . 59))\n ((:tag . "IN") (:stem . "besides") (:form . "besides") (:end . 119)\n (:start . 112) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n (:id . 61))\n ((:tag . "JJ") (:stem . "abdominal") (:form . "abdominal") (:end . 133)\n (:start . 124) (:id . 62))\n ((:tag . "NN") (:stem . "curvature") (:form . "curvature") (:end . 143)\n (:start . 134) (:id . 63))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 144) (:start . 143)\n (:id . 64))\n ((:tag . "DT") (:stem . 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")") (:end . 180) (:start . 179)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n (:id . 74)))@@@1@33@((:hcues ((:id . :x7.48.1) (:span 0 10)))\n (:hscopes ((:id . :x7.48.1) (:span 0 86)))\n (:identifiers (:sid . :s7.48) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102177@unknown@formal@none@1@S@The adgf-a homozygous flies carrying the HS-ADGF-A construct showed survival rates significantly higher than adgf-a even without heat shock, probably due to leaky expression of the HS-ADGF-A construct (Figure 2A).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "adgf-a") (:form . "adgf-a") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 21)\n (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "fly") (:form . 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(:end . 213) (:start . 212)\n (:id . 75)))@@@1@34@((:hcues ((:id . :x7.49.1) (:span 141 149)))\n (:ncues ((:id . :x7.49.2) (:span 121 128)))\n (:hscopes ((:id . :x7.49.1) (:span 141 200)))\n (:nscopes ((:id . :x7.49.2) (:span 121 139)))\n (:identifiers (:sid . :s7.49) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102178@unknown@formal@none@1@S@However, while non-heat shocked animals still produced many melanotic tumors, only 22% of animals that were heat shocked as late embryos/early first instar developed these tumors (Figure 2B).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "JJ") (:stem . "non-heat") (:form . "non-heat") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "JJ") (:stem . 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"]") (:end . 180) (:start . 179)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n (:id . 74)))@@@1@33@((:ncues ((:id . :x7.79.1) (:span 29 32)))\n (:nscopes ((:id . :x7.79.1) (:span 29 90)))\n (:identifiers (:sid . :s7.79) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102208@unknown@formal@none@1@S@However, the lymph glands of adgf-a mutant larvae are already dispersed in the late third instar.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "lymph") (:form . "lymph") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "NNS") (:stem . "gland") (:form . "glands") (:end . 25)\n (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . 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"NN") (:stem . "instar") (:form . "instar") (:end . 96)\n (:start . 90) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.80) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102210@unknown@formal@none@1@S@To analyze hemocytes in living larvae, we used the Hemolectin marker (Hml) [21].@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "analyze") (:form . "analyze") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "hemocyte") (:form . "hemocytes") (:end . 20)\n (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 23) (:start . 21)\n (:id . 45))\n ((:tag . "VBG") (:stem . "live") (:form . "living") (:end . 30) (:start . 24)\n (:id . 46))\n ((:tag . "NNS") (:stem . "larva") (:form . 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"21") (:end . 78) (:start . 76)\n (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 79) (:start . 78)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s7.82) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102211@unknown@formal@none@1@S@We compared the number and distribution of hemocytes stained by GFP in flies carrying hml-Gal4 UAS-GFP in wild-type and mutant backgrounds.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "compare") (:form . "compared") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 22)\n (:start . 16) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . 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"hml-Gal4") (:end . 94)\n (:start . 86) (:id . 56))\n ((:tag . "NN") (:stem . "uas-gfp") (:form . "UAS-GFP") (:end . 102)\n (:start . 95) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 105) (:start . 103)\n (:id . 58))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 115)\n (:start . 106) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 119) (:start . 116)\n (:id . 60))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 126)\n (:start . 120) (:id . 61))\n ((:tag . "NNS") (:stem . "background") (:form . "backgrounds") (:end . 138)\n (:start . 127) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.83) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102212@unknown@formal@none@1@S@While there are relatively few hemocytes, mostly free-floating in the hemolymph, in early third-instar wild-type larvae (see Figure 4I), a much higher number of hemocytes, which are mostly attached to the tissues under the integument (described as sessile hemocytes in [19]), was observed in mutant larvae (see Figure 4J).@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 26)\n (:start . 16) (:id . 45))\n ((:tag . "JJ") (:stem . "few") (:form . 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"larvae") (:end . 305)\n (:start . 299) (:id . 98))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 307) (:start . 306)\n (:id . 99))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 310) (:start . 307)\n (:id . 100))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 317)\n (:start . 311) (:id . 101))\n ((:tag . "NN") (:stem . "4j") (:form . "4J") (:end . 320) (:start . 318)\n (:id . 102))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 321) (:start . 320)\n (:id . 103))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 322) (:start . 321)\n (:id . 104)))@@@1@63@((:identifiers (:sid . :s7.84) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102213@unknown@formal@none@1@S@A similar behavior was detected later in wild-type larvae, toward the end of the third instar (see Figure 4H).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . 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(:end . 110) (:start . 109)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s7.85) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102214@unknown@formal@none@1@S@At this stage, the Hml marker disappeared from the most of the hemocytes in mutants (see Figure 4F and 4G).@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "stage") (:form . "stage") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Hml") (:form . "Hml") (:end . 22) (:start . 19)\n (:id . 47))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 29)\n (:start . 23) (:id . 48))\n ((:tag . "VBD") (:stem . 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(:end . 123) (:start . 122)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.89) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102218@unknown@formal@none@1@S@Each count was repeated five to ten times and the standard error is shown.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "count") (:form . "count") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "VBN") (:stem . "repeat") (:form . "repeated") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 28) (:start . 24)\n (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n (:id . 47))\n ((:tag . "CD") (:stem . "ten") (:form . "ten") (:end . 35) (:start . 32)\n (:id . 48))\n ((:tag . "NNS") (:stem . "time") (:form . 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(:end . 74) (:start . 73)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s7.90) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102220@unknown@formal@none@1@S@(A–E) Differential interference contrast microscopy of living circulating hemocytes (magnification 200×; scale bar, 10 ?m).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A–E") (:form . "A–E") (:end . 4) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "JJ") (:stem . "differential") (:form . "Differential") (:end . 18)\n (:start . 6) (:id . 45))\n ((:tag . "NN") (:stem . "interference") (:form . "interference") (:end . 31)\n (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 40)\n (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "microscopy") (:form . 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(:end . 188) (:start . 187)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s7.96) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102225@unknown@formal@none@1@S@While most of the cells from wild-type larvae are GFP-positive (F), just few of the cells from late third instar adgf-a larvae are stained by GFP at this stage (G).@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 23) (:start . 18)\n (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 28) (:start . 24)\n (:id . 47))\n ((:tag . "JJ") (:stem . "wild-type") (:form . 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"the") (:end . 83) (:start . 80)\n (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 89) (:start . 84)\n (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 94) (:start . 90)\n (:id . 61))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 99) (:start . 95)\n (:id . 62))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 105)\n (:start . 100) (:id . 63))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 112)\n (:start . 106) (:id . 64))\n ((:tag . "NN") (:stem . "adgf-a") (:form . "adgf-a") (:end . 119)\n (:start . 113) (:id . 65))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 126)\n (:start . 120) (:id . 66))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 130) (:start . 127)\n (:id . 67))\n ((:tag . "VBN") (:stem . "stain") (:form . "stained") (:end . 138)\n (:start . 131) (:id . 68))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 141) (:start . 139)\n (:id . 69))\n ((:tag . "NNP") (:stem . "GFP") (:form . "GFP") (:end . 145) (:start . 142)\n (:id . 70))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 148) (:start . 146)\n (:id . 71))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 153) (:start . 149)\n (:id . 72))\n ((:tag . "NN") (:stem . "stage") (:form . "stage") (:end . 159)\n (:start . 154) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 161) (:start . 160)\n (:id . 74))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 162) (:start . 161)\n (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 163) (:start . 162)\n (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s7.97) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102226@unknown@formal@none@1@S@(H–J) Fluorescence microscopy of living larvae with Hml-GFP stained hemocytes (magnification 40×; scale bar, 100 ?m).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "H–J") (:form . "H–J") (:end . 4) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NNP") (:stem . "Fluorescence") (:form . "Fluorescence") (:end . 18)\n (:start . 6) (:id . 45))\n ((:tag . "NN") (:stem . "microscopy") (:form . "microscopy") (:end . 29)\n (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n (:id . 47))\n ((:tag . "VBG") (:stem . "live") (:form . "living") (:end . 39) (:start . 33)\n (:id . 48))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 46)\n (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 51) (:start . 47)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Hml-GFP") (:form . "Hml-GFP") (:end . 59)\n (:start . 52) (:id . 51))\n ((:tag . "VBD") (:stem . "stain") (:form . "stained") (:end . 67)\n (:start . 60) (:id . 52))\n ((:tag . "NNS") (:stem . "hemocyte") (:form . "hemocytes") (:end . 77)\n (:start . 68) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n (:id . 54))\n ((:tag . "NN") (:stem . "magnification") (:form . "magnification")\n (:end . 92) (:start . 79) (:id . 55))\n ((:tag . "CD") (:stem . "40×") (:form . "40×") (:end . 96) (:start . 93)\n (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 97) (:start . 96)\n (:id . 57))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 103) (:start . 98)\n (:id . 58))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 107) (:start . 104)\n (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n (:id . 60))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 112) (:start . 109)\n (:id . 61))\n ((:tag . "NN") (:stem . "?m") (:form . "?m") (:end . 115) (:start . 113)\n (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s7.98) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102227@unknown@formal@none@1@S@Posterior part of late third-instar wild-type larva (H).@(((:tag . "JJ") (:stem . "posterior") (:form . "Posterior") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 14) (:start . 10)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n (:id . 44))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 22) (:start . 18)\n (:id . 45))\n ((:tag . "JJ") (:stem . "third-instar") (:form . "third-instar") (:end . 35)\n (:start . 23) (:id . 46))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 45)\n (:start . 36) (:id . 47))\n ((:tag . "NN") (:stem . "larva") (:form . "larva") (:end . 51) (:start . 46)\n (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 53) (:start . 52)\n (:id . 49))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 54) (:start . 53)\n (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s7.99) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102228@unknown@formal@none@1@S@Middle sections of early third-instar larvae of wild type (I) and adgf-a mutant (J).@(((:tag . "JJ") (:stem . "middle") (:form . "Middle") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 15)\n (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n (:id . 44))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 24) (:start . 19)\n (:id . 45))\n ((:tag . "JJ") (:stem . "third-instar") (:form . "third-instar") (:end . 37)\n (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 44)\n (:start . 38) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n (:id . 48))\n ((:tag . "JJ") (:stem . 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(:end . 84) (:start . 83)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s7.100) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102230@unknown@formal@none@1@S@Crystal cells were visualized by heating larvae of different genotypes at 60 °C for 10 min [46].@(((:tag . "JJ") (:stem . "crystal") (:form . "Crystal") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 13) (:start . 8)\n (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "VBN") (:stem . "visualize") (:form . "visualized") (:end . 29)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 32) (:start . 30)\n (:id . 46))\n ((:tag . "VBG") (:stem . "heat") (:form . "heating") (:end . 40)\n (:start . 33) (:id . 47))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 47)\n (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n (:id . 49))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 60)\n (:start . 51) (:id . 50))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 70)\n (:start . 61) (:id . 51))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 73) (:start . 71)\n (:id . 52))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 76) (:start . 74)\n (:id . 53))\n ((:tag . "NNP") (:stem . "°C") (:form . "°C") (:end . 79) (:start . 77)\n (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 83) (:start . 80)\n (:id . 55))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 86) (:start . 84)\n (:id . 56))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 90) (:start . 87)\n (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 92) (:start . 91)\n (:id . 58))\n ((:tag . "CD") (:stem . "46") (:form . "46") (:end . 94) (:start . 92)\n (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 95) (:start . 94)\n (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s7.102) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102231@unknown@formal@none@1@S@(A) Wild-type larva, (B) adgf-a single mutant, (C) adoR adgf-a double mutant (scale bar, 0.5 mm).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "Wild-type") (:end . 13)\n (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "larva") (:form . "larva") (:end . 19) (:start . 14)\n (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n (:id . 48))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 23) (:start . 22)\n (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 24) (:start . 23)\n (:id . 50))\n ((:tag . "JJ") (:stem . "adgf-a") (:form . "adgf-a") (:end . 31)\n (:start . 25) (:id . 51))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 38)\n (:start . 32) (:id . 52))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 45)\n (:start . 39) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 48) (:start . 47)\n (:id . 55))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 49) (:start . 48)\n (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 50) (:start . 49)\n (:id . 57))\n ((:tag . "NNP") (:stem . "adoR") (:form . "adoR") (:end . 55) (:start . 51)\n (:id . 58))\n ((:tag . "NN") (:stem . "adgf-a") (:form . "adgf-a") (:end . 62)\n (:start . 56) (:id . 59))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 69)\n (:start . 63) (:id . 60))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 76)\n (:start . 70) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n (:id . 62))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 83) (:start . 78)\n (:id . 63))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 87) (:start . 84)\n (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n (:id . 65))\n ((:tag . "CD") (:stem . "0.5") (:form . "0.5") (:end . 92) (:start . 89)\n (:id . 66))\n ((:tag . "NN") (:stem . "mm") (:form . "mm") (:end . 95) (:start . 93)\n (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s7.103) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102232@unknown@formal@none@1@S@The adgf-a Mutant Phenotype Is Rescued by Expression of ADGF-A in the Lymph Glands@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "adgf-a") (:form . "adgf-a") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "mutant") (:form . "Mutant") (:end . 17)\n (:start . 11) (:id . 44))\n ((:tag . "NNP") (:stem . "Phenotype") (:form . "Phenotype") (:end . 27)\n (:start . 18) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "Is") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "VBN") (:stem . "rescue") (:form . "Rescued") (:end . 38)\n (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 41) (:start . 39)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Expression") (:form . "Expression") (:end . 52)\n (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n (:id . 50))\n ((:tag . "NNP") (:stem . "ADGF-A") (:form . "ADGF-A") (:end . 62)\n (:start . 56) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Lymph") (:form . "Lymph") (:end . 75) (:start . 70)\n (:id . 54))\n ((:tag . "NNPS") (:stem . "Glands") (:form . "Glands") (:end . 82)\n (:start . 76) (:id . 55)))@@@1@14@((:identifiers (:sid . :s7.104) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5102233@unknown@formal@none@1@S@To distinguish which tissues require ADGF-A expression for proper development, we tested for rescue of adgf-a lethality by expressing ADGF-A in specific subsets of larval tissues.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "distinguish") (:form . "distinguish") (:end . 14)\n (:start . 3) (:id . 43))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 20) (:start . 15)\n (:id . 44))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 28)\n (:start . 21) (:id . 45))\n ((:tag . "VBP") (:stem . "require") (:form . "require") (:end . 36)\n (:start . 29) (:id . 46))\n ((:tag . "NNP") (:stem . "ADGF-A") (:form . 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"tissues") (:end . 178)\n (:start . 171) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n (:id . 69)))@@@1@28@((:hcues ((:id . :x7.105.1) (:span 82 88)))\n (:hscopes ((:id . :x7.105.1) (:span 82 178)))\n (:identifiers (:sid . :s7.105) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102234@unknown@formal@none@1@S@A transgenic line carrying the UAS-ADGF-A construct on Chromosome II was crossed to lines expressing the Gal4 driver [18] in different tissues (Table 1).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 12)\n (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 17) (:start . 13)\n (:id . 44))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 26)\n (:start . 18) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . 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(:end . 261) (:start . 260)\n (:id . 84)))@@@1@43@((:identifiers (:sid . :s7.107) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102236@unknown@formal@none@1@S@No line expressing the Gal4 driver exclusively in the lymph glands has been reported, so we used a combination of lines sharing in common the feature of Gal4 driver expression in the lymph glands.@(((:tag . "DT") (:stem . "no") (:form . "No") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 18)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "NN") (:stem . "gal4") (:form . "Gal4") (:end . 27) (:start . 23)\n (:id . 46))\n ((:tag . "NN") (:stem . "driver") (:form . "driver") (:end . 34)\n (:start . 28) (:id . 47))\n ((:tag . "RB") (:stem . 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(:end . 196) (:start . 195)\n (:id . 77)))@@@1@36@((:ncues ((:id . :x7.108.1) (:span 0 2)))\n (:nscopes ((:id . :x7.108.1) (:span 0 84)))\n (:identifiers (:sid . :s7.108) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102237@unknown@formal@none@1@S@The results (see Figure 2 and Table 1) clearly demonstrate that expression of ADGF-A in the lymph glands (driven by Cg-Gal4,e33C-Gal4, or c564-Gal4), but not in any other tissue examined, is necessary and sufficient to fully rescue the adgf-a lethality.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 13) (:start . 12)\n (:id . 44))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 16) (:start . 13)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Figure") (:form . 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"lethality") (:end . 252)\n (:start . 243) (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 253) (:start . 252)\n (:id . 89)))@@@1@48@((:ncues ((:id . :x7.109.1) (:span 154 157)))\n (:nscopes ((:id . :x7.109.1) (:span 154 186)))\n (:identifiers (:sid . :s7.109) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102238@unknown@formal@none@1@S@In e33C-Gal4/UAS-ADGF-A, strong expression of ADGF-A in all lobes of developing lymph glands (but not in circulating hemocytes) reduces the number of hemocytes in the hemolymph to almost normal levels (see Figure 3).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "e33c-gal4/uas-adgf-a")\n (:form . "e33C-Gal4/UAS-ADGF-A") (:end . 23) (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n (:id . 44))\n ((:tag . "JJ") (:stem . "strong") (:form . 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"(") (:stem . "(") (:form . "(") (:end . 94) (:start . 93)\n (:id . 56))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 97) (:start . 94)\n (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 101) (:start . 98)\n (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 104) (:start . 102)\n (:id . 59))\n ((:tag . "VBG") (:stem . "circulate") (:form . "circulating") (:end . 116)\n (:start . 105) (:id . 60))\n ((:tag . "NNS") (:stem . "hemocyte") (:form . "hemocytes") (:end . 126)\n (:start . 117) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 127) (:start . 126)\n (:id . 62))\n ((:tag . "VBZ") (:stem . "reduce") (:form . "reduces") (:end . 135)\n (:start . 128) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n (:id . 64))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 146)\n (:start . 140) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . 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"see") (:end . 205) (:start . 202)\n (:id . 76))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 212)\n (:start . 206) (:id . 77))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 214) (:start . 213)\n (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 215) (:start . 214)\n (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n (:id . 80)))@@@1@39@((:identifiers (:sid . :s7.110) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102240@unknown@formal@none@1@S@However, when assayed by survival rate and melanotic tumor formation, the rescue by Cg-Gal4 is full and similar to that of e33C-Gal4 (see Figure 2).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "WRB") (:stem . "when") (:form . 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"NN") (:stem . "rescue") (:form . "rescue") (:end . 80)\n (:start . 74) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 83) (:start . 81)\n (:id . 56))\n ((:tag . "NN") (:stem . "cg-gal4") (:form . "Cg-Gal4") (:end . 91)\n (:start . 84) (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 94) (:start . 92)\n (:id . 58))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 99) (:start . 95)\n (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n (:id . 60))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 111)\n (:start . 104) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 114) (:start . 112)\n (:id . 62))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 119) (:start . 115)\n (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n (:id . 64))\n ((:tag . "NN") (:stem . "e33c-gal4") (:form . "e33C-Gal4") (:end . 132)\n (:start . 123) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n (:id . 66))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 137) (:start . 134)\n (:id . 67))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 144)\n (:start . 138) (:id . 68))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 146) (:start . 145)\n (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s7.112) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102241@unknown@formal@none@1@S@The difference in effectiveness may be explained by the different expression patterns of the drivers.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . 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"it") (:end . 120) (:start . 118)\n (:id . 63))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 125) (:start . 121)\n (:id . 64))\n ((:tag . "RB") (:stem . "fully") (:form . "fully") (:end . 131)\n (:start . 126) (:id . 65))\n ((:tag . "VBD") (:stem . "rescue") (:form . "rescued") (:end . 139)\n (:start . 132) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n (:id . 67))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 150)\n (:start . 144) (:id . 68))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 160)\n (:start . 151) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n (:id . 70)))@@@1@29@((:ncues ((:id . :x7.115.1) (:span 24 27)))\n (:nscopes ((:id . :x7.115.1) (:span 24 62)))\n (:identifiers (:sid . :s7.115) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102244@unknown@formal@none@1@S@We have tried two different insertions of the Dot-Gal4 construct.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBN") (:stem . "try") (:form . "tried") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 17) (:start . 14)\n (:id . 45))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 27)\n (:start . 18) (:id . 46))\n ((:tag . "NNS") (:stem . "insertion") (:form . "insertions") (:end . 38)\n (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n (:id . 49))\n ((:tag . "NN") (:stem . "dot-gal4") (:form . "Dot-Gal4") (:end . 54)\n (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 64)\n (:start . 55) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s7.116) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102245@unknown@formal@none@1@S@The Dot-Gal411C on Chromosome II, which shows weak expression [24], did not rescue the phenotype, but a Dot-Gal443A insertion on Chromosome X, which shows stronger expression, rescued approximately half of the mutant animals (Figure 2).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Dot-Gal411C") (:form . 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(:end . 226) (:start . 225)\n (:id . 76)))@@@1@35@((:hcues ((:id . :x7.118.2) (:span 43 53)))\n (:ncues ((:id . :x7.118.1) (:span 197 200)))\n (:hscopes ((:id . :x7.118.2) (:span 43 179)))\n (:nscopes ((:id . :x7.118.1) (:span 184 225)))\n (:identifiers (:sid . :s7.118) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102247@unknown@formal@none@1@S@Expression of ADGF-A in salivary glands and fat body (as well as in other tissues) is not required for full rescue, as demonstrated by use of the Cg-Gal4,Dot-Gal4, but especially by e33C-Gal4 driver, and is also not sufficient to rescue the phenotype at all, as demonstrated by T110-Gal4 and Lsp2-Gal4 (Table 1).@(((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 43))\n ((:tag . "NNP") (:stem . "ADGF-A") (:form . 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(:end . 297) (:start . 296)\n (:id . 91)))@@@1@50@((:hcues ((:id . :x7.150.2) (:span 110 117)))\n (:ncues ((:id . :x7.150.1) (:span 245 256)))\n (:hscopes ((:id . :x7.150.2) (:span 110 296)))\n (:nscopes ((:id . :x7.150.1) (:span 245 296)))\n (:identifiers (:sid . :s7.150) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102280@unknown@formal@none@1@S@We have identified a putative homolog of the mammalian adenosine receptor family in the Drosophila genome, AdoR, and produced a null mutation in this gene using homologous recombination (adoR; ED, unpublished data).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 18)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . 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(:end . 196) (:start . 195)\n (:id . 74)))@@@1@33@((:hcues ((:id . :x7.154.1) (:span 32 42)))\n (:hscopes ((:id . :x7.154.1) (:span 32 195)))\n (:identifiers (:sid . :s7.154) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102283@unknown@formal@none@1@S@The results show that introducing the adoR mutation into the adgf-a background significantly increases pupariation, as well as adult emerging rate, compared to the adgf-a single mutant (Figure 6B).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n (:id . 45))\n ((:tag . "VBG") (:stem . "introduce") (:form . "introducing") (:end . 33)\n (:start . 22) (:id . 46))\n ((:tag . 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(:end . 244) (:start . 243)\n (:id . 88)))@@@1@47@((:identifiers (:sid . :s7.156) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102285@unknown@formal@none@1@S@Development during the third instar is much less delayed in the double mutant, with most of the larvae pupariating within 1 d after their heterozygous siblings (Figure 7A).@(((:tag . "NNP") (:stem . "Development") (:form . "Development") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 18)\n (:start . 12) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 44))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 28) (:start . 23)\n (:id . 45))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 35)\n (:start . 29) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 38) (:start . 36)\n (:id . 47))\n ((:tag . "RB") (:stem . 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(:end . 147) (:start . 146)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x7.174.2) (:span 99 104)) ((:id . :x7.174.3) (:span 46 55)))\n (:ncues ((:id . :x7.174.1) (:span 105 108)))\n (:hscopes ((:id . :x7.174.2) (:span 99 146))\n ((:id . :x7.174.3) (:span 46 146)))\n (:nscopes ((:id . :x7.174.1) (:span 105 146)))\n (:identifiers (:sid . :s7.174) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102303@unknown@formal@none@1@S@To test this possibility, we tried to rescue the phenotype by feeding mutant larvae 20E, which can initiate pupariation in the ecd1 mutant, which has an extremely low level of ecdysone [30,31].@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "NN") (:stem . "possibility") (:form . 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"JJ") (:stem . "responsive") (:form . "responsive") (:end . 88)\n (:start . 78) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n (:id . 57))\n ((:tag . "NN") (:stem . "ecdysone") (:form . "ecdysone") (:end . 100)\n (:start . 92) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 104) (:start . 101)\n (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 109) (:start . 105)\n (:id . 60))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 114) (:start . 110)\n (:id . 61))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 124)\n (:start . 115) (:id . 62))\n ((:tag . "VBZ") (:stem . "restore") (:form . "restores") (:end . 133)\n (:start . 125) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n (:id . 64))\n ((:tag . "NN") (:stem . "pupariation") (:form . "pupariation") (:end . 149)\n (:start . 138) (:id . 65))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 159)\n (:start . 150) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 162) (:start . 160)\n (:id . 67))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 169)\n (:start . 163) (:id . 68))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 179)\n (:start . 170) (:id . 69))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 185)\n (:start . 180) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s7.176) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102305@unknown@formal@none@1@S@The delay in development is also significantly reduced (Figure 7A).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "delay") (:form . "delay") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 12) (:start . 10)\n (:id . 44))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 24)\n (:start . 13) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 32) (:start . 28)\n (:id . 47))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 46) (:start . 33) (:id . 48))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 54)\n (:start . 47) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n (:id . 50))\n ((:tag . "NN") (:stem . "figure") (:form . "Figure") (:end . 62)\n (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "7a") (:form . "7A") (:end . 65) (:start . 63)\n (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 66) (:start . 65)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s7.177) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102306@unknown@formal@none@1@S@Since the adgf-a mutant shows certain precocious metamorphic changes (macrophage differentiation and fat body disintegration), we speculated that a reduced ecdysteroid level could be caused by precocious degeneration of the prothoracic part of the ring gland.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "adgf-a") (:form . "adgf-a") (:end . 16)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 23)\n (:start . 17) (:id . 45))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 29) (:start . 24)\n (:id . 46))\n ((:tag . "JJ") (:stem . "certain") (:form . 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"could") (:end . 179)\n (:start . 174) (:id . 67))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 182) (:start . 180)\n (:id . 68))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 189)\n (:start . 183) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 192) (:start . 190)\n (:id . 70))\n ((:tag . "JJ") (:stem . "precocious") (:form . "precocious") (:end . 203)\n (:start . 193) (:id . 71))\n ((:tag . "NN") (:stem . "degeneration") (:form . "degeneration") (:end . 216)\n (:start . 204) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 219) (:start . 217)\n (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 223) (:start . 220)\n (:id . 74))\n ((:tag . "JJ") (:stem . "prothoracic") (:form . "prothoracic") (:end . 235)\n (:start . 224) (:id . 75))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 240) (:start . 236)\n (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 243) (:start . 241)\n (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 247) (:start . 244)\n (:id . 78))\n ((:tag . "NN") (:stem . "ring") (:form . "ring") (:end . 252) (:start . 248)\n (:id . 79))\n ((:tag . "NN") (:stem . "gland") (:form . "gland") (:end . 258)\n (:start . 253) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 259) (:start . 258)\n (:id . 81)))@@@1@40@((:hcues ((:id . :x7.178.1) (:span 174 179))\n ((:id . :x7.178.2) (:span 130 140)))\n (:hscopes ((:id . :x7.178.1) (:span 146 258))\n ((:id . :x7.178.2) (:span 130 258)))\n (:identifiers (:sid . :s7.178) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102307@unknown@formal@none@1@S@However, the overall structure of the ring gland is not visibly affected even in the oldest larvae (10 d, i.e., 5 d after the heterozygous siblings pupariated) with a fully disintegrated fat body (Figure 7B and 7C).@(((:tag . 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"FW") (:stem . "i.e.") (:form . "i.e.") (:end . 110) (:start . 106)\n (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n (:id . 65))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 113) (:start . 112)\n (:id . 66))\n ((:tag . "NN") (:stem . "d") (:form . "d") (:end . 115) (:start . 114)\n (:id . 67))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 121)\n (:start . 116) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n (:id . 69))\n ((:tag . "JJ") (:stem . "heterozygous") (:form . "heterozygous") (:end . 138)\n (:start . 126) (:id . 70))\n ((:tag . "NNS") (:stem . "sibling") (:form . "siblings") (:end . 147)\n (:start . 139) (:id . 71))\n ((:tag . "VBN") (:stem . "pupariate") (:form . "pupariated") (:end . 158)\n (:start . 148) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 159) (:start . 158)\n (:id . 73))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 164) (:start . 160)\n (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 166) (:start . 165)\n (:id . 75))\n ((:tag . "RB") (:stem . "fully") (:form . "fully") (:end . 172)\n (:start . 167) (:id . 76))\n ((:tag . "VBN") (:stem . "disintegrate") (:form . "disintegrated")\n (:end . 186) (:start . 173) (:id . 77))\n ((:tag . "NN") (:stem . "fat") (:form . "fat") (:end . 190) (:start . 187)\n (:id . 78))\n ((:tag . "NN") (:stem . "body") (:form . "body") (:end . 195) (:start . 191)\n (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 197) (:start . 196)\n (:id . 80))\n ((:tag . "NN") (:stem . "figure") (:form . "Figure") (:end . 203)\n (:start . 197) (:id . 81))\n ((:tag . "NN") (:stem . "7b") (:form . "7B") (:end . 206) (:start . 204)\n (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 210) (:start . 207)\n (:id . 83))\n ((:tag . "NN") (:stem . "7c") (:form . "7C") (:end . 213) (:start . 211)\n (:id . 84))\n ((:tag . 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"Toll") (:end . 167) (:start . 163)\n (:id . 67))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 175)\n (:start . 168) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n (:id . 69)))@@@1@28@((:hcues ((:id . :x7.189.1) (:span 3 15)))\n (:hscopes ((:id . :x7.189.1) (:span 3 175)))\n (:identifiers (:sid . :s7.189) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102318@unknown@formal@none@1@S@To test this hypothesis, we crossed transgenic flies carrying ADGF-A gene under the control of a heat-shock promoter on Chromosome II (HS-ADGF-A) with cactE8 (a lethal allele of cact on Chromosome II, which, in combination with cactD13, results in a zygotic null combination, or, with cactIIIG, results in zygotic hypomorphic combination).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "test") (:form . 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"the") (:end . 161) (:start . 158)\n (:id . 66))\n ((:tag . "NNP") (:stem . "HS-ADGF-A") (:form . "HS-ADGF-A") (:end . 171)\n (:start . 162) (:id . 67))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 181)\n (:start . 172) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s7.197) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102326@unknown@formal@none@1@S@(A) The bar graph shows the percentage of the pupae (blue bars) and adult flies (purple bars) demonstrating the larval and pupal survival of each genotype.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . 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"bars") (:end . 62) (:start . 58)\n (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n (:id . 58))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 73) (:start . 68)\n (:id . 59))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 79) (:start . 74)\n (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 81) (:start . 80)\n (:id . 61))\n ((:tag . "JJ") (:stem . "purple") (:form . "purple") (:end . 87)\n (:start . 81) (:id . 62))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 92) (:start . 88)\n (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n (:id . 64))\n ((:tag . "VBG") (:stem . "demonstrate") (:form . "demonstrating")\n (:end . 107) (:start . 94) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n (:id . 66))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 118)\n (:start . 112) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n (:id . 68))\n ((:tag . "JJ") (:stem . "pupal") (:form . "pupal") (:end . 128)\n (:start . 123) (:id . 69))\n ((:tag . "NN") (:stem . "survival") (:form . "survival") (:end . 137)\n (:start . 129) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 140) (:start . 138)\n (:id . 71))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 145) (:start . 141)\n (:id . 72))\n ((:tag . "NN") (:stem . "genotype") (:form . "genotype") (:end . 154)\n (:start . 146) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s7.198) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102327@unknown@formal@none@1@S@The x-axis shows the genotypes and is shared with (B).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "x-axis") (:form . "x-axis") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 16) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 30)\n (:start . 21) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 37) (:start . 35)\n (:id . 48))\n ((:tag . "VBN") (:stem . "share") (:form . "shared") (:end . 44)\n (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 49) (:start . 45)\n (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 51) (:start . 50)\n (:id . 51))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 52) (:start . 51)\n (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 53) (:start . 52)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 54) (:start . 53)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s7.199) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102328@unknown@formal@none@1@S@Flies heterozygous for the cact mutation were used as a control.@(((:tag . "NNS") (:stem . "fly") (:form . "Flies") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "heterozygous") (:form . "heterozygous") (:end . 18)\n (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 22) (:start . 19)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 45))\n ((:tag . "NN") (:stem . "cact") (:form . "cact") (:end . 31) (:start . 27)\n (:id . 46))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 40)\n (:start . 32) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 45) (:start . 41)\n (:id . 48))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 50) (:start . 46)\n (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 53) (:start . 51)\n (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 55) (:start . 54)\n (:id . 51))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 63)\n (:start . 56) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 64) (:start . 63)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s7.200) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102330@unknown@formal@none@1@S@Discussion@(((:tag . "NN") (:stem . "discussion") (:form . "Discussion") (:end . 10)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s7.202) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5102331@unknown@formal@none@1@S@ADA Deficiency in Drosophila Causes Abnormal Hemocyte Development, Melanotic Tumor Formation, Fat Body Degeneration, and Delayed Development@(((:tag . "NNP") (:stem . "ADA") (:form . "ADA") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Deficiency") (:form . "Deficiency") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 17) (:start . 15)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 28)\n (:start . 18) (:id . 45))\n ((:tag . "NNP") (:stem . "Causes") (:form . "Causes") (:end . 35)\n (:start . 29) (:id . 46))\n ((:tag . "NNP") (:stem . "Abnormal") (:form . "Abnormal") (:end . 44)\n (:start . 36) (:id . 47))\n ((:tag . "NNP") (:stem . "Hemocyte") (:form . "Hemocyte") (:end . 53)\n (:start . 45) (:id . 48))\n ((:tag . "NNP") (:stem . "Development") (:form . "Development") (:end . 65)\n (:start . 54) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Melanotic") (:form . "Melanotic") (:end . 76)\n (:start . 67) (:id . 51))\n ((:tag . "NNP") (:stem . "Tumor") (:form . "Tumor") (:end . 82) (:start . 77)\n (:id . 52))\n ((:tag . "NNP") (:stem . "Formation") (:form . "Formation") (:end . 92)\n (:start . 83) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Fat") (:form . "Fat") (:end . 97) (:start . 94)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Body") (:form . "Body") (:end . 102) (:start . 98)\n (:id . 56))\n ((:tag . "NNP") (:stem . "Degeneration") (:form . "Degeneration")\n (:end . 115) (:start . 103) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n (:id . 59))\n ((:tag . "NNP") (:stem . "Delayed") (:form . "Delayed") (:end . 128)\n (:start . 121) (:id . 60))\n ((:tag . "NNP") (:stem . "Development") (:form . "Development") (:end . 140)\n (:start . 129) (:id . 61)))@@@1@20@((:identifiers (:sid . :s7.203) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5102332@unknown@formal@none@1@S@We have established an ADA deficiency model in Drosophila in order to study the effects of altered adenosine levels in vivo.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBN") (:stem . "establish") (:form . "established") (:end . 19)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . 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"effect") (:form . "effects") (:end . 87)\n (:start . 80) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n (:id . 57))\n ((:tag . "VBN") (:stem . "alter") (:form . "altered") (:end . 98)\n (:start . 91) (:id . 58))\n ((:tag . "NN") (:stem . "adenosine") (:form . "adenosine") (:end . 108)\n (:start . 99) (:id . 59))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 115)\n (:start . 109) (:id . 60))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 118) (:start . 116)\n (:id . 61))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 123) (:start . 119)\n (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.204) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102333@unknown@formal@none@1@S@We produced a loss-of-function mutation in the ADGF-A gene, which produces a product (ADGF-A) with ADA activity.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n (:id . 44))\n ((:tag . "JJ") (:stem . "loss-of-function") (:form . "loss-of-function")\n (:end . 30) (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 39)\n (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . 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"with") (:end . 98) (:start . 94)\n (:id . 59))\n ((:tag . "NNP") (:stem . "ADA") (:form . "ADA") (:end . 102) (:start . 99)\n (:id . 60))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 111)\n (:start . 103) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s7.205) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102334@unknown@formal@none@1@S@When homozygous, the mutation causes abnormal hemocyte development, leading to melanotic tumor formation [36], as well as fat-body disintegration associated with death during the larval stage or delayed transition to the pupal stage of development.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 15)\n (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 29)\n (:start . 21) (:id . 46))\n ((:tag . "VBZ") (:stem . "cause") (:form . "causes") (:end . 36)\n (:start . 30) (:id . 47))\n ((:tag . "JJ") (:stem . "abnormal") (:form . "abnormal") (:end . 45)\n (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "hemocyte") (:form . "hemocyte") (:end . 54)\n (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 66)\n (:start . 55) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n (:id . 51))\n ((:tag . "VBG") (:stem . "lead") (:form . "leading") (:end . 75)\n (:start . 68) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n (:id . 53))\n ((:tag . "JJ") (:stem . "melanotic") (:form . "melanotic") (:end . 88)\n (:start . 79) (:id . 54))\n ((:tag . "NN") (:stem . "tumor") (:form . "tumor") (:end . 94) (:start . 89)\n (:id . 55))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 104)\n (:start . 95) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 106) (:start . 105)\n (:id . 57))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 108) (:start . 106)\n (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 109) (:start . 108)\n (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n (:id . 60))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 113) (:start . 111)\n (:id . 61))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 118) (:start . 114)\n (:id . 62))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 121) (:start . 119)\n (:id . 63))\n ((:tag . "NN") (:stem . "fat-body") (:form . "fat-body") (:end . 130)\n (:start . 122) (:id . 64))\n ((:tag . "NN") (:stem . "disintegration") (:form . "disintegration")\n (:end . 145) (:start . 131) (:id . 65))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 156)\n (:start . 146) (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 161) (:start . 157)\n (:id . 67))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 167)\n (:start . 162) (:id . 68))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 174)\n (:start . 168) (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 178) (:start . 175)\n (:id . 70))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 185)\n (:start . 179) (:id . 71))\n ((:tag . "NN") (:stem . "stage") (:form . "stage") (:end . 191)\n (:start . 186) (:id . 72))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 194) (:start . 192)\n (:id . 73))\n ((:tag . "VBN") (:stem . "delay") (:form . "delayed") (:end . 202)\n (:start . 195) (:id . 74))\n ((:tag . "NN") (:stem . "transition") (:form . "transition") (:end . 213)\n (:start . 203) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 216) (:start . 214)\n (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 220) (:start . 217)\n (:id . 77))\n ((:tag . "JJ") (:stem . "pupal") (:form . "pupal") (:end . 226)\n (:start . 221) (:id . 78))\n ((:tag . "NN") (:stem . "stage") (:form . "stage") (:end . 232)\n (:start . 227) (:id . 79))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 235) (:start . 233)\n (:id . 80))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 247)\n (:start . 236) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 248) (:start . 247)\n (:id . 82)))@@@1@41@((:identifiers (:sid . :s7.206) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102335@unknown@formal@none@1@S@In agreement with our previous study using cells cultured in vitro [16], here we have shown that ADA enzymatic activity is essential for ADGF-A function in vivo, when this function is assayed by testing for rescue of the mutant phenotype.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 17) (:start . 13)\n (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 21) (:start . 18)\n (:id . 45))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 30)\n (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "study") (:form . 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(:end . 238) (:start . 237)\n (:id . 86)))@@@1@45@((:identifiers (:sid . :s7.207) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102336@unknown@formal@none@1@S@Just as increased levels of both ADA substrates, adenosine and deoxyadenosine, are found in blood of SCID patients [5], adgf-a mutant larvae also have elevated levels of adenosine and deoxyadenosine, indicating that the mutant phenotype is caused by disturbance in the turnover of these nucleosides.@(((:tag . "RB") (:stem . "just") (:form . "Just") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 17)\n (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 24)\n (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . 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"of") (:end . 87) (:start . 85)\n (:id . 57))\n ((:tag . "JJ") (:stem . "overactive") (:form . "overactive") (:end . 98)\n (:start . 88) (:id . 58))\n ((:tag . "NNP") (:stem . "Toll") (:form . "Toll") (:end . 103) (:start . 99)\n (:id . 59))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 113)\n (:start . 104) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n (:id . 61))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 125)\n (:start . 115) (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 130) (:start . 126)\n (:id . 63))\n ((:tag . "NNP") (:stem . "ADGF-A") (:form . "ADGF-A") (:end . 137)\n (:start . 131) (:id . 64))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 143)\n (:start . 138) (:id . 65))\n ((:tag . "VB") (:stem . "function") (:form . "function") (:end . 152)\n (:start . 144) (:id . 66))\n ((:tag . "RB") (:stem . "downstream") (:form . "downstream") (:end . 163)\n (:start . 153) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 166) (:start . 164)\n (:id . 68))\n ((:tag . "NNP") (:stem . "Toll") (:form . "Toll") (:end . 171) (:start . 167)\n (:id . 69))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 181)\n (:start . 172) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 184) (:start . 182)\n (:id . 71))\n ((:tag . "VB") (:stem . "control") (:form . "control") (:end . 192)\n (:start . 185) (:id . 72))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 196) (:start . 193)\n (:id . 73))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 204)\n (:start . 197) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n (:id . 75)))@@@1@34@((:hcues ((:id . :x7.222.1) (:span 138 143))\n ((:id . :x7.222.2) (:span 115 125)))\n (:hscopes ((:id . :x7.222.1) (:span 138 204))\n ((:id . :x7.222.2) (:span 115 204)))\n (:identifiers (:sid . :s7.222) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102351@unknown@formal@none@1@S@This conclusion is consistent with the existence of a putative binding site for Dorsal (one of two known effectors of Toll signaling) in the ADGF-A promoter (Figure 9).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "conclusion") (:form . "conclusion") (:end . 15)\n (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n (:id . 44))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 29)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 34) (:start . 30)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n (:id . 47))\n ((:tag . "NN") (:stem . "existence") (:form . "existence") (:end . 48)\n (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n (:id . 50))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 62)\n (:start . 54) (:id . 51))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 70)\n (:start . 63) (:id . 52))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 75) (:start . 71)\n (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 79) (:start . 76)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Dorsal") (:form . "Dorsal") (:end . 86)\n (:start . 80) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 88) (:start . 87)\n (:id . 56))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 91) (:start . 88)\n (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n (:id . 58))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 98) (:start . 95)\n (:id . 59))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 104) (:start . 99)\n (:id . 60))\n ((:tag . "NNS") (:stem . "effector") (:form . "effectors") (:end . 114)\n (:start . 105) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 117) (:start . 115)\n (:id . 62))\n ((:tag . "NNP") (:stem . "Toll") (:form . "Toll") (:end . 122) (:start . 118)\n (:id . 63))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 132)\n (:start . 123) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 136) (:start . 134)\n (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n (:id . 67))\n ((:tag . "NNP") (:stem . "ADGF-A") (:form . "ADGF-A") (:end . 147)\n (:start . 141) (:id . 68))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 156)\n (:start . 148) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 158) (:start . 157)\n (:id . 70))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 164)\n (:start . 158) (:id . 71))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 166) (:start . 165)\n (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s7.223) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102352@unknown@formal@none@1@S@It will be important to explore this connection further, since recent studies suggest an interaction between adenosine signaling and the NF-?B signaling pathway, which is the mammalian counterpart of the Toll pathway [37].@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 10) (:start . 8)\n (:id . 44))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 20)\n (:start . 11) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n (:id . 46))\n ((:tag . "VB") (:stem . "explore") (:form . "explore") (:end . 31)\n (:start . 24) (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 36) (:start . 32)\n (:id . 48))\n ((:tag . "NN") (:stem . "connection") (:form . "connection") (:end . 47)\n (:start . 37) (:id . 49))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 55)\n (:start . 48) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n (:id . 51))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 62) (:start . 57)\n (:id . 52))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 69)\n (:start . 63) (:id . 53))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 77)\n (:start . 70) (:id . 54))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 85)\n (:start . 78) (:id . 55))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 88) (:start . 86)\n (:id . 56))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 100)\n (:start . 89) (:id . 57))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 108)\n (:start . 101) (:id . 58))\n ((:tag . "NN") (:stem . "adenosine") (:form . "adenosine") (:end . 118)\n (:start . 109) (:id . 59))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 128)\n (:start . 119) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n (:id . 62))\n ((:tag . "NN") (:stem . "NF-?B") (:form . "NF-?B") (:end . 142)\n (:start . 137) (:id . 63))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 152)\n (:start . 143) (:id . 64))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 160)\n (:start . 153) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n (:id . 66))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 167)\n (:start . 162) (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 170) (:start . 168)\n (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 174) (:start . 171)\n (:id . 69))\n ((:tag . "JJ") (:stem . "mammalian") (:form . "mammalian") (:end . 184)\n (:start . 175) (:id . 70))\n ((:tag . "NN") (:stem . "counterpart") (:form . "counterpart") (:end . 196)\n (:start . 185) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 199) (:start . 197)\n (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 203) (:start . 200)\n (:id . 73))\n ((:tag . "NNP") (:stem . "Toll") (:form . "Toll") (:end . 208) (:start . 204)\n (:id . 74))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 216)\n (:start . 209) (:id . 75))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 218) (:start . 217)\n (:id . 76))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 220) (:start . 218)\n (:id . 77))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 221) (:start . 220)\n (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n (:id . 79)))@@@1@38@((:hcues ((:id . :x7.224.1) (:span 78 85)))\n (:hscopes ((:id . :x7.224.1) (:span 78 216)))\n (:identifiers (:sid . :s7.224) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102353@unknown@formal@none@1@S@Schematic Map of the ADGF-A Gene with Promoter Analysis@(((:tag . "JJ") (:stem . "schematic") (:form . "Schematic") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Map") (:form . "Map") (:end . 13) (:start . 10)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "NNP") (:stem . "ADGF-A") (:form . "ADGF-A") (:end . 27)\n (:start . 21) (:id . 46))\n ((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 32) (:start . 28)\n (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 37) (:start . 33)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Promoter") (:form . "Promoter") (:end . 46)\n (:start . 38) (:id . 49))\n ((:tag . "NNP") (:stem . "Analysis") (:form . "Analysis") (:end . 55)\n (:start . 47) (:id . 50)))@@@1@9@((:identifiers (:sid . :s7.225) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5102354@unknown@formal@none@1@S@The ADGF-A gene contains four exons and two transcriptional starts [17,47].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "ADGF-A") (:form . "ADGF-A") (:end . 10)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 24)\n (:start . 16) (:id . 45))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 29) (:start . 25)\n (:id . 46))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 35) (:start . 30)\n (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 43) (:start . 40)\n (:id . 49))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n (:end . 59) (:start . 44) (:id . 50))\n ((:tag . "NNS") (:stem . "start") (:form . "starts") (:end . 66)\n (:start . 60) (:id . 51))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 68) (:start . 67)\n (:id . 52))\n ((:tag . "CD") (:stem . "17,47") (:form . "17,47") (:end . 73) (:start . 68)\n (:id . 53))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 74) (:start . 73)\n (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s7.226) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102355@unknown@formal@none@1@S@We analyzed sequences preceding both transcriptional starts for the presence of known transcriptional factor binding sites using the software program Gene2Promoter (Genomatix Software GmbH).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "analyze") (:form . "analyzed") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 21)\n (:start . 12) (:id . 44))\n ((:tag . "VBG") (:stem . "precede") (:form . "preceding") (:end . 31)\n (:start . 22) (:id . 45))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 36) (:start . 32)\n (:id . 46))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n (:end . 52) (:start . 37) (:id . 47))\n ((:tag . "NNS") (:stem . "start") (:form . "starts") (:end . 59)\n (:start . 53) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 63) (:start . 60)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n (:id . 50))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 76)\n (:start . 68) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n (:id . 52))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 85) (:start . 80)\n (:id . 53))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n (:end . 101) (:start . 86) (:id . 54))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 108)\n (:start . 102) (:id . 55))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 116)\n (:start . 109) (:id . 56))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 122)\n (:start . 117) (:id . 57))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 128) (:start . 123)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n (:id . 59))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 141)\n (:start . 133) (:id . 60))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 149)\n (:start . 142) (:id . 61))\n ((:tag . "NNP") (:stem . "Gene2Promoter") (:form . "Gene2Promoter")\n (:end . 163) (:start . 150) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 165) (:start . 164)\n (:id . 63))\n ((:tag . "NNP") (:stem . "Genomatix") (:form . "Genomatix") (:end . 174)\n (:start . 165) (:id . 64))\n ((:tag . "NNP") (:stem . "Software") (:form . "Software") (:end . 183)\n (:start . 175) (:id . 65))\n ((:tag . "NNP") (:stem . "GmbH") (:form . "GmbH") (:end . 188) (:start . 184)\n (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s7.227) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102356@unknown@formal@none@1@S@Selected sites are represented by color bars in approximate positions of promoter regions.@(((:tag . "VBN") (:stem . "select") (:form . "Selected") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 14) (:start . 9)\n (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 18) (:start . 15)\n (:id . 44))\n ((:tag . "VBN") (:stem . "represent") (:form . "represented") (:end . 30)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 33) (:start . 31)\n (:id . 46))\n ((:tag . "NN") (:stem . "color") (:form . "color") (:end . 39) (:start . 34)\n (:id . 47))\n ((:tag . "NNS") (:stem . 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(:end . 90) (:start . 89)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s7.228) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102357@unknown@formal@none@1@S@The legend under the sequence show the names of transcription factors binding to matching colored binding sites.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "legend") (:form . "legend") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 16) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 29)\n (:start . 21) (:id . 46))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 34) (:start . 30)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n (:id . 48))\n ((:tag . 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(:end . 234) (:start . 233)\n (:id . 84)))@@@1@43@((:identifiers (:sid . :s7.237) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102366@unknown@formal@none@1@S@They also showed that the interaction of hemocytes with the fat body is mediated by a 120-kDa membrane protein localized specifically on pupal hemocytes [40].@(((:tag . "PRP") (:stem . "they") (:form . "They") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 16) (:start . 10)\n (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 46))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 37)\n (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . 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(:end . 158) (:start . 157)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s7.238) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102367@unknown@formal@none@1@S@This protein was suggested to be a scavenger receptor, but it does not seem to be homologous to Drosophila Croquemort (unpublished data).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "VBN") (:stem . "suggest") (:form . "suggested") (:end . 26)\n (:start . 17) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 32) (:start . 30)\n (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . 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(:end . 137) (:start . 136)\n (:id . 67)))@@@1@26@((:hcues ((:id . :x7.239.2) (:span 71 75)) ((:id . :x7.239.3) (:span 17 26)))\n (:ncues ((:id . :x7.239.1) (:span 67 70)))\n (:hscopes ((:id . :x7.239.2) (:span 59 117))\n ((:id . :x7.239.3) (:span 0 53)))\n (:nscopes ((:id . :x7.239.1) (:span 59 117)))\n (:identifiers (:sid . :s7.239) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102368@unknown@formal@none@1@S@Work by Franc et al. [27] is consistent with the idea that more than one scavenger receptor is involved in this process.@(((:tag . "NN") (:stem . "work") (:form . "Work") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Franc") (:form . "Franc") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "FW") (:stem . "al.") (:form . 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(:end . 120) (:start . 119)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.240) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102370@unknown@formal@none@1@S@The precocious metamorphic changes that appear to occur in response to elevated adenosine in the adgf-a mutant larvae lead to the suggestion that adenosine may act as a regulatory signal for these processes during normal development.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "precocious") (:form . "precocious") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "metamorphic") (:form . "metamorphic") (:end . 26)\n (:start . 15) (:id . 44))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 34)\n (:start . 27) (:id . 45))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 39) (:start . 35)\n (:id . 46))\n ((:tag . "VBP") (:stem . "appear") (:form . 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(:end . 233) (:start . 232)\n (:id . 78)))@@@1@37@((:hcues ((:id . :x7.242.1) (:span 156 159))\n ((:id . :x7.242.2) (:span 130 140)) ((:id . :x7.242.3) (:span 40 46)))\n (:hscopes ((:id . :x7.242.1) (:span 156 232))\n ((:id . :x7.242.2) (:span 130 232)) ((:id . :x7.242.3) (:span 35 117)))\n (:identifiers (:sid . :s7.242) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102371@unknown@formal@none@1@S@One possibility is that adenosine acts as a downstream effector of ecdysone-regulated prepupal changes, and that the increase in adenosine concentration is mediated by ecdysone-induced down-regulation of ADGF-A expression.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n (:id . 44))\n ((:tag . "IN") (:stem . 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(:end . 222) (:start . 221)\n (:id . 72)))@@@1@31@((:hcues ((:id . :x7.243.1) (:span 4 15)))\n (:hscopes ((:id . :x7.243.1) (:span 4 221)))\n (:identifiers (:sid . :s7.243) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102372@unknown@formal@none@1@S@This is supported by the presence of multiple sites for ecdysone-inducible transcription regulators in the ADGF-A promoter (Figure 9).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "VBN") (:stem . "support") (:form . "supported") (:end . 17)\n (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 20) (:start . 18)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n (:id . 46))\n ((:tag . "NN") (:stem . "presence") (:form . 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(:end . 134) (:start . 133)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.244) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102373@unknown@formal@none@1@S@Adenosine could serve as a signal for macrophage differentiation, and the lack of adenosine deaminase activity due to the adgf-a mutation could cause precocious differentiation of these cells in mutant larvae.@(((:tag . "NNP") (:stem . "Adenosine") (:form . "Adenosine") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 15) (:start . 10)\n (:id . 43))\n ((:tag . "VB") (:stem . "serve") (:form . "serve") (:end . 21) (:start . 16)\n (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 24) (:start . 22)\n (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n (:id . 46))\n ((:tag . "NN") (:stem . "signal") (:form . 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(:end . 209) (:start . 208)\n (:id . 74)))@@@1@33@((:hcues ((:id . :x7.245.1) (:span 138 143))\n ((:id . :x7.245.3) (:span 10 15)))\n (:ncues ((:id . :x7.245.2) (:span 74 78)))\n (:hscopes ((:id . :x7.245.1) (:span 138 208))\n ((:id . :x7.245.3) (:span 10 64)))\n (:nscopes ((:id . :x7.245.2) (:span 74 110)))\n (:identifiers (:sid . :s7.245) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102374@unknown@formal@none@1@S@We are now carrying out direct tests of the idea that the differentiation of hemocytes in mutant larvae is caused by elevated adenosine.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 10) (:start . 7)\n (:id . 44))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 19)\n (:start . 11) (:id . 45))\n ((:tag . 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(:end . 136) (:start . 135)\n (:id . 65)))@@@1@24@((:hcues ((:id . :x7.246.1) (:span 44 48)))\n (:hscopes ((:id . :x7.246.1) (:span 44 135)))\n (:identifiers (:sid . :s7.246) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102375@unknown@formal@none@1@S@If confirmed, this effect would have general significance, since in ADA-deficient mice, inflammatory changes in the lungs include an accumulation of activated alveolar macrophages [41], and this could also be mediated by elevated adenosine.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 18) (:start . 14)\n (:id . 45))\n ((:tag . "NN") (:stem . "effect") (:form . 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(:end . 79) (:start . 78)\n (:id . 54)))@@@1@13@((:hcues ((:id . :x7.253.1) (:span 3 10)))\n (:hscopes ((:id . :x7.253.1) (:span 3 78)))\n (:identifiers (:sid . :s7.253) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102382@unknown@formal@none@1@S@Other mutants with hormonal dysregulation show delayed larval development and failure to pupariate [42,43].@(((:tag . "JJ") (:stem . "other") (:form . "Other") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 13)\n (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "JJ") (:stem . "hormonal") (:form . "hormonal") (:end . 27)\n (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "dysregulation") (:form . "dysregulation")\n (:end . 41) (:start . 28) (:id . 46))\n ((:tag . "NN") (:stem . "show") (:form . 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(:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n (:id . 58)))@@@1@17@((:ncues ((:id . :x7.254.1) (:span 78 85)))\n (:nscopes ((:id . :x7.254.1) (:span 78 98)))\n (:identifiers (:sid . :s7.254) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102383@unknown@formal@none@1@S@Presumably the elevated adenosine in the adgf-a mutant blocks the production or release of ecdysone from the ring gland by an unknown mechanism.@(((:tag . "RB") (:stem . "presumably") (:form . "Presumably") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n (:id . 43))\n ((:tag . "JJ") (:stem . "elevated") (:form . "elevated") (:end . 23)\n (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "adenosine") (:form . "adenosine") (:end . 33)\n (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n (:id . 46))\n ((:tag . "DT") (:stem . 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(:end . 144) (:start . 143)\n (:id . 65)))@@@1@24@((:hcues ((:id . :x7.255.1) (:span 0 10)))\n (:hscopes ((:id . :x7.255.1) (:span 0 143)))\n (:identifiers (:sid . :s7.255) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102384@unknown@formal@none@1@S@This idea is supported by our finding that both pupariation rate and survival of the adgf-a mutant can also be improved by feeding the mutant larvae with 20E in the diet (see Figure 7A).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "idea") (:form . "idea") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n (:id . 44))\n ((:tag . "VBN") (:stem . "support") (:form . "supported") (:end . 22)\n (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 25) (:start . 23)\n (:id . 46))\n ((:tag . "PRP$") (:stem . 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"these") (:end . 71) (:start . 66)\n (:id . 53))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 79)\n (:start . 72) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n (:id . 55)))@@@1@14@((:hcues ((:id . :x7.262.1) (:span 12 26)))\n (:hscopes ((:id . :x7.262.1) (:span 12 79)))\n (:identifiers (:sid . :s7.262) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102391@unknown@formal@none@1@S@Drosophila, now with the advantage of the well-characterized adgf-a mutant, could serve as an ideal model system in which to investigate this mechanism.@(((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 43))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . 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"serve") (:end . 87) (:start . 82)\n (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 90) (:start . 88)\n (:id . 56))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 93) (:start . 91)\n (:id . 57))\n ((:tag . "JJ") (:stem . "ideal") (:form . "ideal") (:end . 99) (:start . 94)\n (:id . 58))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 105)\n (:start . 100) (:id . 59))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 112)\n (:start . 106) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 121)\n (:start . 116) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 124) (:start . 122)\n (:id . 63))\n ((:tag . "VB") (:stem . "investigate") (:form . "investigate") (:end . 136)\n (:start . 125) (:id . 64))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 141) (:start . 137)\n (:id . 65))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 151)\n (:start . 142) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n (:id . 67)))@@@1@26@((:hcues ((:id . :x7.263.1) (:span 76 81)))\n (:hscopes ((:id . :x7.263.1) (:span 76 151)))\n (:identifiers (:sid . :s7.263) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102392@unknown@formal@none@1@S@Concluding Remarks@(((:tag . "VBG") (:stem . "conclude") (:form . "Concluding") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "remark") (:form . "Remarks") (:end . 18)\n (:start . 11) (:id . 43)))@@@1@2@((:identifiers (:sid . :s7.264) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5102393@unknown@formal@none@1@S@In our previous work using cells cultured in vitro, we showed that, as in mammals, adenosine can block proliferation and/or survival of some Drosophila cell types [16].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 15)\n (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 26) (:start . 21)\n (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 32) (:start . 27)\n (:id . 47))\n ((:tag . "VBN") (:stem . 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",") (:form . ",") (:end . 82) (:start . 81)\n (:id . 59))\n ((:tag . "NN") (:stem . "adenosine") (:form . "adenosine") (:end . 92)\n (:start . 83) (:id . 60))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 96) (:start . 93)\n (:id . 61))\n ((:tag . "VB") (:stem . "block") (:form . "block") (:end . 102) (:start . 97)\n (:id . 62))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n (:end . 116) (:start . 103) (:id . 63))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 123)\n (:start . 117) (:id . 64))\n ((:tag . "NN") (:stem . "survival") (:form . "survival") (:end . 132)\n (:start . 124) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 135) (:start . 133)\n (:id . 66))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 140) (:start . 136)\n (:id . 67))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 151)\n (:start . 141) (:id . 68))\n ((:tag . "NN") (:stem . "cell") (:form . 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(:end . 232) (:start . 231)\n (:id . 82)))@@@1@41@((:identifiers (:sid . :s7.266) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102395@unknown@formal@none@1@S@Although the adgf-a mutation leads to larval or pupal death, we have shown that this is not due to the adenosine or deoxyadenosine simply blocking cellular proliferation or survival, as the experiments in vitro would suggest.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 43))\n ((:tag . "JJ") (:stem . "adgf-a") (:form . "adgf-a") (:end . 19)\n (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 28)\n (:start . 20) (:id . 45))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 34) (:start . 29)\n (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . 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(:end . 173) (:start . 172)\n (:id . 72)))@@@1@31@((:identifiers (:sid . :s7.268) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102397@unknown@formal@none@1@S@Hemocytes also differentiate and are released from the lymph glands during systemic infection [19].@(((:tag . "NNP") (:stem . "Hemocyte") (:form . "Hemocytes") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 14) (:start . 10)\n (:id . 43))\n ((:tag . "VBP") (:stem . "differentiate") (:form . "differentiate")\n (:end . 28) (:start . 15) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 36) (:start . 33)\n (:id . 46))\n ((:tag . "VBN") (:stem . "release") (:form . "released") (:end . 45)\n (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . 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(:end . 99) (:start . 98)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s7.269) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102398@unknown@formal@none@1@S@Together with our result suggesting an interaction between Toll signaling and ADGF-A, this leads to the hypothesis that adenosine controls hemocyte differentiation in response to infection, and that it signals through the adenosine receptor to postpone the next developmental step, metamorphosis.@(((:tag . "RB") (:stem . "together") (:form . "Together") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 13) (:start . 9)\n (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 24)\n (:start . 18) (:id . 45))\n ((:tag . "VBG") (:stem . "suggest") (:form . 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(:end . 296) (:start . 295)\n (:id . 86)))@@@1@45@((:hcues ((:id . :x7.270.1) (:span 104 114))\n ((:id . :x7.270.2) (:span 25 35)))\n (:hscopes ((:id . :x7.270.1) (:span 104 295))\n ((:id . :x7.270.2) (:span 25 84)))\n (:identifiers (:sid . :s7.270) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102400@unknown@formal@none@1@S@A similar process of hemocyte differentiation and release from the lymph glands normally takes place at the onset of metamorphosis, when pupal macrophages remove histolyzing tissues.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 9)\n (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 17)\n (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 45))\n ((:tag . "NN") (:stem . "hemocyte") (:form . 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"remove") (:end . 161)\n (:start . 155) (:id . 66))\n ((:tag . "VBG") (:stem . "histolyze") (:form . "histolyzing") (:end . 173)\n (:start . 162) (:id . 67))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 181)\n (:start . 174) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s7.272) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102401@unknown@formal@none@1@S@The ADGF-A promoter contains consensus binding sites for effectors of both Toll and ecdysone signaling.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "ADGF-A") (:form . "ADGF-A") (:end . 10)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 19)\n (:start . 11) (:id . 44))\n ((:tag . "VBZ") (:stem . "contain") (:form . 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(:end . 125) (:start . 124)\n (:id . 64)))@@@1@23@((:hcues ((:id . :x7.274.1) (:span 5 27)))\n (:hscopes ((:id . :x7.274.1) (:span 5 124)))\n (:identifiers (:sid . :s7.274) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102403@unknown@formal@none@1@S@Materials and Methods@(((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 13) (:start . 10)\n (:id . 43))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 21)\n (:start . 14) (:id . 44)))@@@1@3@((:identifiers (:sid . :s7.275) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011 5102404@unknown@formal@none@1@S@Fly strains and genetics@(((:tag . "RB") (:stem . "fly") (:form . "Fly") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "strain") (:form . "strains") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "NNS") (:stem . "genetic") (:form . "genetics") (:end . 24)\n (:start . 16) (:id . 45)))@@@1@4@((:identifiers (:sid . :s7.276) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5102405@unknown@formal@none@1@S@For standard procedures, flies were raised at 25 °C on a standard cornmeal-agar-yeast-molasses diet supplemented with 0.3% Nipagin to retard mold growth.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "procedure") (:form . "procedures") (:end . 23)\n (:start . 13) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n (:id . 45))\n ((:tag . "NNS") (:stem . 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(:end . 153) (:start . 152)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.277) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102406@unknown@formal@none@1@S@Oregon flies were used as the wild-type Drosophila strain, but in most cases the y w strain was used as a control since most mutations were carried in the y w background.@(((:tag . "NNP") (:stem . "Oregon") (:form . "Oregon") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 12) (:start . 7)\n (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n (:id . 44))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 22) (:start . 18)\n (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 25) (:start . 23)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n (:id . 47))\n ((:tag . "JJ") (:stem . "wild-type") (:form . 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"carried") (:end . 147)\n (:start . 140) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 150) (:start . 148)\n (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n (:id . 71))\n ((:tag . "NN") (:stem . "y") (:form . "y") (:end . 156) (:start . 155)\n (:id . 72))\n ((:tag . "NN") (:stem . "w") (:form . "w") (:end . 158) (:start . 157)\n (:id . 73))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 169)\n (:start . 159) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s7.278) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102407@unknown@formal@none@1@S@A mutation in the ADGF-A gene on Chromosome III was obtained as described earlier [17].@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . 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(:end . 115) (:start . 114)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.280) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102410@unknown@formal@none@1@S@Transgenic flies carrying HS-ADGF-A,UAS-ADGF-Amyc, and UAS-mutADGF-Amyc construct (see description below) were produced by a modified P-element transformation method [45].@(((:tag . "JJ") (:stem . "transgenic") (:form . "Transgenic") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 16) (:start . 11)\n (:id . 43))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 25)\n (:start . 17) (:id . 44))\n ((:tag . "NNP") (:stem . "HS-ADGF-A,UAS-ADGF-Amyc")\n (:form . "HS-ADGF-A,UAS-ADGF-Amyc") (:end . 49) (:start . 26) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . 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(:end . 171) (:start . 170)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.282) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102411@unknown@formal@none@1@S@HS-ADGF-A,UAS-ADGF-Amyc[2A],UAS-ADGF-Amyc[7A],UAS-mutADGF-Amyc[1A], andUAS-mutADGF-Amyc[3B], all insertions on Chromosome II, were isolated and used in this work.@(((:tag . "NNP")\n (:stem\n . "HS-ADGF-A,UAS-ADGF-Amyc[2A],UAS-ADGF-Amyc[7A],UAS-mutADGF-Amyc[1A")\n (:form\n . "HS-ADGF-A,UAS-ADGF-Amyc[2A],UAS-ADGF-Amyc[7A],UAS-mutADGF-Amyc[1A")\n (:end . 65) (:start . 0) (:id . 42))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 66) (:start . 65)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n (:id . 44))\n ((:tag . "NNP") (:stem . "andUAS-mutADGF-Amyc[3B")\n (:form . "andUAS-mutADGF-Amyc[3B") (:end . 90) (:start . 68) (:id . 45))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 91) (:start . 90)\n (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n (:id . 47))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 96) (:start . 93)\n (:id . 48))\n ((:tag . "NNS") (:stem . "insertion") (:form . "insertions") (:end . 107)\n (:start . 97) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 110) (:start . 108)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Chromosome") (:form . "Chromosome") (:end . 121)\n (:start . 111) (:id . 51))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 124) (:start . 122)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 130) (:start . 126)\n (:id . 54))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 139)\n (:start . 131) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n (:id . 56))\n ((:tag . 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(:end . 162) (:start . 161)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s7.283) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102412@unknown@formal@none@1@S@The following markers and mutations were obtained from the Bloomington stock center, accessible at http://fly.bio.indiana.edu/ (stock numbers provided in parentheses): Hml-GFP marker (Hml-Gal4/UAS-GFP) expressing GFP in embryonic and larval hemocytes on Chromosome II (BL-6397), the l(3)hem1 mutation on Chromosome III (BL-6184), and the crqKG01679 mutation in the crq gene on Chromosome II (BL-14900).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "marker") (:form . "markers") (:end . 21)\n (:start . 14) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . 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(:end . 349) (:start . 348)\n (:id . 115)))@@@1@74@((:identifiers (:sid . :s7.287) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102416@unknown@formal@none@1@S@The Pen2.4-GAL4e33C lethal insertion on Chromosome III was obtained from Dr. N. Perrimon's lab, and the Dmef2-Gal4 driver on II from Dr. A. Michelson.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Pen2.4-GAL4e33C") (:form . "Pen2.4-GAL4e33C")\n (:end . 19) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "lethal") (:form . "lethal") (:end . 26)\n (:start . 20) (:id . 44))\n ((:tag . "NN") (:stem . "insertion") (:form . "insertion") (:end . 36)\n (:start . 27) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 39) (:start . 37)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Chromosome") (:form . "Chromosome") (:end . 50)\n (:start . 40) (:id . 47))\n ((:tag . "CD") (:stem . 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"the") (:form . "the") (:end . 103) (:start . 100)\n (:id . 59))\n ((:tag . "NN") (:stem . "dmef2-gal4") (:form . "Dmef2-Gal4") (:end . 114)\n (:start . 104) (:id . 60))\n ((:tag . "NN") (:stem . "driver") (:form . "driver") (:end . 121)\n (:start . 115) (:id . 61))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 124) (:start . 122)\n (:id . 62))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 127) (:start . 125)\n (:id . 63))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 132) (:start . 128)\n (:id . 64))\n ((:tag . "NNP") (:stem . "Dr.") (:form . "Dr.") (:end . 136) (:start . 133)\n (:id . 65))\n ((:tag . "NNP") (:stem . "A.") (:form . "A.") (:end . 139) (:start . 137)\n (:id . 66))\n ((:tag . "NNP") (:stem . "Michelson") (:form . "Michelson") (:end . 149)\n (:start . 140) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s7.288) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102417@unknown@formal@none@1@S@Expression information of these Gal4 drivers is provided in Table 1.@(((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 22)\n (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 31) (:start . 26)\n (:id . 45))\n ((:tag . "NN") (:stem . "gal4") (:form . "Gal4") (:end . 36) (:start . 32)\n (:id . 46))\n ((:tag . "NNS") (:stem . "driver") (:form . "drivers") (:end . 44)\n (:start . 37) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 47) (:start . 45)\n (:id . 48))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 56)\n (:start . 48) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n (:id . 50))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 65) (:start . 60)\n (:id . 51))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 67) (:start . 66)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s7.289) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102418@unknown@formal@none@1@S@A stock carrying the ubiquitous actin-Gal4 driver (P-actin-Gal4 UAS-GFP/CyO; lethal insertion on Chromosome II) was obtained from Dr. R. Sousa.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "stock") (:form . "stock") (:end . 7) (:start . 2)\n (:id . 43))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 16)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "JJ") (:stem . "ubiquitous") (:form . "ubiquitous") (:end . 31)\n (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "actin-gal4") (:form . "actin-Gal4") (:end . 42)\n (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "driver") (:form . "driver") (:end . 49)\n (:start . 43) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 51) (:start . 50)\n (:id . 49))\n ((:tag . "NNP") (:stem . "P-actin-Gal4") (:form . "P-actin-Gal4") (:end . 63)\n (:start . 51) (:id . 50))\n ((:tag . "NNP") (:stem . "UAS-GFP/CyO") (:form . "UAS-GFP/CyO") (:end . 75)\n (:start . 64) (:id . 51))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 76) (:start . 75)\n (:id . 52))\n ((:tag . "JJ") (:stem . "lethal") (:form . "lethal") (:end . 83)\n (:start . 77) (:id . 53))\n ((:tag . "NN") (:stem . "insertion") (:form . "insertion") (:end . 93)\n (:start . 84) (:id . 54))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 96) (:start . 94)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Chromosome") (:form . "Chromosome") (:end . 107)\n (:start . 97) (:id . 56))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 110) (:start . 108)\n (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 115) (:start . 112)\n (:id . 59))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 124)\n (:start . 116) (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 129) (:start . 125)\n (:id . 61))\n ((:tag . "NNP") (:stem . "Dr.") (:form . "Dr.") (:end . 133) (:start . 130)\n (:id . 62))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 136) (:start . 134)\n (:id . 63))\n ((:tag . "NNP") (:stem . "Sousa") (:form . "Sousa") (:end . 142)\n (:start . 137) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.290) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102420@unknown@formal@none@1@S@Transgenic flies SgsGFP-1 (insertion on Chromosome X) and SgsGFP-2 (insertion on Chromosome II) containing the chimeric gene construct Sgs?3-GFP were obtained from Dr. A. J. Andres.@(((:tag . "JJ") (:stem . "transgenic") (:form . "Transgenic") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 16) (:start . 11)\n (:id . 43))\n ((:tag . "NN") (:stem . "sgsgfp-1") (:form . "SgsGFP-1") (:end . 25)\n (:start . 17) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n (:id . 45))\n ((:tag . "NN") (:stem . "insertion") (:form . "insertion") (:end . 36)\n (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 39) (:start . 37)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Chromosome") (:form . "Chromosome") (:end . 50)\n (:start . 40) (:id . 48))\n ((:tag . "NNP") (:stem . "X") (:form . "X") (:end . 52) (:start . 51)\n (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 53) (:start . 52)\n (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n (:id . 51))\n ((:tag . "NN") (:stem . "sgsgfp-2") (:form . "SgsGFP-2") (:end . 66)\n (:start . 58) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n (:id . 53))\n ((:tag . "NN") (:stem . "insertion") (:form . "insertion") (:end . 77)\n (:start . 68) (:id . 54))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 80) (:start . 78)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Chromosome") (:form . "Chromosome") (:end . 91)\n (:start . 81) (:id . 56))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 94) (:start . 92)\n (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 95) (:start . 94)\n (:id . 58))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 106)\n (:start . 96) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n (:id . 60))\n ((:tag . "JJ") (:stem . "chimeric") (:form . "chimeric") (:end . 119)\n (:start . 111) (:id . 61))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 124) (:start . 120)\n (:id . 62))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 134)\n (:start . 125) (:id . 63))\n ((:tag . "NNP") (:stem . "Sgs?3-GFP") (:form . "Sgs?3-GFP") (:end . 144)\n (:start . 135) (:id . 64))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 149) (:start . 145)\n (:id . 65))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 158)\n (:start . 150) (:id . 66))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 163) (:start . 159)\n (:id . 67))\n ((:tag . "NNP") (:stem . "Dr.") (:form . "Dr.") (:end . 167) (:start . 164)\n (:id . 68))\n ((:tag . "NNP") (:stem . "A.") (:form . "A.") (:end . 170) (:start . 168)\n (:id . 69))\n ((:tag . "NNP") (:stem . "J.") (:form . "J.") (:end . 173) (:start . 171)\n (:id . 70))\n ((:tag . "NNP") (:stem . "Andres") (:form . "Andres") (:end . 180)\n (:start . 174) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n (:id . 72)))@@@1@31@((:identifiers (:sid . :s7.292) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102421@unknown@formal@none@1@S@For expression of ADGF-A using the HS-ADGF-A construct, flies were heat shocked as late embryos/early first instars at 37 °C for 30 min.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n (:id . 44))\n ((:tag . "NNP") (:stem . "ADGF-A") (:form . "ADGF-A") (:end . 24)\n (:start . 18) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 30) (:start . 25)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "NNP") (:stem . "HS-ADGF-A") (:form . "HS-ADGF-A") (:end . 44)\n (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 54)\n (:start . 45) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n (:id . 50))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 61) (:start . 56)\n (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 66) (:start . 62)\n (:id . 52))\n ((:tag . "NN") (:stem . "heat") (:form . "heat") (:end . 71) (:start . 67)\n (:id . 53))\n ((:tag . "VBD") (:stem . "shock") (:form . "shocked") (:end . 79)\n (:start . 72) (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 82) (:start . 80)\n (:id . 55))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 87) (:start . 83)\n (:id . 56))\n ((:tag . "JJ") (:stem . "embryos/early") (:form . "embryos/early")\n (:end . 101) (:start . 88) (:id . 57))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 107)\n (:start . 102) (:id . 58))\n ((:tag . "NNS") (:stem . "instar") (:form . "instars") (:end . 115)\n (:start . 108) (:id . 59))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 118) (:start . 116)\n (:id . 60))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 121) (:start . 119)\n (:id . 61))\n ((:tag . "NNP") (:stem . "°C") (:form . "°C") (:end . 124) (:start . 122)\n (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 128) (:start . 125)\n (:id . 63))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 131) (:start . 129)\n (:id . 64))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 135) (:start . 132)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.293) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102422@unknown@formal@none@1@S@In all rescue experiments, 30 freshly hatched homozygous first-instar larvae were selected using a GFP dissecting microscope and transferred into fresh vials (at least four vials for each variant).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 13) (:start . 7)\n (:id . 44))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 25)\n (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n (:id . 46))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 29) (:start . 27)\n (:id . 47))\n ((:tag . "RB") (:stem . "freshly") (:form . "freshly") (:end . 37)\n (:start . 30) (:id . 48))\n ((:tag . "VBN") (:stem . "hatch") (:form . "hatched") (:end . 45)\n (:start . 38) (:id . 49))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 56)\n (:start . 46) (:id . 50))\n ((:tag . "JJ") (:stem . "first-instar") (:form . "first-instar") (:end . 69)\n (:start . 57) (:id . 51))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 76)\n (:start . 70) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 81) (:start . 77)\n (:id . 53))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 90)\n (:start . 82) (:id . 54))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 96) (:start . 91)\n (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 98) (:start . 97)\n (:id . 56))\n ((:tag . "NNP") (:stem . "GFP") (:form . "GFP") (:end . 102) (:start . 99)\n (:id . 57))\n ((:tag . "VBG") (:stem . "dissect") (:form . "dissecting") (:end . 113)\n (:start . 103) (:id . 58))\n ((:tag . "NN") (:stem . "microscope") (:form . "microscope") (:end . 124)\n (:start . 114) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n (:id . 60))\n ((:tag . "VBN") (:stem . "transfer") (:form . "transferred") (:end . 140)\n (:start . 129) (:id . 61))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 145) (:start . 141)\n (:id . 62))\n ((:tag . "JJ") (:stem . "fresh") (:form . "fresh") (:end . 151)\n (:start . 146) (:id . 63))\n ((:tag . "NNS") (:stem . "vial") (:form . "vials") (:end . 157)\n (:start . 152) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 159) (:start . 158)\n (:id . 65))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 161) (:start . 159)\n (:id . 66))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 167)\n (:start . 162) (:id . 67))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 172) (:start . 168)\n (:id . 68))\n ((:tag . "NNS") (:stem . "vial") (:form . "vials") (:end . 178)\n (:start . 173) (:id . 69))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 182) (:start . 179)\n (:id . 70))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 187) (:start . 183)\n (:id . 71))\n ((:tag . "NN") (:stem . "variant") (:form . "variant") (:end . 195)\n (:start . 188) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 196) (:start . 195)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n (:id . 74)))@@@1@33@((:identifiers (:sid . :s7.294) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102423@unknown@formal@none@1@S@They were left to develop at 25 °C and examined as wandering third-instar larvae, pupae, and adults.@(((:tag . "PRP") (:stem . "they") (:form . "They") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . "VBN") (:stem . "leave") (:form . "left") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 17) (:start . 15)\n (:id . 45))\n ((:tag . "VB") (:stem . "develop") (:form . "develop") (:end . 25)\n (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 28) (:start . 26)\n (:id . 47))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 31) (:start . 29)\n (:id . 48))\n ((:tag . "NNP") (:stem . "°C") (:form . "°C") (:end . 34) (:start . 32)\n (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n (:id . 50))\n ((:tag . "VBN") (:stem . "examine") (:form . "examined") (:end . 47)\n (:start . 39) (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 50) (:start . 48)\n (:id . 52))\n ((:tag . "VBG") (:stem . "wander") (:form . "wandering") (:end . 60)\n (:start . 51) (:id . 53))\n ((:tag . "JJ") (:stem . "third-instar") (:form . "third-instar") (:end . 73)\n (:start . 61) (:id . 54))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 80)\n (:start . 74) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n (:id . 56))\n ((:tag . "NNS") (:stem . "pupa") (:form . "pupae") (:end . 87) (:start . 82)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n (:id . 59))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 99)\n (:start . 93) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s7.295) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102424@unknown@formal@none@1@S@Ecdysone treatment@(((:tag . "NNP") (:stem . "Ecdysone") (:form . "Ecdysone") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 18)\n (:start . 9) (:id . 43)))@@@1@2@((:identifiers (:sid . :s7.296) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5102425@unknown@formal@none@1@S@Mutant larvae were raised on plates with yeast paste at 25 °C and transferred to vials with glucose-yeast medium (control) or with glucose-yeast medium containing 20-hydroxyecdysone (H-5142; Sigma-Aldrich, St.@(((:tag . "JJ") (:stem . "mutant") (:form . "Mutant") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "larva") (:form . 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"l2/l3") (:form . "L2/L3") (:end . 87) (:start . 82)\n (:id . 58))\n ((:tag . "NN") (:stem . "molt") (:form . "molt") (:end . 92) (:start . 88)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s7.298) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102427@unknown@formal@none@1@S@Numbers of puparia were counted at 12-h intervals after the 120-h time point (when the first control larvae start to pupariate).@(((:tag . "NNPS") (:stem . "Number") (:form . "Numbers") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n (:id . 43))\n ((:tag . "NN") (:stem . "puparia") (:form . "puparia") (:end . 18)\n (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 23) (:start . 19)\n (:id . 45))\n ((:tag . "VBN") (:stem . "count") (:form . 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(:end . 128) (:start . 127)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.299) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102428@unknown@formal@none@1@S@The ecd1 flies (Bloomington stock BL-218) served as a control for the functional 20E diet [31]: flies were raised at 22 °C (permissive temperature for the temperature-sensitive ecd1 mutation) and transferred to vials with control or 20E-containing diet and raised at 29 °C (restrictive temperature).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "ecd1") (:form . "ecd1") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 16) (:start . 15)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Bloomington") (:form . "Bloomington") (:end . 27)\n (:start . 16) (:id . 46))\n ((:tag . 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"observations") (:end . 32)\n (:start . 20) (:id . 45)))@@@1@4@((:identifiers (:sid . :s7.305) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5102434@unknown@formal@none@1@S@Circulating hemocytes were obtained by opening two late third-instar larvae in 30 ?l of PBS.@(((:tag . "VBG") (:stem . "circulate") (:form . "Circulating") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "hemocyte") (:form . "hemocytes") (:end . 21)\n (:start . 12) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 26) (:start . 22)\n (:id . 44))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 35)\n (:start . 27) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 38) (:start . 36)\n (:id . 46))\n ((:tag . "VBG") (:stem . "open") (:form . "opening") (:end . 46)\n (:start . 39) (:id . 47))\n ((:tag . "CD") (:stem . "two") (:form . 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(:end . 92) (:start . 91)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s7.306) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102435@unknown@formal@none@1@S@This allowed us to collect all hemolymph from the larvae in a defined volume.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "allow") (:form . "allowed") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 18) (:start . 16)\n (:id . 45))\n ((:tag . "VB") (:stem . "collect") (:form . "collect") (:end . 26)\n (:start . 19) (:id . 46))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 30) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "hemolymph") (:form . "hemolymph") (:end . 40)\n (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . 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(:end . 77) (:start . 76)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s7.307) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102436@unknown@formal@none@1@S@The solution with circulating hemocytes was mixed by gently pipetting, and part was transferred into the chamber of an improved Neubauer hemocytometer.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "solution") (:form . "solution") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 17) (:start . 13)\n (:id . 44))\n ((:tag . "VBG") (:stem . "circulate") (:form . "circulating") (:end . 29)\n (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "hemocyte") (:form . "hemocytes") (:end . 39)\n (:start . 30) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 43) (:start . 40)\n (:id . 47))\n ((:tag . "VBN") (:stem . "mix") (:form . 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(:end . 51) (:start . 50)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s7.309) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102438@unknown@formal@none@1@S@Hemocyte morphology was observed by differential interference contrast microscopy of living cells in Shields and Sang Insect Medium (Sigma-Aldrich) obtained by the same procedure as for counting.@(((:tag . "NNP") (:stem . "Hemocyte") (:form . "Hemocyte") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 19)\n (:start . 9) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 23) (:start . 20)\n (:id . 44))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 32)\n (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 35) (:start . 33)\n (:id . 46))\n ((:tag . "JJ") (:stem . "differential") (:form . 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"(") (:end . 269) (:start . 268)\n (:id . 85))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 270) (:start . 269)\n (:id . 86))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 271) (:start . 270)\n (:id . 87))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 275) (:start . 272)\n (:id . 88))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 282)\n (:start . 276) (:id . 89))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 287) (:start . 283)\n (:id . 90))\n ((:tag . "NNP") (:stem . "XbaI") (:form . "XbaI") (:end . 292) (:start . 288)\n (:id . 91))\n ((:tag . "NN") (:stem . "tail") (:form . "tail") (:end . 297) (:start . 293)\n (:id . 92))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 298) (:start . 297)\n (:id . 93))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 302) (:start . 299)\n (:id . 94))\n ((:tag . "CD") (:stem . "5?-") (:form . "5?-") (:end . 306) (:start . 303)\n (:id . 95))\n ((:tag . "NN") (:stem . 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")") (:end . 373) (:start . 372)\n (:id . 106))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 374) (:start . 373)\n (:id . 107)))@@@1@66@((:identifiers (:sid . :s7.315) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102444@unknown@formal@none@1@S@The PCR product was cloned into the pGEM-T Easy vector (Promega, Madison, Wisconsin, United States), and the resulting plasmid (ADGF-A-pGEM) was cut by NotI/SpeI restriction enzymes.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "product") (:form . "product") (:end . 15)\n (:start . 8) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "VBN") (:stem . "clone") (:form . "cloned") (:end . 26)\n (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . 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(:end . 182) (:start . 181)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s7.316) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102445@unknown@formal@none@1@S@The ADGF-A fragment was then cloned into the pCaSpeR-hs) vector cut by NotI/XbaI to obtain the HS-ADGF-A construct.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "ADGF-A") (:form . "ADGF-A") (:end . 10)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 19)\n (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 28) (:start . 24)\n (:id . 46))\n ((:tag . "VBN") (:stem . "clone") (:form . "cloned") (:end . 35)\n (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "into") (:form . 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(:end . 238) (:start . 237)\n (:id . 82))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 242) (:start . 239)\n (:id . 83))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 247) (:start . 243)\n (:id . 84))\n ((:tag . "NNP") (:stem . "XbaI") (:form . "XbaI") (:end . 252) (:start . 248)\n (:id . 85))\n ((:tag . "NN") (:stem . "tail") (:form . "tail") (:end . 257) (:start . 253)\n (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 258) (:start . 257)\n (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 259) (:start . 258)\n (:id . 88)))@@@1@47@((:identifiers (:sid . :s7.319) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102448@unknown@formal@none@1@S@The fragment was cut by XhoI/XbaI and cloned into the pUAST vector modified by MZ.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "fragment") (:form . 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"modify") (:form . "modified") (:end . 75)\n (:start . 67) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 78) (:start . 76)\n (:id . 55))\n ((:tag . "NNP") (:stem . "MZ") (:form . "MZ") (:end . 81) (:start . 79)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s7.320) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102450@unknown@formal@none@1@S@A mutated version—UAS-mutADGF-Amyc—was prepared in the same way as UAS-ADGF-Amyc, but pBLUESCRIPT containing mutated ADGF-A cDNA was used as a template.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 9)\n (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 17)\n (:start . 10) (:id . 44))\n ((:tag . "JJ") (:stem . "—") (:form . 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"a") (:end . 142) (:start . 141)\n (:id . 66))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 151)\n (:start . 143) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s7.322) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102451@unknown@formal@none@1@S@The mutated version of ADGF-A (carrying a mutation causing the substitution of two amino acids—His386 and Ala387 for Glu and Leu, respectively) in the catalytic domain, shown to abolish adenosine deaminase activity [16], was prepared by recombinant PCR using the following recombinant primers: 5?- TCTACTTCGAGCTCGGAGAAACAAACTGGTTCGGT-3? and 5?- CTCCGAGCTCGAAGTAGAAATCAATGTCATCG-3? and the same 5? and 3? end primers as above.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "mutate") (:form . 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(:end . 425) (:start . 424)\n (:id . 114)))@@@1@73@((:identifiers (:sid . :s7.323) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102452@unknown@formal@none@1@S@Adenosine and deoxyadenosine concentrations measurement@(((:tag . "NNP") (:stem . "Adenosine") (:form . "Adenosine") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 13) (:start . 10)\n (:id . 43))\n ((:tag . "NN") (:stem . "deoxyadenosine") (:form . "deoxyadenosine")\n (:end . 28) (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n (:end . 43) (:start . 29) (:id . 45))\n ((:tag . "NN") (:stem . "measurement") (:form . "measurement") (:end . 55)\n (:start . 44) (:id . 46)))@@@1@5@((:identifiers (:sid . :s7.324) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5102453@unknown@formal@none@1@S@The detection method used liquid chromatography and mass spectrometry (LC/MS method) of deproteinated hemolymph samples.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "detection") (:form . "detection") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 20)\n (:start . 14) (:id . 44))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 25) (:start . 21)\n (:id . 45))\n ((:tag . "NN") (:stem . "liquid") (:form . "liquid") (:end . 32)\n (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . "chromatography") (:form . "chromatography")\n (:end . 47) (:start . 33) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . 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(:end . 133) (:start . 132)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s8.5) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102464@unknown@formal@none@1@S@The core cell death pathway was first defined through genetic analysis in the nematode Caenorhabditis elegans and has since been found to be conserved in species as diverse as Drosophila melanogaster and Homo sapiens.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 19) (:start . 14)\n (:id . 45))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 27)\n (:start . 20) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 31) (:start . 28)\n (:id . 47))\n ((:tag . 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(:end . 217) (:start . 216)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s8.6) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102465@unknown@formal@none@1@S@The rapid progress of the various genome sequencing projects has greatly accelerated the discovery of homologs for key components of the cell death pathway as well as for its regulators.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "progress") (:form . "progress") (:end . 18)\n (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 46))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 33)\n (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . 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"VBP") (:stem . "act") (:form . "act") (:end . 87) (:start . 84)\n (:id . 56))\n ((:tag . "RB") (:stem . "mainly") (:form . "mainly") (:end . 94)\n (:start . 88) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 97) (:start . 95)\n (:id . 58))\n ((:tag . "NN") (:stem . "apoptosis") (:form . "apoptosis") (:end . 107)\n (:start . 98) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s8.17) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102476@unknown@formal@none@1@S@Class 2 has been further subdivided into two groups: upstream or initiator caspases (group 1), and downstream or effector caspases (group 2).@(((:tag . "NNP") (:stem . "Class") (:form . "Class") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 7) (:start . 6)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . 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"caspases") (:end . 130)\n (:start . 122) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 132) (:start . 131)\n (:id . 66))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 137)\n (:start . 132) (:id . 67))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 139) (:start . 138)\n (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 140) (:start . 139)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s8.18) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102477@unknown@formal@none@1@S@Initiator caspases are thought to be at the beginning of a proteolytic cascade that amplifies the cell death signal and results in the activation of the effector caspases.@(((:tag . "NNP") (:stem . "Initiator") (:form . "Initiator") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "caspas") (:form . 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"cascade") (:form . "cascade") (:end . 78)\n (:start . 71) (:id . 54))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 83) (:start . 79)\n (:id . 55))\n ((:tag . "VBZ") (:stem . "amplify") (:form . "amplifies") (:end . 93)\n (:start . 84) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n (:id . 57))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 102) (:start . 98)\n (:id . 58))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 108)\n (:start . 103) (:id . 59))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 115)\n (:start . 109) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 119) (:start . 116)\n (:id . 61))\n ((:tag . "VBZ") (:stem . "result") (:form . "results") (:end . 127)\n (:start . 120) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 130) (:start . 128)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n (:id . 64))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 145)\n (:start . 135) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 148) (:start . 146)\n (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n (:id . 67))\n ((:tag . "NN") (:stem . "effector") (:form . "effector") (:end . 161)\n (:start . 153) (:id . 68))\n ((:tag . "NNS") (:stem . "caspas") (:form . "caspases") (:end . 170)\n (:start . 162) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x8.19.1) (:span 23 30)))\n (:hscopes ((:id . :x8.19.1) (:span 0 170)))\n (:identifiers (:sid . :s8.19) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102478@unknown@formal@none@1@S@Initiator caspases usually have long pro-domains, while effector caspases have short pro-domains.@(((:tag . "NNP") (:stem . "Initiator") (:form . "Initiator") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "caspas") (:form . "caspases") (:end . 18)\n (:start . 10) (:id . 43))\n ((:tag . "RB") (:stem . "usually") (:form . "usually") (:end . 26)\n (:start . 19) (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 31) (:start . 27)\n (:id . 45))\n ((:tag . "JJ") (:stem . "long") (:form . "long") (:end . 36) (:start . 32)\n (:id . 46))\n ((:tag . "NNS") (:stem . "pro-domain") (:form . "pro-domains") (:end . 48)\n (:start . 37) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n (:id . 48))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 55) (:start . 50)\n (:id . 49))\n ((:tag . "NN") (:stem . "effector") (:form . "effector") (:end . 64)\n (:start . 56) (:id . 50))\n ((:tag . "NNS") (:stem . "caspas") (:form . "caspases") (:end . 73)\n (:start . 65) (:id . 51))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 78) (:start . 74)\n (:id . 52))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 84) (:start . 79)\n (:id . 53))\n ((:tag . "NNS") (:stem . "pro-domain") (:form . "pro-domains") (:end . 96)\n (:start . 85) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s8.20) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102480@unknown@formal@none@1@S@C. elegans appears to have only a single caspase - CED-3 - that is essential for all developmental cell death, despite having three other caspases in its genome [8,9].@(((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 18)\n (:start . 11) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 26) (:start . 22)\n (:id . 46))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 31) (:start . 27)\n (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n (:id . 48))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 40)\n (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "caspase") (:form . "caspase") (:end . 48)\n (:start . 41) (:id . 50))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 50) (:start . 49)\n (:id . 51))\n ((:tag . "NNP") (:stem . "CED-3") (:form . "CED-3") (:end . 56) (:start . 51)\n (:id . 52))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 58) (:start . 57)\n (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 63) (:start . 59)\n (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 66) (:start . 64)\n (:id . 55))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 76)\n (:start . 67) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 80) (:start . 77)\n (:id . 57))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 84) (:start . 81)\n (:id . 58))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n (:end . 98) (:start . 85) (:id . 59))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 103) (:start . 99)\n (:id . 60))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 109)\n (:start . 104) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n (:id . 62))\n ((:tag . "IN") (:stem . "despite") (:form . "despite") (:end . 118)\n (:start . 111) (:id . 63))\n ((:tag . "VBG") (:stem . "have") (:form . "having") (:end . 125)\n (:start . 119) (:id . 64))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 131)\n (:start . 126) (:id . 65))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 137)\n (:start . 132) (:id . 66))\n ((:tag . "NNS") (:stem . "caspas") (:form . "caspases") (:end . 146)\n (:start . 138) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n (:id . 68))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 153) (:start . 150)\n (:id . 69))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 160)\n (:start . 154) (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 162) (:start . 161)\n (:id . 71))\n ((:tag . "CD") (:stem . "8,9") (:form . "8,9") (:end . 165) (:start . 162)\n (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 166) (:start . 165)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n (:id . 74)))@@@1@33@((:hcues ((:id . :x8.22.1) (:span 11 18)))\n (:hscopes ((:id . :x8.22.1) (:span 0 109)))\n (:identifiers (:sid . :s8.22) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102481@unknown@formal@none@1@S@Three Drosophila caspases - Dcp-2/Dredd, Dronc, and one known only as a sequence in the genome database - have long pro-domains and are thus likely initiator caspases; another four - Dcp-1, drICE, Decay, and another one found in the genome database - have short pro-domains and are probably effector caspases.@(((:tag . "CD") (:stem . "three") (:form . "Three") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 16)\n (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "caspas") (:form . "caspases") (:end . 25)\n (:start . 17) (:id . 44))\n ((:tag . "HYPH") (:stem . "-") (:form . 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"drICE") (:end . 195)\n (:start . 190) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 196) (:start . 195)\n (:id . 78))\n ((:tag . "NNP") (:stem . "Decay") (:form . "Decay") (:end . 202)\n (:start . 197) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 203) (:start . 202)\n (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 207) (:start . 204)\n (:id . 81))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 215)\n (:start . 208) (:id . 82))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 219) (:start . 216)\n (:id . 83))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 225)\n (:start . 220) (:id . 84))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 228) (:start . 226)\n (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 232) (:start . 229)\n (:id . 86))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 239)\n (:start . 233) (:id . 87))\n ((:tag . "NN") (:stem . 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(:end . 309) (:start . 308)\n (:id . 98)))@@@1@57@((:hcues ((:id . :x8.23.1) (:span 282 290))\n ((:id . :x8.23.2) (:span 141 147)))\n (:hscopes ((:id . :x8.23.1) (:span 282 308))\n ((:id . :x8.23.2) (:span 141 166)))\n (:identifiers (:sid . :s8.23) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102482@unknown@formal@none@1@S@In addition, Dcp-1 has a substrate specificity that is very similar to that of two effector caspases, mammalian caspase 3 and C. elegans CED-3 [10].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Dcp-1") (:form . "Dcp-1") (:end . 18) (:start . 13)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 22) (:start . 19)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 24) (:start . 23)\n (:id . 47))\n ((:tag . "NN") (:stem . "substrate") (:form . "substrate") (:end . 34)\n (:start . 25) (:id . 48))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 46)\n (:start . 35) (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 51) (:start . 47)\n (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 54) (:start . 52)\n (:id . 51))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 59) (:start . 55)\n (:id . 52))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 67)\n (:start . 60) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 70) (:start . 68)\n (:id . 54))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 75) (:start . 71)\n (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n (:id . 56))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 82) (:start . 79)\n (:id . 57))\n ((:tag . "NN") (:stem . "effector") (:form . "effector") (:end . 91)\n (:start . 83) (:id . 58))\n ((:tag . "NNS") (:stem . "caspas") (:form . "caspases") (:end . 100)\n (:start . 92) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n (:id . 60))\n ((:tag . "JJ") (:stem . "mammalian") (:form . "mammalian") (:end . 111)\n (:start . 102) (:id . 61))\n ((:tag . "NN") (:stem . "caspase") (:form . "caspase") (:end . 119)\n (:start . 112) (:id . 62))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 121) (:start . 120)\n (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n (:id . 64))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 128) (:start . 126)\n (:id . 65))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 136)\n (:start . 129) (:id . 66))\n ((:tag . "NNP") (:stem . "CED-3") (:form . "CED-3") (:end . 142)\n (:start . 137) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 144) (:start . 143)\n (:id . 68))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 146) (:start . 144)\n (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 147) (:start . 146)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n (:id . 71)))@@@1@30@((:identifiers (:sid . :s8.24) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102483@unknown@formal@none@1@S@Interestingly, Dronc appears to have a substrate specificity that is so far unique among caspases: while all other known caspases have only been shown to cleave after aspartate residues, Dronc can also cleave after glutamate residues [11].@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Dronc") (:form . "Dronc") (:end . 20) (:start . 15)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 28)\n (:start . 21) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n (:id . 46))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 36) (:start . 32)\n (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n (:id . 48))\n ((:tag . "NN") (:stem . "substrate") (:form . "substrate") (:end . 48)\n (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 60)\n (:start . 49) (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 65) (:start . 61)\n (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 68) (:start . 66)\n (:id . 52))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 71) (:start . 69)\n (:id . 53))\n ((:tag . "RB") (:stem . "far") (:form . "far") (:end . 75) (:start . 72)\n (:id . 54))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 82)\n (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 88) (:start . 83)\n (:id . 56))\n ((:tag . "NNS") (:stem . "caspas") (:form . "caspases") (:end . 97)\n (:start . 89) (:id . 57))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 98) (:start . 97)\n (:id . 58))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 104) (:start . 99)\n (:id . 59))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 108) (:start . 105)\n (:id . 60))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 114)\n (:start . 109) (:id . 61))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 120)\n (:start . 115) (:id . 62))\n ((:tag . "NNS") (:stem . "caspas") (:form . "caspases") (:end . 129)\n (:start . 121) (:id . 63))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 134) (:start . 130)\n (:id . 64))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 139) (:start . 135)\n (:id . 65))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 144) (:start . 140)\n (:id . 66))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 150)\n (:start . 145) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 153) (:start . 151)\n (:id . 68))\n ((:tag . "VB") (:stem . "cleave") (:form . "cleave") (:end . 160)\n (:start . 154) (:id . 69))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 166)\n (:start . 161) (:id . 70))\n ((:tag . "NN") (:stem . "aspartate") (:form . "aspartate") (:end . 176)\n (:start . 167) (:id . 71))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 185)\n (:start . 177) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 186) (:start . 185)\n (:id . 73))\n ((:tag . "NNP") (:stem . "Dronc") (:form . "Dronc") (:end . 192)\n (:start . 187) (:id . 74))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 196) (:start . 193)\n (:id . 75))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 201) (:start . 197)\n (:id . 76))\n ((:tag . "VB") (:stem . "cleave") (:form . "cleave") (:end . 208)\n (:start . 202) (:id . 77))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 214)\n (:start . 209) (:id . 78))\n ((:tag . "NN") (:stem . "glutamate") (:form . "glutamate") (:end . 224)\n (:start . 215) (:id . 79))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 233)\n (:start . 225) (:id . 80))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 235) (:start . 234)\n (:id . 81))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 237) (:start . 235)\n (:id . 82))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 238) (:start . 237)\n (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 239) (:start . 238)\n (:id . 84)))@@@1@43@((:hcues ((:id . :x8.25.1) (:span 21 28)))\n (:hscopes ((:id . :x8.25.1) (:span 15 97)))\n (:identifiers (:sid . :s8.25) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102484@unknown@formal@none@1@S@This unusual substrate specificity may explain why Dronc is resistant to inhibition by the pan-caspase inhibitor p35.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "unusual") (:form . "unusual") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "substrate") (:form . "substrate") (:end . 22)\n (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 34)\n (:start . 23) (:id . 45))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 38) (:start . 35)\n (:id . 46))\n ((:tag . "VB") (:stem . "explain") (:form . "explain") (:end . 46)\n (:start . 39) (:id . 47))\n ((:tag . "WRB") (:stem . "why") (:form . "why") (:end . 50) (:start . 47)\n (:id . 48))\n ((:tag . "NNP") (:stem . "Dronc") (:form . "Dronc") (:end . 56) (:start . 51)\n (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 59) (:start . 57)\n (:id . 50))\n ((:tag . "JJ") (:stem . "resistant") (:form . "resistant") (:end . 69)\n (:start . 60) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n (:id . 52))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 83)\n (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 86) (:start . 84)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n (:id . 55))\n ((:tag . "NN") (:stem . "pan-caspase") (:form . "pan-caspase") (:end . 102)\n (:start . 91) (:id . 56))\n ((:tag . "NN") (:stem . "inhibitor") (:form . "inhibitor") (:end . 112)\n (:start . 103) (:id . 57))\n ((:tag . "NN") (:stem . "p35") (:form . "p35") (:end . 116) (:start . 113)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n (:id . 59)))@@@1@18@((:hcues ((:id . :x8.26.1) (:span 35 38)))\n (:hscopes ((:id . :x8.26.1) (:span 35 116)))\n (:identifiers (:sid . :s8.26) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102485@unknown@formal@none@1@S@On the basis of current data, it seems that CED-4 functions to help activate the caspase CED-3, and CED-9 blocks this activation through physical interaction with CED-4.@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "basis") (:form . "basis") (:end . 12) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 23)\n (:start . 16) (:id . 46))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 28) (:start . 24)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n (:id . 48))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 32) (:start . 30)\n (:id . 49))\n ((:tag . "VBZ") (:stem . "seem") (:form . "seems") (:end . 38) (:start . 33)\n (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 43) (:start . 39)\n (:id . 51))\n ((:tag . "NN") (:stem . "ced-4") (:form . "CED-4") (:end . 49) (:start . 44)\n (:id . 52))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 59)\n (:start . 50) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 62) (:start . 60)\n (:id . 54))\n ((:tag . "VB") (:stem . "help") (:form . "help") (:end . 67) (:start . 63)\n (:id . 55))\n ((:tag . "VB") (:stem . "activate") (:form . "activate") (:end . 76)\n (:start . 68) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n (:id . 57))\n ((:tag . "NN") (:stem . "caspase") (:form . "caspase") (:end . 88)\n (:start . 81) (:id . 58))\n ((:tag . "NN") (:stem . "ced-3") (:form . "CED-3") (:end . 94) (:start . 89)\n (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n (:id . 61))\n ((:tag . "NNP") (:stem . "CED-9") (:form . "CED-9") (:end . 105)\n (:start . 100) (:id . 62))\n ((:tag . "NNS") (:stem . "block") (:form . "blocks") (:end . 112)\n (:start . 106) (:id . 63))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 117) (:start . 113)\n (:id . 64))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 128)\n (:start . 118) (:id . 65))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 136)\n (:start . 129) (:id . 66))\n ((:tag . "JJ") (:stem . "physical") (:form . "physical") (:end . 145)\n (:start . 137) (:id . 67))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 157)\n (:start . 146) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 162) (:start . 158)\n (:id . 69))\n ((:tag . "NN") (:stem . "ced-4") (:form . "CED-4") (:end . 168)\n (:start . 163) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n (:id . 71)))@@@1@30@((:hcues ((:id . :x8.27.1) (:span 33 38)))\n (:hscopes ((:id . :x8.27.1) (:span 33 168)))\n (:identifiers (:sid . :s8.27) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102486@unknown@formal@none@1@S@Endogenous CED-4 is normally localized to the mitochondria by CED-9, unless EGL-1 is expressed [12,13].@(((:tag . "JJ") (:stem . "endogenous") (:form . "Endogenous") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "ced-4") (:form . "CED-4") (:end . 16) (:start . 11)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 19) (:start . 17)\n (:id . 44))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 28)\n (:start . 20) (:id . 45))\n ((:tag . "JJ") (:stem . "localized") (:form . "localized") (:end . 38)\n (:start . 29) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n (:id . 48))\n ((:tag . "NNS") (:stem . "mitochondrion") (:form . "mitochondria")\n (:end . 58) (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 61) (:start . 59)\n (:id . 50))\n ((:tag . "NNP") (:stem . "CED-9") (:form . "CED-9") (:end . 67) (:start . 62)\n (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n (:id . 52))\n ((:tag . "IN") (:stem . "unless") (:form . "unless") (:end . 75)\n (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "egl-1") (:form . "EGL-1") (:end . 81) (:start . 76)\n (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 84) (:start . 82)\n (:id . 55))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 94)\n (:start . 85) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 96) (:start . 95)\n (:id . 57))\n ((:tag . "CD") (:stem . "12,13") (:form . "12,13") (:end . 101) (:start . 96)\n (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 102) (:start . 101)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s8.28) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102487@unknown@formal@none@1@S@If EGL-1 is expressed, the interaction between CED-4 and CED-9 ceases, and CED-4 translocates to the nuclear membrane where it activates CED-3, resulting in programmed cell death.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "egl-1") (:form . "EGL-1") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 21)\n (:start . 12) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 47))\n ((:tag . "NN") (:stem . "interaction") (:form . 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(:end . 124) (:start . 123)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s8.30) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102490@unknown@formal@none@1@S@Knock-out studies have shown that mice deficient for Apaf-1 have reduced cell death in certain tissues, further supporting a role for Apaf-1 in programmed cell death.@(((:tag . "JJ") (:stem . "knock-out") (:form . "Knock-out") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 17)\n (:start . 10) (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 22) (:start . 18)\n (:id . 44))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 28) (:start . 23)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n (:id . 46))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 38) (:start . 34)\n (:id . 47))\n ((:tag . "JJ") (:stem . 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(:end . 183) (:start . 182)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s8.38) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102497@unknown@formal@none@1@S@CED-9 has mammalian counterparts in the anti-apoptotic subgroup of Bcl-2 family members, while EGL-1 has mammalian counterparts in the pro-apoptotic subgroup.@(((:tag . "NNP") (:stem . "CED-9") (:form . "CED-9") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "JJ") (:stem . "mammalian") (:form . "mammalian") (:end . 19)\n (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "counterpart") (:form . "counterparts") (:end . 32)\n (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 47))\n ((:tag . "JJ") (:stem . 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(:end . 254) (:start . 253)\n (:id . 85)))@@@1@44@((:hcues ((:id . :x8.40.1) (:span 126 134)))\n (:hscopes ((:id . :x8.40.1) (:span 85 234)))\n (:identifiers (:sid . :s8.40) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102500@unknown@formal@none@1@S@Indeed, most mitochondria released all their cytochrome c within a one minute period in a temperature-independent manner, suggesting that an enzymatic transport mechanism is probably not involved.@(((:tag . "RB") (:stem . "indeed") (:form . "Indeed") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "NNS") (:stem . "mitochondrion") (:form . "mitochondria")\n (:end . 25) (:start . 13) (:id . 45))\n ((:tag . "VBD") (:stem . "release") (:form . "released") (:end . 34)\n (:start . 26) (:id . 46))\n ((:tag . 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"c") (:end . 234) (:start . 233)\n (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 237) (:start . 235)\n (:id . 77))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 248)\n (:start . 238) (:id . 78))\n ((:tag . "NN") (:stem . "cultured-cell") (:form . "cultured-cell")\n (:end . 262) (:start . 249) (:id . 79))\n ((:tag . "NNS") (:stem . "lysate") (:form . "lysates") (:end . 270)\n (:start . 263) (:id . 80))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 272) (:start . 271)\n (:id . 81))\n ((:tag . "CD") (:stem . "19,20") (:form . "19,20") (:end . 277)\n (:start . 272) (:id . 82))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 278) (:start . 277)\n (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 279) (:start . 278)\n (:id . 84)))@@@1@43@((:hcues ((:id . :x8.44.1) (:span 115 118)))\n (:hscopes ((:id . :x8.44.1) (:span 115 168)))\n (:identifiers (:sid . :s8.44) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102503@unknown@formal@none@1@S@There is no apparent need for cytochrome c release in C. elegans, since CED-4 does not require it to activate CED-3.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n (:id . 43))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "JJ") (:stem . "apparent") (:form . "apparent") (:end . 20)\n (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "need") (:form . "need") (:end . 25) (:start . 21)\n (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 29) (:start . 26)\n (:id . 47))\n ((:tag . 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"not") (:end . 86) (:start . 83)\n (:id . 58))\n ((:tag . "VB") (:stem . "require") (:form . "require") (:end . 94)\n (:start . 87) (:id . 59))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 97) (:start . 95)\n (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n (:id . 61))\n ((:tag . "VB") (:stem . "activate") (:form . "activate") (:end . 109)\n (:start . 101) (:id . 62))\n ((:tag . "NNP") (:stem . "CED-3") (:form . "CED-3") (:end . 115)\n (:start . 110) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n (:id . 64)))@@@1@23@((:ncues ((:id . :x8.45.1) (:span 83 86)) ((:id . :x8.45.2) (:span 9 11)))\n (:nscopes ((:id . :x8.45.1) (:span 83 115)) ((:id . :x8.45.2) (:span 9 64)))\n (:identifiers (:sid . :s8.45) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102504@unknown@formal@none@1@S@Recently, a pro-apoptotic Drosophila Bcl-2 family member was identified with the help of the database of genomic sequence; this gene is most closely related to mammalian Bok and potentially regulates apoptosis in the fly [21,22,23,24].@(((:tag . "RB") (:stem . "recently") (:form . "Recently") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 11) (:start . 10)\n (:id . 44))\n ((:tag . "JJ") (:stem . "pro-apoptotic") (:form . "pro-apoptotic")\n (:end . 25) (:start . 12) (:id . 45))\n ((:tag . 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"closely") (:end . 148)\n (:start . 141) (:id . 66))\n ((:tag . "JJ") (:stem . "related") (:form . "related") (:end . 156)\n (:start . 149) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 159) (:start . 157)\n (:id . 68))\n ((:tag . "JJ") (:stem . "mammalian") (:form . "mammalian") (:end . 169)\n (:start . 160) (:id . 69))\n ((:tag . "NNP") (:stem . "Bok") (:form . "Bok") (:end . 173) (:start . 170)\n (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 177) (:start . 174)\n (:id . 71))\n ((:tag . "RB") (:stem . "potentially") (:form . "potentially") (:end . 189)\n (:start . 178) (:id . 72))\n ((:tag . "VBZ") (:stem . "regulate") (:form . "regulates") (:end . 199)\n (:start . 190) (:id . 73))\n ((:tag . "NN") (:stem . "apoptosis") (:form . "apoptosis") (:end . 209)\n (:start . 200) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 212) (:start . 210)\n (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 216) (:start . 213)\n (:id . 76))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 220) (:start . 217)\n (:id . 77))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 222) (:start . 221)\n (:id . 78))\n ((:tag . "CD") (:stem . "21,22,23,24") (:form . "21,22,23,24") (:end . 233)\n (:start . 222) (:id . 79))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 234) (:start . 233)\n (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 235) (:start . 234)\n (:id . 81)))@@@1@40@((:hcues ((:id . :x8.46.1) (:span 178 189)))\n (:hscopes ((:id . :x8.46.1) (:span 178 220)))\n (:identifiers (:sid . :s8.46) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102505@unknown@formal@none@1@S@The Drosophila Bok homolog interacts with several anti-apoptotic, but not with several pro-apoptotic, Bcl-2 family members and, therefore, possibly functions by antagonizing pro-survival proteins.@(((:tag . 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(:end . 196) (:start . 195)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x8.47.1) (:span 139 147)))\n (:ncues ((:id . :x8.47.2) (:span 70 73)))\n (:hscopes ((:id . :x8.47.1) (:span 139 195)))\n (:nscopes ((:id . :x8.47.2) (:span 70 122)))\n (:identifiers (:sid . :s8.47) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102506@unknown@formal@none@1@S@Ectopic expression of Bok protein promotes apoptosis in transgenic flies as well as in cultured cells.@(((:tag . "JJ") (:stem . "ectopic") (:form . "Ectopic") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 18)\n (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Bok") (:form . "Bok") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 33)\n (:start . 26) (:id . 46))\n ((:tag . 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"cells") (:end . 101) (:start . 96)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s8.48) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102507@unknown@formal@none@1@S@While one group reports that the caspase inhibitor p35 can block apoptosis induced by Drosophila Bok [22], another group did not see p35 inhibition [23].@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 15) (:start . 10)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "report") (:form . "reports") (:end . 23)\n (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . 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(:end . 120) (:start . 119)\n (:id . 61)))@@@1@20@((:hcues ((:id . :x8.50.1) (:span 16 19)))\n (:hscopes ((:id . :x8.50.1) (:span 16 119)))\n (:identifiers (:sid . :s8.50) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102510@unknown@formal@none@1@S@Interestingly, ectopic expression of Drosophila Bok sensitizes the developing eye to cell death induced by ultraviolet irradiation [21].@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 43))\n ((:tag . "JJ") (:stem . "ectopic") (:form . "ectopic") (:end . 22)\n (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 33)\n (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . 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"grim") (:end . 236) (:start . 232)\n (:id . 84))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 238) (:start . 237)\n (:id . 85))\n ((:tag . "CD") (:stem . "22") (:form . "22") (:end . 240) (:start . 238)\n (:id . 86))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 241) (:start . 240)\n (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 242) (:start . 241)\n (:id . 88)))@@@1@47@((:hcues ((:id . :x8.53.1) (:span 156 158)) ((:id . :x8.53.2) (:span 82 84))\n ((:id . :x8.53.3) (:span 49 56)))\n (:hscopes ((:id . :x8.53.1) (:span 141 173)) ((:id . :x8.53.2) (:span 69 99))\n ((:id . :x8.53.3) (:span 13 236)))\n (:identifiers (:sid . :s8.53) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102512@unknown@formal@none@1@S@The core components of the cell death pathway are illustrated in Figure 1.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . 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(:end . 156) (:start . 155)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x8.60.1) (:span 85 92)))\n (:hscopes ((:id . :x8.60.1) (:span 75 155)))\n (:identifiers (:sid . :s8.60) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102520@unknown@formal@none@1@S@Regulation of programmed cell death@(((:tag . "NN") (:stem . "regulation") (:form . "Regulation") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 43))\n ((:tag . "VBN") (:stem . "program") (:form . "programmed") (:end . 24)\n (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 29) (:start . 25)\n (:id . 45))\n ((:tag . "NN") (:stem . "death") (:form . 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"JJ") (:stem . "known") (:form . "known") (:end . 208)\n (:start . 203) (:id . 78))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 217)\n (:start . 209) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n (:id . 80)))@@@1@39@((:ncues ((:id . :x8.66.1) (:span 194 196)))\n (:nscopes ((:id . :x8.66.1) (:span 194 217)))\n (:identifiers (:sid . :s8.66) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102525@unknown@formal@none@1@S@Each of these three genes can induce programmed cell death when overexpressed in the developing Drosophila eye or in various tissue-culture assays.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 19) (:start . 14)\n (:id . 45))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 25) (:start . 20)\n (:id . 46))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 29) (:start . 26)\n (:id . 47))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 36)\n (:start . 30) (:id . 48))\n ((:tag . "VBN") (:stem . "program") (:form . "programmed") (:end . 47)\n (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 52) (:start . 48)\n (:id . 50))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 58) (:start . 53)\n (:id . 51))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 63) (:start . 59)\n (:id . 52))\n ((:tag . "VBN") (:stem . "overexpresse") (:form . "overexpressed")\n (:end . 77) (:start . 64) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . 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(:end . 147) (:start . 146)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s8.67) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102526@unknown@formal@none@1@S@In addition, Reaper, Hid and Grim are able to induce apoptosis in heterologous systems, suggesting that vertebrate homologs of these proteins exist (reviewed in [26]).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Reaper") (:form . "Reaper") (:end . 19)\n (:start . 13) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Hid") (:form . "Hid") (:end . 24) (:start . 21)\n (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . 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"VBG") (:stem . "suggest") (:form . "suggesting") (:end . 98)\n (:start . 88) (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 103) (:start . 99)\n (:id . 60))\n ((:tag . "NN") (:stem . "vertebrate") (:form . "vertebrate") (:end . 114)\n (:start . 104) (:id . 61))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 123)\n (:start . 115) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n (:id . 63))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 132)\n (:start . 127) (:id . 64))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 141)\n (:start . 133) (:id . 65))\n ((:tag . "VBP") (:stem . "exist") (:form . "exist") (:end . 147)\n (:start . 142) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 149) (:start . 148)\n (:id . 67))\n ((:tag . "VBN") (:stem . "review") (:form . "reviewed") (:end . 157)\n (:start . 149) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 160) (:start . 158)\n (:id . 69))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 162) (:start . 161)\n (:id . 70))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 164) (:start . 162)\n (:id . 71))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 165) (:start . 164)\n (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 166) (:start . 165)\n (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n (:id . 74)))@@@1@33@((:hcues ((:id . :x8.68.1) (:span 88 98)))\n (:hscopes ((:id . :x8.68.1) (:span 88 147)))\n (:identifiers (:sid . :s8.68) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102527@unknown@formal@none@1@S@Further evidence for the existence of vertebrate homologs of Reaper, Hid, and Grim come from observations that these three proteins are able to bind a class of inhibitors of apoptosis, or IAPs.@(((:tag . "JJ") (:stem . "further") (:form . "Further") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 16)\n (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 20) (:start . 17)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n (:id . 45))\n ((:tag . "NN") (:stem . "existence") (:form . "existence") (:end . 34)\n (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n (:id . 47))\n ((:tag . "NN") (:stem . "vertebrate") (:form . "vertebrate") (:end . 48)\n (:start . 38) (:id . 48))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 57)\n (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n (:id . 50))\n ((:tag . "NNP") (:stem . "Reaper") (:form . "Reaper") (:end . 67)\n (:start . 61) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n (:id . 52))\n ((:tag . "NNP") (:stem . "Hid") (:form . "Hid") (:end . 72) (:start . 69)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n (:id . 55))\n ((:tag . "NNP") (:stem . "Grim") (:form . "Grim") (:end . 82) (:start . 78)\n (:id . 56))\n ((:tag . "VBP") (:stem . "come") (:form . "come") (:end . 87) (:start . 83)\n (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 92) (:start . 88)\n (:id . 58))\n ((:tag . "NNS") (:stem . "observation") (:form . "observations") (:end . 105)\n (:start . 93) (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 110) (:start . 106)\n (:id . 60))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 116)\n (:start . 111) (:id . 61))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 122)\n (:start . 117) (:id . 62))\n ((:tag . "NNS") (:stem . "protein") (:form . 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",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n (:id . 74))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 187) (:start . 185)\n (:id . 75))\n ((:tag . "NNP") (:stem . "IAP") (:form . "IAPs") (:end . 192) (:start . 188)\n (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n (:id . 77)))@@@1@36@((:identifiers (:sid . :s8.69) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102528@unknown@formal@none@1@S@IAPs were first discovered in baculovirus, but have since been shown to play a vital role in blocking apoptosis in Drosophila as well as in mammals (reviewed in [27]).@(((:tag . "NNP") (:stem . "IAP") (:form . "IAPs") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 9) (:start . 5)\n (:id . 43))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 15) (:start . 10)\n (:id . 44))\n ((:tag . "VBN") (:stem . 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"DT") (:stem . "a") (:form . "a") (:end . 78) (:start . 77)\n (:id . 56))\n ((:tag . "JJ") (:stem . "vital") (:form . "vital") (:end . 84) (:start . 79)\n (:id . 57))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 89) (:start . 85)\n (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n (:id . 59))\n ((:tag . "VBG") (:stem . "block") (:form . "blocking") (:end . 101)\n (:start . 93) (:id . 60))\n ((:tag . "NN") (:stem . "apoptosis") (:form . "apoptosis") (:end . 111)\n (:start . 102) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n (:id . 62))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 125)\n (:start . 115) (:id . 63))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 128) (:start . 126)\n (:id . 64))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 133) (:start . 129)\n (:id . 65))\n ((:tag . "IN") (:stem . "as") (:form . 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(:end . 167) (:start . 166)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s8.70) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102530@unknown@formal@none@1@S@More recently, reports of a potential functional mammalian analog of Reaper, Hid, and Grim have been published [30,31].@(((:tag . "RBR") (:stem . "more") (:form . "More") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 44))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 22)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 27) (:start . 26)\n (:id . 47))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 37)\n (:start . 28) (:id . 48))\n ((:tag . 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(:end . 119) (:start . 118)\n (:id . 65)))@@@1@24@((:hcues ((:id . :x8.72.1) (:span 28 37)))\n (:hscopes ((:id . :x8.72.1) (:span 28 90)))\n (:identifiers (:sid . :s8.72) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102531@unknown@formal@none@1@S@Although Diablo/Smac shares no sequence homology with Reaper, Hid, or Grim, it too can bind IAPs, preventing them from inhibiting caspase activation, and thereby inducing apoptosis.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Diablo/Smac") (:form . "Diablo/Smac") (:end . 20)\n (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "share") (:form . "shares") (:end . 27)\n (:start . 21) (:id . 44))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 30) (:start . 28)\n (:id . 45))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 39)\n (:start . 31) (:id . 46))\n ((:tag . 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"can") (:form . "can") (:end . 86) (:start . 83)\n (:id . 58))\n ((:tag . "VB") (:stem . "bind") (:form . "bind") (:end . 91) (:start . 87)\n (:id . 59))\n ((:tag . "NNS") (:stem . "iap") (:form . "IAPs") (:end . 96) (:start . 92)\n (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n (:id . 61))\n ((:tag . "VBG") (:stem . "prevent") (:form . "preventing") (:end . 108)\n (:start . 98) (:id . 62))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 113) (:start . 109)\n (:id . 63))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 118) (:start . 114)\n (:id . 64))\n ((:tag . "VBG") (:stem . "inhibit") (:form . "inhibiting") (:end . 129)\n (:start . 119) (:id . 65))\n ((:tag . "NN") (:stem . "caspase") (:form . "caspase") (:end . 137)\n (:start . 130) (:id . 66))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 148)\n (:start . 138) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 153) (:start . 150)\n (:id . 69))\n ((:tag . "RB") (:stem . "thereby") (:form . "thereby") (:end . 161)\n (:start . 154) (:id . 70))\n ((:tag . "VBG") (:stem . "induce") (:form . "inducing") (:end . 170)\n (:start . 162) (:id . 71))\n ((:tag . "NN") (:stem . "apoptosis") (:form . "apoptosis") (:end . 180)\n (:start . 171) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n (:id . 73)))@@@1@32@((:ncues ((:id . :x8.73.1) (:span 28 30)))\n (:nscopes ((:id . :x8.73.1) (:span 28 74)))\n (:identifiers (:sid . :s8.73) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102532@unknown@formal@none@1@S@Furthermore, Diablo/Smac interacts through its amino terminus with the BIR (baculovirus IAP repeat) domains of IAPs, similar to Reaper, Hid, and Grim [32,33].@(((:tag . "RB") (:stem . 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"to") (:form . "to") (:end . 127) (:start . 125)\n (:id . 63))\n ((:tag . "NNP") (:stem . "Reaper") (:form . "Reaper") (:end . 134)\n (:start . 128) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n (:id . 65))\n ((:tag . "NNP") (:stem . "Hid") (:form . "Hid") (:end . 139) (:start . 136)\n (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 144) (:start . 141)\n (:id . 68))\n ((:tag . "NNP") (:stem . "Grim") (:form . "Grim") (:end . 149) (:start . 145)\n (:id . 69))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 151) (:start . 150)\n (:id . 70))\n ((:tag . "CD") (:stem . "32,33") (:form . "32,33") (:end . 156)\n (:start . 151) (:id . 71))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 157) (:start . 156)\n (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s8.74) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102533@unknown@formal@none@1@S@An important difference between the function of Diablo/Smac and Reaper, Hid, and Grim is that Diablo/Smac is not pro-apoptotic by itself when overexpressed, but instead requires a death-inducing stimulus to promote apoptosis, unlike the three Drosophila proteins.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 23)\n (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 31)\n (:start . 24) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n (:id . 46))\n ((:tag . "NN") (:stem . 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"but") (:end . 160) (:start . 157)\n (:id . 68))\n ((:tag . "RB") (:stem . "instead") (:form . "instead") (:end . 168)\n (:start . 161) (:id . 69))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 177)\n (:start . 169) (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 179) (:start . 178)\n (:id . 71))\n ((:tag . "JJ") (:stem . "death-inducing") (:form . "death-inducing")\n (:end . 194) (:start . 180) (:id . 72))\n ((:tag . "NN") (:stem . "stimulus") (:form . "stimulus") (:end . 203)\n (:start . 195) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 206) (:start . 204)\n (:id . 74))\n ((:tag . "VB") (:stem . "promote") (:form . "promote") (:end . 214)\n (:start . 207) (:id . 75))\n ((:tag . "NN") (:stem . "apoptosis") (:form . "apoptosis") (:end . 224)\n (:start . 215) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 225) (:start . 224)\n (:id . 77))\n ((:tag . "IN") (:stem . "unlike") (:form . "unlike") (:end . 232)\n (:start . 226) (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 236) (:start . 233)\n (:id . 79))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 242)\n (:start . 237) (:id . 80))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 253)\n (:start . 243) (:id . 81))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 262)\n (:start . 254) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 263) (:start . 262)\n (:id . 83)))@@@1@42@((:ncues ((:id . :x8.75.1) (:span 109 112)))\n (:nscopes ((:id . :x8.75.1) (:span 109 155)))\n (:identifiers (:sid . :s8.75) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102534@unknown@formal@none@1@S@Table 1 provides a summary of the conserved regulators of cell death across species.@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . 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(:form . ".") (:end . 175) (:start . 174)\n (:id . 76)))@@@1@35@((:hcues ((:id . :x8.83.1) (:span 41 46)))\n (:hscopes ((:id . :x8.83.1) (:span 41 169)))\n (:identifiers (:sid . :s8.83) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102542@unknown@formal@none@1@S@A second class of key apoptotic regulators in Drosophila is the IAP family.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 8) (:start . 2)\n (:id . 43))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n (:id . 45))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "JJ") (:stem . "apoptotic") (:form . "apoptotic") (:end . 31)\n (:start . 22) (:id . 47))\n ((:tag . "NNS") (:stem . 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(:end . 75) (:start . 74)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s8.84) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102543@unknown@formal@none@1@S@IAPs contain at least one, and up to three, BIR domains, which are important for protein-protein interactions, and often a carboxy-terminal RING domain (reviewed in [27]).@(((:tag . "NNS") (:stem . "iap") (:form . "IAPs") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 21) (:start . 16)\n (:id . 45))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 25) (:start . 22)\n (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . 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(:end . 171) (:start . 170)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s8.85) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102544@unknown@formal@none@1@S@While several IAPs have been implicated in inhibiting apoptosis, proteins with single BIR domains can also have functions in cell cycle regulation and cytokinesis [39,40].@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 13)\n (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "iap") (:form . "IAPs") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 23) (:start . 19)\n (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 28) (:start . 24)\n (:id . 46))\n ((:tag . "VBN") (:stem . "implicate") (:form . "implicated") (:end . 39)\n (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . 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(:end . 378) (:start . 377)\n (:id . 106)))@@@1@65@((:hcues ((:id . :x8.87.1) (:span 197 207)))\n (:ncues ((:id . :x8.87.2) (:span 43 50 60 63)))\n (:hscopes ((:id . :x8.87.1) (:span 197 284)))\n (:nscopes ((:id . :x8.87.2) (:span 43 84)))\n (:identifiers (:sid . :s8.87) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102546@unknown@formal@none@1@S@Three Drosophila BIRPs have been shown to be inhibitors of apoptosis, Diap1, Diap2, and Deterin [42,43,44,45].@(((:tag . "CD") (:stem . "three") (:form . "Three") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 16)\n (:start . 6) (:id . 43))\n ((:tag . "NNPS") (:stem . "BIRP") (:form . "BIRPs") (:end . 22) (:start . 17)\n (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 27) (:start . 23)\n (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . 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")") (:stem . ")") (:form . ")") (:end . 242) (:start . 241)\n (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 243) (:start . 242)\n (:id . 86)))@@@1@45@((:hcues ((:id . :x8.93.1) (:span 21 28)))\n (:hscopes ((:id . :x8.93.1) (:span 12 223)))\n (:identifiers (:sid . :s8.93) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102552@unknown@formal@none@1@S@Reaper, Hid, Grim, and Diablo/Smac can physically interact with IAPs, thereby inhibiting the anti-apoptotic activity of IAPs and allowing caspase activation.@(((:tag . "NNP") (:stem . "Reaper") (:form . "Reaper") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "NNP") (:stem . "Hid") (:form . "Hid") (:end . 11) (:start . 8)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Grim") (:form . 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"requires") (:end . 139)\n (:start . 131) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n (:id . 65))\n ((:tag . "NN") (:stem . "ring") (:form . "RING") (:end . 148) (:start . 144)\n (:id . 66))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 155)\n (:start . 149) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 157) (:start . 156)\n (:id . 68))\n ((:tag . "CD") (:stem . "51") (:form . "51") (:end . 159) (:start . 157)\n (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 160) (:start . 159)\n (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n (:id . 71)))@@@1@30@((:hcues ((:id . :x8.98.1) (:span 67 75)))\n (:hscopes ((:id . :x8.98.1) (:span 67 104)))\n (:identifiers (:sid . :s8.98) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102557@unknown@formal@none@1@S@The exact role of the ubiquitination pathway in regulating apoptosis is still unclear.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "exact") (:form . "exact") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "NN") (:stem . "ubiquitination") (:form . "ubiquitination")\n (:end . 36) (:start . 22) (:id . 47))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 44)\n (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "VBG") (:stem . "regulate") (:form . "regulating") (:end . 58)\n (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "apoptosis") (:form . "apoptosis") (:end . 68)\n (:start . 59) (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 71) (:start . 69)\n (:id . 52))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 77) (:start . 72)\n (:id . 53))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 85)\n (:start . 78) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n (:id . 55)))@@@1@14@((:hcues ((:id . :x8.99.1) (:span 78 85)))\n (:hscopes ((:id . :x8.99.1) (:span 0 85)))\n (:identifiers (:sid . :s8.99) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102558@unknown@formal@none@1@S@Even the role of the RING domain in IAPs is open to debate: mutations in the RING domain of endogenous diap1 can be either pro- or anti-apoptotic, depending on the death-inducing stimulus ([49] and J. Agapite, L. Goyal, K. McCall and H.S., unpublished observations).@(((:tag . "RB") (:stem . "even") (:form . "Even") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . 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(:end . 266) (:start . 265)\n (:id . 95)))@@@1@54@((:hcues ((:id . :x8.100.1) (:span 116 122 128 130))\n ((:id . :x8.100.3) (:span 109 112)))\n (:hscopes ((:id . :x8.100.1) (:span 116 145))\n ((:id . :x8.100.3) (:span 109 145)))\n (:identifiers (:sid . :s8.100) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102560@unknown@formal@none@1@S@Strengths and limitations of genomic analysis@(((:tag . "NNS") (:stem . "strength") (:form . "Strengths") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 13) (:start . 10)\n (:id . 43))\n ((:tag . "NNS") (:stem . "limitation") (:form . "limitations") (:end . 25)\n (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n (:id . 45))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 36)\n (:start . 29) (:id . 46))\n ((:tag . "NN") (:stem . "analysis") (:form . 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(:end . 189) (:start . 188)\n (:id . 78)))@@@1@37@((:identifiers (:sid . :s9.16) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102590@unknown@formal@none@1@S@The Drosophila dosage compensation complex@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "dosage") (:form . "dosage") (:end . 21)\n (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "compensation") (:form . "compensation") (:end . 34)\n (:start . 22) (:id . 45))\n ((:tag . "NN") (:stem . "complex") (:form . 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(:end . 254) (:start . 253)\n (:id . 86)))@@@1@45@((:hcues ((:id . :x9.23.1) (:span 201 204))\n ((:id . :x9.23.2) (:span 121 123)))\n (:hscopes ((:id . :x9.23.1) (:span 201 246))\n ((:id . :x9.23.2) (:span 107 128)))\n (:identifiers (:sid . :s9.23) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102596@unknown@formal@none@1@S@Moreover, the DCCs can spread, by several hundred kilobases, into neighboring autosomal DNA.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "NNPS") (:stem . "DCC") (:form . "DCCs") (:end . 18) (:start . 14)\n (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 22) (:start . 19)\n (:id . 46))\n ((:tag . "VB") (:stem . "spread") (:form . 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(:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s9.24) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102597@unknown@formal@none@1@S@These experiments indicated that the roX genes might function as nuclear entry sites for the assembly of the MSL proteins on the X chromosome.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 17)\n (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "indicate") (:form . "indicated") (:end . 27)\n (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n (:id . 46))\n ((:tag . "NNP") (:stem . "roX") (:form . "roX") (:end . 40) (:start . 37)\n (:id . 47))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 46) (:start . 41)\n (:id . 48))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 52) (:start . 47)\n (:id . 49))\n ((:tag . "VB") (:stem . "function") (:form . "function") (:end . 61)\n (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 64) (:start . 62)\n (:id . 51))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 72)\n (:start . 65) (:id . 52))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 78) (:start . 73)\n (:id . 53))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 84) (:start . 79)\n (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 88) (:start . 85)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n (:id . 56))\n ((:tag . "NN") (:stem . "assembly") (:form . "assembly") (:end . 101)\n (:start . 93) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n (:id . 59))\n ((:tag . "NNP") (:stem . "MSL") (:form . "MSL") (:end . 112) (:start . 109)\n (:id . 60))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 121)\n (:start . 113) (:id . 61))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 124) (:start . 122)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 128) (:start . 125)\n (:id . 63))\n ((:tag . "NNP") (:stem . "X") (:form . "X") (:end . 130) (:start . 129)\n (:id . 64))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 141)\n (:start . 131) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x9.25.1) (:span 47 52)) ((:id . :x9.25.2) (:span 18 32)))\n (:hscopes ((:id . :x9.25.1) (:span 47 141))\n ((:id . :x9.25.2) (:span 18 141)))\n (:identifiers (:sid . :s9.25) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102598@unknown@formal@none@1@S@Little was known, however, about the specific role of the roX RNAs during the formation of the DCC.@(((:tag . "NNP") (:stem . "Little") (:form . "Little") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 10) (:start . 7)\n (:id . 43))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 16) (:start . 11)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 25)\n (:start . 18) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n (:id . 47))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 32) (:start . 27)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n (:id . 49))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 45)\n (:start . 37) (:id . 50))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 50) (:start . 46)\n (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n (:id . 53))\n ((:tag . "NNP") (:stem . "roX") (:form . "roX") (:end . 61) (:start . 58)\n (:id . 54))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNAs") (:end . 66) (:start . 62)\n (:id . 55))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 73)\n (:start . 67) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n (:id . 57))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 87)\n (:start . 78) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n (:id . 60))\n ((:tag . "NNP") (:stem . "DCC") (:form . "DCC") (:end . 98) (:start . 95)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.26) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102600@unknown@formal@none@1@S@Meller et al. [1] took advantage of the fact that dosage compensation can be initiated and analyzed in females ectopically expressing the male-specific MSL2 protein.@(((:tag . "NNP") (:stem . "Meller") (:form . "Meller") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 9) (:start . 7)\n (:id . 43))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 15) (:start . 14)\n (:id . 45))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 16) (:start . 15)\n (:id . 46))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 17) (:start . 16)\n (:id . 47))\n ((:tag . "VBD") (:stem . "take") (:form . "took") (:end . 22) (:start . 18)\n (:id . 48))\n ((:tag . "NN") (:stem . "advantage") (:form . "advantage") (:end . 32)\n (:start . 23) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 51))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 44) (:start . 40)\n (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 49) (:start . 45)\n (:id . 53))\n ((:tag . "NN") (:stem . "dosage") (:form . "dosage") (:end . 56)\n (:start . 50) (:id . 54))\n ((:tag . "NN") (:stem . "compensation") (:form . "compensation") (:end . 69)\n (:start . 57) (:id . 55))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 73) (:start . 70)\n (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 76) (:start . 74)\n (:id . 57))\n ((:tag . "VBN") (:stem . "initiate") (:form . "initiated") (:end . 86)\n (:start . 77) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n (:id . 59))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 99)\n (:start . 91) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 102) (:start . 100)\n (:id . 61))\n ((:tag . "NNS") (:stem . "female") (:form . "females") (:end . 110)\n (:start . 103) (:id . 62))\n ((:tag . "RB") (:stem . "ectopically") (:form . "ectopically") (:end . 122)\n (:start . 111) (:id . 63))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 133)\n (:start . 123) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n (:id . 65))\n ((:tag . "JJ") (:stem . "male-specific") (:form . "male-specific")\n (:end . 151) (:start . 138) (:id . 66))\n ((:tag . "NN") (:stem . "msl2") (:form . "MSL2") (:end . 156) (:start . 152)\n (:id . 67))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 164)\n (:start . 157) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s9.28) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102601@unknown@formal@none@1@S@These females hypertranscribe their two X chromosomes and therefore die during development, but they can be rescued if any other msl mutation is present.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "female") (:form . "females") (:end . 13)\n (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "hypertranscribe") (:form . "hypertranscribe")\n (:end . 29) (:start . 14) (:id . 44))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 35)\n (:start . 30) (:id . 45))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 39) (:start . 36)\n (:id . 46))\n ((:tag . "NNP") (:stem . "X") (:form . "X") (:end . 41) (:start . 40)\n (:id . 47))\n ((:tag . "NNS") (:stem . "chromosome") (:form . "chromosomes") (:end . 53)\n (:start . 42) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n (:id . 49))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 67)\n (:start . 58) (:id . 50))\n ((:tag . "VBP") (:stem . "die") (:form . "die") (:end . 71) (:start . 68)\n (:id . 51))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 78)\n (:start . 72) (:id . 52))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 90)\n (:start . 79) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n (:id . 54))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 95) (:start . 92)\n (:id . 55))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 100) (:start . 96)\n (:id . 56))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 104) (:start . 101)\n (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 107) (:start . 105)\n (:id . 58))\n ((:tag . "VBN") (:stem . "rescue") (:form . "rescued") (:end . 115)\n (:start . 108) (:id . 59))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 118) (:start . 116)\n (:id . 60))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 122) (:start . 119)\n (:id . 61))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 128)\n (:start . 123) (:id . 62))\n ((:tag . "NN") (:stem . "msl") (:form . "msl") (:end . 132) (:start . 129)\n (:id . 63))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 141)\n (:start . 133) (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 144) (:start . 142)\n (:id . 65))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 152)\n (:start . 145) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s9.29) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102602@unknown@formal@none@1@S@It has been shown previously, using a similar strategy, that the DCC is assembled in an ordered sequence (Figure 1).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 17) (:start . 12)\n (:id . 45))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 28)\n (:start . 18) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 35) (:start . 30)\n (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n (:id . 49))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 45)\n (:start . 38) (:id . 50))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 54)\n (:start . 46) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 60) (:start . 56)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n (:id . 54))\n ((:tag . "NNP") (:stem . "DCC") (:form . "DCC") (:end . 68) (:start . 65)\n (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 71) (:start . 69)\n (:id . 56))\n ((:tag . "VBN") (:stem . "assemble") (:form . "assembled") (:end . 81)\n (:start . 72) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 87) (:start . 85)\n (:id . 59))\n ((:tag . "VBN") (:stem . "order") (:form . "ordered") (:end . 95)\n (:start . 88) (:id . 60))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 104)\n (:start . 96) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 112)\n (:start . 106) (:id . 63))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 114) (:start . 113)\n (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s9.30) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102603@unknown@formal@none@1@S@For example, MSL1 and MSL2 are the first proteins to bind to the X chromosome; in the absence of all other MSL proteins they associate with about 35 sites, the so-called chromatin entry sites.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "NNP") (:stem . "MSL1") (:form . "MSL1") (:end . 17) (:start . 13)\n (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "NNP") (:stem . "MSL2") (:form . "MSL2") (:end . 26) (:start . 22)\n (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 30) (:start . 27)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 49))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 40) (:start . 35)\n (:id . 50))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 49)\n (:start . 41) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n (:id . 52))\n ((:tag . "VB") (:stem . "bind") (:form . "bind") (:end . 57) (:start . 53)\n (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n (:id . 55))\n ((:tag . "NNP") (:stem . "X") (:form . "X") (:end . 66) (:start . 65)\n (:id . 56))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 77)\n (:start . 67) (:id . 57))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 78) (:start . 77)\n (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n (:id . 60))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 93)\n (:start . 86) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n (:id . 62))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 100) (:start . 97)\n (:id . 63))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 106)\n (:start . 101) (:id . 64))\n ((:tag . "NNP") (:stem . "MSL") (:form . "MSL") (:end . 110) (:start . 107)\n (:id . 65))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 119)\n (:start . 111) (:id . 66))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 124) (:start . 120)\n (:id . 67))\n ((:tag . "VBP") (:stem . "associate") (:form . "associate") (:end . 134)\n (:start . 125) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 139) (:start . 135)\n (:id . 69))\n ((:tag . "RB") (:stem . "about") (:form . "about") (:end . 145)\n (:start . 140) (:id . 70))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 148) (:start . 146)\n (:id . 71))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 154)\n (:start . 149) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 155) (:start . 154)\n (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n (:id . 74))\n ((:tag . "JJ") (:stem . "so-called") (:form . "so-called") (:end . 169)\n (:start . 160) (:id . 75))\n ((:tag . "NN") (:stem . "chromatin") (:form . "chromatin") (:end . 179)\n (:start . 170) (:id . 76))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 185)\n (:start . 180) (:id . 77))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 191)\n (:start . 186) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n (:id . 79)))@@@1@38@((:identifiers (:sid . :s9.31) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102604@unknown@formal@none@1@S@MSL1 and MSL2 are interdependent, however: they require each other for binding [15].@(((:tag . "NNP") (:stem . "MSL1") (:form . "MSL1") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "NNP") (:stem . "MSL2") (:form . "MSL2") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 17) (:start . 14)\n (:id . 45))\n ((:tag . "JJ") (:stem . "interdependent") (:form . "interdependent")\n (:end . 32) (:start . 18) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n (:id . 47))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 41)\n (:start . 34) (:id . 48))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 42) (:start . 41)\n (:id . 49))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 47) (:start . 43)\n (:id . 50))\n ((:tag . "VBP") (:stem . "require") (:form . "require") (:end . 55)\n (:start . 48) (:id . 51))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 60) (:start . 56)\n (:id . 52))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 66) (:start . 61)\n (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 70) (:start . 67)\n (:id . 54))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 78)\n (:start . 71) (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 80) (:start . 79)\n (:id . 56))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 82) (:start . 80)\n (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 83) (:start . 82)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s9.32) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102605@unknown@formal@none@1@S@MLE appears to be the next protein to join the growing DCC as it is found at reduced levels at some of these 35 sites when the remaining two proteins, MSL3 and MOF, are absent [16].@(((:tag . "NNP") (:stem . "MLE") (:form . "MLE") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 17) (:start . 15)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "JJ") (:stem . "next") (:form . "next") (:end . 26) (:start . 22)\n (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 34)\n (:start . 27) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n (:id . 49))\n ((:tag . "VB") (:stem . "join") (:form . "join") (:end . 42) (:start . 38)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n (:id . 51))\n ((:tag . "VBG") (:stem . "grow") (:form . "growing") (:end . 54)\n (:start . 47) (:id . 52))\n ((:tag . "NNP") (:stem . "DCC") (:form . "DCC") (:end . 58) (:start . 55)\n (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 61) (:start . 59)\n (:id . 54))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 64) (:start . 62)\n (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 67) (:start . 65)\n (:id . 56))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 73) (:start . 68)\n (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 76) (:start . 74)\n (:id . 58))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 84)\n (:start . 77) (:id . 59))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 91)\n (:start . 85) (:id . 60))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 94) (:start . 92)\n (:id . 61))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 99) (:start . 95)\n (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n (:id . 63))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 108)\n (:start . 103) (:id . 64))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 111) (:start . 109)\n (:id . 65))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 117)\n (:start . 112) (:id . 66))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 122) (:start . 118)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n (:id . 68))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 136)\n (:start . 127) (:id . 69))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 140) (:start . 137)\n (:id . 70))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 149)\n (:start . 141) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n (:id . 72))\n ((:tag . "NNP") (:stem . "MSL3") (:form . "MSL3") (:end . 155) (:start . 151)\n (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n (:id . 74))\n ((:tag . "NNP") (:stem . "MOF") (:form . "MOF") (:end . 163) (:start . 160)\n (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 164) (:start . 163)\n (:id . 76))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 168) (:start . 165)\n (:id . 77))\n ((:tag . "JJ") (:stem . "absent") (:form . "absent") (:end . 175)\n (:start . 169) (:id . 78))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 177) (:start . 176)\n (:id . 79))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 179) (:start . 177)\n (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 180) (:start . 179)\n (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n (:id . 82)))@@@1@41@((:hcues ((:id . :x9.33.1) (:span 4 11)))\n (:hscopes ((:id . :x9.33.1) (:span 0 58)))\n (:identifiers (:sid . :s9.33) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102606@unknown@formal@none@1@S@These latter two proteins require all the other MSL proteins to be present to enable them to associate with the X chromosome.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "latter") (:form . "latter") (:end . 12) (:start . 6)\n (:id . 43))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 25)\n (:start . 17) (:id . 45))\n ((:tag . "VBP") (:stem . "require") (:form . "require") (:end . 33)\n (:start . 26) (:id . 46))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 37) (:start . 34)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n (:id . 48))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 47) (:start . 42)\n (:id . 49))\n ((:tag . "NNP") (:stem . "MSL") (:form . "MSL") (:end . 51) (:start . 48)\n (:id . 50))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 60)\n (:start . 52) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 66) (:start . 64)\n (:id . 53))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 74)\n (:start . 67) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 77) (:start . 75)\n (:id . 55))\n ((:tag . "VB") (:stem . "enable") (:form . "enable") (:end . 84)\n (:start . 78) (:id . 56))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 89) (:start . 85)\n (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 92) (:start . 90)\n (:id . 58))\n ((:tag . "VB") (:stem . "associate") (:form . "associate") (:end . 102)\n (:start . 93) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 107) (:start . 103)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n (:id . 61))\n ((:tag . "NNP") (:stem . "X") (:form . "X") (:end . 113) (:start . 112)\n (:id . 62))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 124)\n (:start . 114) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s9.34) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102607@unknown@formal@none@1@S@Importantly, all MSLs are required to generate the normal DCC distribution to the hundreds of sites throughout the entire X chromosome.@(((:tag . "RB") (:stem . "importantly") (:form . "Importantly") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 43))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "NNPS") (:stem . "MSL") (:form . "MSLs") (:end . 21) (:start . 17)\n (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 25) (:start . 22)\n (:id . 46))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 34)\n (:start . 26) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n (:id . 48))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 46)\n (:start . 38) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n (:id . 50))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 57)\n (:start . 51) (:id . 51))\n ((:tag . "NNP") (:stem . "DCC") (:form . "DCC") (:end . 61) (:start . 58)\n (:id . 52))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 74)\n (:start . 62) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 77) (:start . 75)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n (:id . 55))\n ((:tag . "NNS") (:stem . "hundred") (:form . "hundreds") (:end . 90)\n (:start . 82) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n (:id . 57))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 99) (:start . 94)\n (:id . 58))\n ((:tag . "IN") (:stem . "throughout") (:form . "throughout") (:end . 110)\n (:start . 100) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n (:id . 60))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 121)\n (:start . 115) (:id . 61))\n ((:tag . "NN") (:stem . "x") (:form . "X") (:end . 123) (:start . 122)\n (:id . 62))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 134)\n (:start . 124) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s9.35) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102608@unknown@formal@none@1@S@Meller et al. [1] have now analyzed and compared roX RNA and MSL protein distribution in females ectopically expressing MSL2 but lacking other MSL proteins.@(((:tag . "NNP") (:stem . "Meller") (:form . "Meller") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 9) (:start . 7)\n (:id . 43))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 15) (:start . 14)\n (:id . 45))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 16) (:start . 15)\n (:id . 46))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 17) (:start . 16)\n (:id . 47))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 22) (:start . 18)\n (:id . 48))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 26) (:start . 23)\n (:id . 49))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 35)\n (:start . 27) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n (:id . 51))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 48)\n (:start . 40) (:id . 52))\n ((:tag . "NNP") (:stem . "roX") (:form . "roX") (:end . 52) (:start . 49)\n (:id . 53))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 56) (:start . 53)\n (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n (:id . 55))\n ((:tag . "NNP") (:stem . "MSL") (:form . "MSL") (:end . 64) (:start . 61)\n (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 72)\n (:start . 65) (:id . 57))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 85)\n (:start . 73) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n (:id . 59))\n ((:tag . "NNS") (:stem . "female") (:form . "females") (:end . 96)\n (:start . 89) (:id . 60))\n ((:tag . "RB") (:stem . "ectopically") (:form . "ectopically") (:end . 108)\n (:start . 97) (:id . 61))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 119)\n (:start . 109) (:id . 62))\n ((:tag . "NN") (:stem . "msl2") (:form . "MSL2") (:end . 124) (:start . 120)\n (:id . 63))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 128) (:start . 125)\n (:id . 64))\n ((:tag . "VBG") (:stem . "lack") (:form . "lacking") (:end . 136)\n (:start . 129) (:id . 65))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 142)\n (:start . 137) (:id . 66))\n ((:tag . "NN") (:stem . "msl") (:form . "MSL") (:end . 146) (:start . 143)\n (:id . 67))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 155)\n (:start . 147) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n (:id . 69)))@@@1@28@((:ncues ((:id . :x9.36.1) (:span 129 136)))\n (:nscopes ((:id . :x9.36.1) (:span 129 155)))\n (:identifiers (:sid . :s9.36) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102610@unknown@formal@none@1@S@When the MLE protein, which encodes an RNA helicase, was absent, both roX RNAs were found only at their site of transcription but not in any other of the 35 entry sites where MSL1 and MSL2 were present, suggesting that neither of the roX RNAs can be integrated in a minimal MSL1-MSL2 complex.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "mle") (:form . "MLE") (:end . 12) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 20)\n (:start . 13) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n (:id . 46))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 27) (:start . 22)\n (:id . 47))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 35)\n (:start . 28) (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 38) (:start . 36)\n (:id . 49))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 42) (:start . 39)\n (:id . 50))\n ((:tag . "NN") (:stem . "helicase") (:form . "helicase") (:end . 51)\n (:start . 43) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 56) (:start . 53)\n (:id . 53))\n ((:tag . "JJ") (:stem . "absent") (:form . "absent") (:end . 63)\n (:start . 57) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n (:id . 55))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 69) (:start . 65)\n (:id . 56))\n ((:tag . "NNP") (:stem . "roX") (:form . "roX") (:end . 73) (:start . 70)\n (:id . 57))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNAs") (:end . 78) (:start . 74)\n (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 83) (:start . 79)\n (:id . 59))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 89) (:start . 84)\n (:id . 60))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 94) (:start . 90)\n (:id . 61))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 97) (:start . 95)\n (:id . 62))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 103)\n (:start . 98) (:id . 63))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 108) (:start . 104)\n (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n (:id . 65))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n (:end . 125) (:start . 112) (:id . 66))\n ((:tag . "CC") (:stem . "but") (:form . 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(:end . 116) (:start . 115)\n (:id . 64)))@@@1@23@((:hcues ((:id . :x9.44.1) (:span 66 75)))\n (:hscopes ((:id . :x9.44.1) (:span 66 115)))\n (:identifiers (:sid . :s9.44) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102617@unknown@formal@none@1@S@MOF is the crucial component that links the DCC to the X-chromosome-specific acetylated form of histone H4.@(((:tag . "NNP") (:stem . "MOF") (:form . "MOF") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 6) (:start . 4)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n (:id . 44))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 18)\n (:start . 11) (:id . 45))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 28)\n (:start . 19) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . 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",") (:end . 215) (:start . 214)\n (:id . 72))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 219) (:start . 216)\n (:id . 73))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 224) (:start . 220)\n (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 228) (:start . 225)\n (:id . 75))\n ((:tag . "JJ") (:stem . "amino-terminal") (:form . "amino-terminal")\n (:end . 243) (:start . 229) (:id . 76))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 250)\n (:start . 244) (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 254) (:start . 251)\n (:id . 78))\n ((:tag . "NN") (:stem . "hat") (:form . "HAT") (:end . 258) (:start . 255)\n (:id . 79))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 265)\n (:start . 259) (:id . 80))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 270) (:start . 266)\n (:id . 81))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 274) (:start . 271)\n (:id . 82))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 284)\n (:start . 275) (:id . 83))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 288) (:start . 285)\n (:id . 84))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 293) (:start . 289)\n (:id . 85))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 305)\n (:start . 294) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 306) (:start . 305)\n (:id . 87)))@@@1@46@((:hcues ((:id . :x9.48.2) (:span 120 134)))\n (:ncues ((:id . :x9.48.1) (:span 271 274)))\n (:hscopes ((:id . :x9.48.2) (:span 120 305)))\n (:nscopes ((:id . :x9.48.1) (:span 271 305)))\n (:identifiers (:sid . :s9.48) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102621@unknown@formal@none@1@S@Akthar et al. [2] then tested the putative RNA-binding property of MOF directly using electromobility shift assays.@(((:tag . "NNP") (:stem . "Akthar") (:form . "Akthar") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 9) (:start . 7)\n (:id . 43))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 13) (:start . 10)\n (:id . 44))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 15) (:start . 14)\n (:id . 45))\n ((:tag . "LS") (:stem . "2") (:form . "2") (:end . 16) (:start . 15)\n (:id . 46))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 17) (:start . 16)\n (:id . 47))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 22) (:start . 18)\n (:id . 48))\n ((:tag . "VBD") (:stem . "test") (:form . "tested") (:end . 29) (:start . 23)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 50))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 42)\n (:start . 34) (:id . 51))\n ((:tag . "JJ") (:stem . "rna-binding") (:form . "RNA-binding") (:end . 54)\n (:start . 43) (:id . 52))\n ((:tag . "NN") (:stem . "property") (:form . "property") (:end . 63)\n (:start . 55) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n (:id . 54))\n ((:tag . "NNP") (:stem . "MOF") (:form . "MOF") (:end . 70) (:start . 67)\n (:id . 55))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 79)\n (:start . 71) (:id . 56))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 85) (:start . 80)\n (:id . 57))\n ((:tag . "NN") (:stem . "electromobility") (:form . "electromobility")\n (:end . 101) (:start . 86) (:id . 58))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 107)\n (:start . 102) (:id . 59))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 114)\n (:start . 108) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n (:id . 61)))@@@1@20@((:hcues ((:id . :x9.49.1) (:span 34 42)))\n (:hscopes ((:id . :x9.49.1) (:span 34 70)))\n (:identifiers (:sid . :s9.49) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102622@unknown@formal@none@1@S@MOF appeared to bind to RNA rather non-specifically, but preferred RNA to DNA.@(((:tag . "NNP") (:stem . "MOF") (:form . "MOF") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "appear") (:form . "appeared") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "VB") (:stem . "bind") (:form . "bind") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n (:id . 46))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 27) (:start . 24)\n (:id . 47))\n ((:tag . "RB") (:stem . "rather") (:form . 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(:end . 162) (:start . 161)\n (:id . 68)))@@@1@27@((:hcues ((:id . :x9.55.1) (:span 120 125)) ((:id . :x9.55.2) (:span 102 109))\n ((:id . :x9.55.3) (:span 41 48)))\n (:hscopes ((:id . :x9.55.1) (:span 120 156))\n ((:id . :x9.55.2) (:span 102 156)) ((:id . :x9.55.3) (:span 0 48)))\n (:identifiers (:sid . :s9.55) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102628@unknown@formal@none@1@S@Thus, the data by Akthar et al. [2] suggests a new and rather unexpected role for these modules in RNA binding.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n (:id . 44))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 14) (:start . 10)\n (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . 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"rather") (:end . 61)\n (:start . 55) (:id . 57))\n ((:tag . "JJ") (:stem . "unexpected") (:form . "unexpected") (:end . 72)\n (:start . 62) (:id . 58))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 77) (:start . 73)\n (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 81) (:start . 78)\n (:id . 60))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 87) (:start . 82)\n (:id . 61))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 95)\n (:start . 88) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n (:id . 63))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 102) (:start . 99)\n (:id . 64))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 110)\n (:start . 103) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n (:id . 66)))@@@1@25@((:hcues ((:id . :x9.56.1) (:span 36 44)))\n (:hscopes ((:id . :x9.56.1) (:span 36 110)))\n (:identifiers (:sid . :s9.56) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102630@unknown@formal@none@1@S@Ordered assembly of MSL proteins and roX RNA increases stability of the DCC.@(((:tag . "VBN") (:stem . "order") (:form . "Ordered") (:end . 7) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "assembly") (:form . "assembly") (:end . 16)\n (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n (:id . 44))\n ((:tag . "NNP") (:stem . "MSL") (:form . "MSL") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 32)\n (:start . 24) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n (:id . 47))\n ((:tag . "NNP") (:stem . "roX") (:form . 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(:end . 76) (:start . 75)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s9.58) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5102631@unknown@formal@none@1@S@The first step of assembly involves the recognition of about 35 chromosomal entry sites by a preDCC consisting of MSL1 and MSL2.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "assembly") (:form . "assembly") (:end . 26)\n (:start . 18) (:id . 46))\n ((:tag . "VBZ") (:stem . "involve") (:form . "involves") (:end . 35)\n (:start . 27) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . 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(:end . 60) (:start . 59)\n (:id . 53)))@@@1@12@((:ncues ((:id . :x9.60.1) (:span 22 25)))\n (:nscopes ((:id . :x9.60.1) (:span 22 59)))\n (:identifiers (:sid . :s9.60) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102633@unknown@formal@none@1@S@In the next step, roX2 and MLE enter the complex to form a more stable primary DCC (PrimDCC) at these 35 sites.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "next") (:form . "next") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 16) (:start . 12)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 46))\n ((:tag . "NN") (:stem . "rox2") (:form . "roX2") (:end . 22) (:start . 18)\n (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . 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"DCC") (:form . "DCC") (:end . 82) (:start . 79)\n (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n (:id . 60))\n ((:tag . "NNP") (:stem . "PrimDCC") (:form . "PrimDCC") (:end . 91)\n (:start . 84) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 92) (:start . 91)\n (:id . 62))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 95) (:start . 93)\n (:id . 63))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 101) (:start . 96)\n (:id . 64))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 104) (:start . 102)\n (:id . 65))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 110)\n (:start . 105) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s9.61) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102634@unknown@formal@none@1@S@Spreading throughout the entire X chromosome requires the formation of the complete complex by addition of MOF and MSL3.@(((:tag . "VBG") (:stem . "spread") (:form . "Spreading") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "throughout") (:form . "throughout") (:end . 20)\n (:start . 10) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n (:id . 44))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 31)\n (:start . 25) (:id . 45))\n ((:tag . "NN") (:stem . "x") (:form . "X") (:end . 33) (:start . 32)\n (:id . 46))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 44)\n (:start . 34) (:id . 47))\n ((:tag . "VBZ") (:stem . "require") (:form . 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"the") (:end . 215) (:start . 212)\n (:id . 76))\n ((:tag . "NNP") (:stem . "DCC") (:form . "DCC") (:end . 219) (:start . 216)\n (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n (:id . 78)))@@@1@37@((:hcues ((:id . :x9.63.1) (:span 70 75)))\n (:hscopes ((:id . :x9.63.1) (:span 70 219)))\n (:identifiers (:sid . :s9.63) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102636@unknown@formal@none@1@S@MLE might be removed in vitro (for example, by elevated ionic strength) without destroying the entire complex, because of the stabilizing presence of MOF-MSL3.@(((:tag . "NNP") (:stem . "MLE") (:form . "MLE") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 12) (:start . 10)\n (:id . 44))\n ((:tag . "VBN") (:stem . "remove") (:form . 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")") (:form . ")") (:end . 71) (:start . 70)\n (:id . 56))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 79)\n (:start . 72) (:id . 57))\n ((:tag . "VBG") (:stem . "destroy") (:form . "destroying") (:end . 90)\n (:start . 80) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n (:id . 59))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 101)\n (:start . 95) (:id . 60))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 109)\n (:start . 102) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n (:id . 62))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 118)\n (:start . 111) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n (:id . 65))\n ((:tag . "VBG") (:stem . "stabilize") (:form . "stabilizing") (:end . 137)\n (:start . 126) (:id . 66))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 146)\n (:start . 138) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 149) (:start . 147)\n (:id . 68))\n ((:tag . "NNP") (:stem . "MOF-MSL3") (:form . "MOF-MSL3") (:end . 158)\n (:start . 150) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x9.64.2) (:span 4 9)))\n (:ncues ((:id . :x9.64.1) (:span 72 79)))\n (:hscopes ((:id . :x9.64.2) (:span 0 158)))\n (:nscopes ((:id . :x9.64.1) (:span 72 109)))\n (:identifiers (:sid . :s9.64) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102637@unknown@formal@none@1@S@The role of roX1 RNA is not clear, but it is integrated late in this process, together with or after MOF and MSL3; roX1 might provide additional stability to the mature DCC (MatDCC).@(((:tag . 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(:end . 182) (:start . 181)\n (:id . 80)))@@@1@39@((:hcues ((:id . :x9.65.1) (:span 120 125)) ((:id . :x9.65.2) (:span 92 94))\n ((:id . :x9.65.3) (:span 24 33)))\n (:hscopes ((:id . :x9.65.1) (:span 120 181))\n ((:id . :x9.65.2) (:span 78 100)) ((:id . :x9.65.3) (:span 0 33)))\n (:identifiers (:sid . :s9.65) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102638@unknown@formal@none@1@S@So, roX1 and roX2 might be partially redundant.@(((:tag . "RB") (:stem . "so") (:form . "So") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 3) (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "rox1") (:form . "roX1") (:end . 8) (:start . 4)\n (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 12) (:start . 9)\n (:id . 45))\n ((:tag . "NN") (:stem . "rox2") (:form . "roX2") (:end . 17) (:start . 13)\n (:id . 46))\n ((:tag . "MD") (:stem . "might") (:form . 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"without") (:end . 276)\n (:start . 269) (:id . 87))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 284)\n (:start . 277) (:id . 88))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 294)\n (:start . 285) (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 295) (:start . 294)\n (:id . 90)))@@@1@49@((:hcues ((:id . :x9.69.2) (:span 173 180)) ((:id . :x9.69.4) (:span 10 15)))\n (:ncues ((:id . :x9.69.1) (:span 269 276))\n ((:id . :x9.69.3) (:span 181 184)))\n (:hscopes ((:id . :x9.69.2) (:span 153 200))\n ((:id . :x9.69.4) (:span 10 200)))\n (:nscopes ((:id . :x9.69.1) (:span 269 294))\n ((:id . :x9.69.3) (:span 153 200)))\n (:identifiers (:sid . :s9.69) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102642@unknown@formal@none@1@S@The soluble DCCs from these extracts are therefore not necessarily functional and might differ from those in males.@(((:tag . "DT") (:stem . 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(:end . 115) (:start . 114)\n (:id . 60)))@@@1@19@((:hcues ((:id . :x9.70.1) (:span 82 87)))\n (:ncues ((:id . :x9.70.2) (:span 51 54)))\n (:hscopes ((:id . :x9.70.1) (:span 82 114)))\n (:nscopes ((:id . :x9.70.2) (:span 51 77)))\n (:identifiers (:sid . :s9.70) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102643@unknown@formal@none@1@S@Second, the interaction between roX RNA and MOF protein appears to lack specificity.@(((:tag . "RB") (:stem . "second") (:form . "Second") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n (:id . 44))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 23)\n (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 31)\n (:start . 24) (:id . 46))\n ((:tag . "NNP") (:stem . "roX") (:form . 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(:end . 84) (:start . 83)\n (:id . 56)))@@@1@15@((:hcues ((:id . :x9.71.2) (:span 56 63)))\n (:ncues ((:id . :x9.71.1) (:span 67 71)))\n (:hscopes ((:id . :x9.71.2) (:span 8 83)))\n (:nscopes ((:id . :x9.71.1) (:span 67 83)))\n (:identifiers (:sid . :s9.71) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102644@unknown@formal@none@1@S@The lack of specificity might be attributed to a number of reasons, such as the absence of other MSL components, the presence of other RNAs interacting with MOF, or worse, it might reflect a property of MOF without functional significance: that is, MOF might not contact RNA at all in vivo.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "lack") (:form . "lack") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . 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"vivo") (:form . "vivo") (:end . 289) (:start . 285)\n (:id . 98))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 290) (:start . 289)\n (:id . 99)))@@@1@58@((:hcues ((:id . :x9.72.2) (:span 253 258)) ((:id . :x9.72.4) (:span 175 180))\n ((:id . :x9.72.7) (:span 24 29)))\n (:ncues ((:id . :x9.72.1) (:span 259 262)) ((:id . :x9.72.3) (:span 207 214))\n ((:id . :x9.72.5) (:span 80 87)) ((:id . :x9.72.6) (:span 4 8)))\n (:hscopes ((:id . :x9.72.2) (:span 253 289))\n ((:id . :x9.72.4) (:span 175 289)) ((:id . :x9.72.7) (:span 4 23)))\n (:nscopes ((:id . :x9.72.1) (:span 259 289))\n ((:id . :x9.72.3) (:span 207 238)) ((:id . :x9.72.5) (:span 80 111))\n ((:id . :x9.72.6) (:span 4 160)))\n (:identifiers (:sid . :s9.72) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102645@unknown@formal@none@1@S@Keeping this cautious note in mind, a more attractive alternative could be envisioned.@(((:tag . "VBG") (:stem . "keep") (:form . "Keeping") (:end . 7) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 12) (:start . 8)\n (:id . 43))\n ((:tag . "JJ") (:stem . "cautious") (:form . "cautious") (:end . 21)\n (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "note") (:form . "note") (:end . 26) (:start . 22)\n (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "NN") (:stem . "mind") (:form . "mind") (:end . 34) (:start . 30)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n (:id . 49))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 42) (:start . 38)\n (:id . 50))\n ((:tag . "JJ") (:stem . "attractive") (:form . "attractive") (:end . 53)\n (:start . 43) (:id . 51))\n ((:tag . "NN") (:stem . "alternative") (:form . "alternative") (:end . 65)\n (:start . 54) (:id . 52))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 71) (:start . 66)\n (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 74) (:start . 72)\n (:id . 54))\n ((:tag . "VBN") (:stem . "envision") (:form . "envisioned") (:end . 85)\n (:start . 75) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n (:id . 56)))@@@1@15@((:hcues ((:id . :x9.73.1) (:span 66 71)))\n (:hscopes ((:id . :x9.73.1) (:span 36 85)))\n (:identifiers (:sid . :s9.73) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102646@unknown@formal@none@1@S@The main proposition of this model is that roX2 can interact with both MLE and MOF, and perhaps even other MSL proteins, as both roX RNAs are certainly large enough to accommodate binding sites for several proteins [6].@(((:tag . "DT") (:stem . "the") (:form . 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"becomes") (:end . 208)\n (:start . 201) (:id . 78))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 213) (:start . 209)\n (:id . 79))\n ((:tag . "JJ") (:stem . "stable") (:form . "stable") (:end . 220)\n (:start . 214) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 221) (:start . 220)\n (:id . 81)))@@@1@40@((:hcues ((:id . :x9.75.2) (:span 121 128)) ((:id . :x9.75.3) (:span 96 101)))\n (:ncues ((:id . :x9.75.1) (:span 129 132)))\n (:hscopes ((:id . :x9.75.2) (:span 121 153))\n ((:id . :x9.75.3) (:span 96 115)))\n (:nscopes ((:id . :x9.75.1) (:span 129 153)))\n (:identifiers (:sid . :s9.75) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102648@unknown@formal@none@1@S@The addition of each new component might therefore strengthen existing interactions by optimizing contacts between binding surfaces through adjustments in the higher-order structure of the components (Figure 1).@(((:tag . 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"interactions") (:end . 83)\n (:start . 71) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 86) (:start . 84)\n (:id . 53))\n ((:tag . "VBG") (:stem . "optimize") (:form . "optimizing") (:end . 97)\n (:start . 87) (:id . 54))\n ((:tag . "NNS") (:stem . "contact") (:form . "contacts") (:end . 106)\n (:start . 98) (:id . 55))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 114)\n (:start . 107) (:id . 56))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 122)\n (:start . 115) (:id . 57))\n ((:tag . "NNS") (:stem . "surface") (:form . "surfaces") (:end . 131)\n (:start . 123) (:id . 58))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 139)\n (:start . 132) (:id . 59))\n ((:tag . "NNS") (:stem . "adjustment") (:form . "adjustments") (:end . 151)\n (:start . 140) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 154) (:start . 152)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 158) (:start . 155)\n (:id . 62))\n ((:tag . "JJR") (:stem . "higher-ord") (:form . "higher-order") (:end . 171)\n (:start . 159) (:id . 63))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 181)\n (:start . 172) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 184) (:start . 182)\n (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 188) (:start . 185)\n (:id . 66))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 199)\n (:start . 189) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 201) (:start . 200)\n (:id . 68))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 207)\n (:start . 201) (:id . 69))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 209) (:start . 208)\n (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 210) (:start . 209)\n (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n (:id . 72)))@@@1@31@((:hcues ((:id . :x9.76.1) (:span 35 40)))\n (:hscopes ((:id . :x9.76.1) (:span 35 199)))\n (:identifiers (:sid . :s9.76) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102650@unknown@formal@none@1@S@The addition of both MLE and roX2 RNA might allow the formation of a primary complex (the primDCC), which might be stabilized by the direct interaction of a structural motif of roX2 RNA with the MLE protein, as well as interactions of this complex with MSL1 and MSL2.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "NNP") (:stem . "MLE") (:form . 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"DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n (:id . 68))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 139)\n (:start . 133) (:id . 69))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 151)\n (:start . 140) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 154) (:start . 152)\n (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 156) (:start . 155)\n (:id . 72))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 167)\n (:start . 157) (:id . 73))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 173)\n (:start . 168) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 176) (:start . 174)\n (:id . 75))\n ((:tag . "NN") (:stem . "rox2") (:form . "roX2") (:end . 181) (:start . 177)\n (:id . 76))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 185) (:start . 182)\n (:id . 77))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 190) (:start . 186)\n (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 194) (:start . 191)\n (:id . 79))\n ((:tag . "NN") (:stem . "mle") (:form . "MLE") (:end . 198) (:start . 195)\n (:id . 80))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 206)\n (:start . 199) (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 207) (:start . 206)\n (:id . 82))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 210) (:start . 208)\n (:id . 83))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 215) (:start . 211)\n (:id . 84))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 218) (:start . 216)\n (:id . 85))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 231)\n (:start . 219) (:id . 86))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 234) (:start . 232)\n (:id . 87))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 239) (:start . 235)\n (:id . 88))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 247)\n (:start . 240) (:id . 89))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 252) (:start . 248)\n (:id . 90))\n ((:tag . "NNP") (:stem . "MSL1") (:form . "MSL1") (:end . 257) (:start . 253)\n (:id . 91))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 261) (:start . 258)\n (:id . 92))\n ((:tag . "NNP") (:stem . "MSL2") (:form . "MSL2") (:end . 266) (:start . 262)\n (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 267) (:start . 266)\n (:id . 94)))@@@1@53@((:hcues ((:id . :x9.78.1) (:span 106 111)) ((:id . :x9.78.2) (:span 38 43)))\n (:hscopes ((:id . :x9.78.1) (:span 100 266))\n ((:id . :x9.78.2) (:span 38 98)))\n (:identifiers (:sid . :s9.78) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102651@unknown@formal@none@1@S@The primDCC might then be reinforced by the addition of the remaining two proteins, MSL3 and MOF, one or both of which might recognize other motifs within the roX2 RNA, to form the mature complex (matDCC).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "primdcc") (:form . "primDCC") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 17) (:start . 12)\n (:id . 44))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 22) (:start . 18)\n (:id . 45))\n ((:tag . "VB") (:stem . 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(:end . 205) (:start . 204)\n (:id . 83)))@@@1@42@((:hcues ((:id . :x9.79.1) (:span 119 124)) ((:id . :x9.79.2) (:span 102 104))\n ((:id . :x9.79.3) (:span 12 17)))\n (:hscopes ((:id . :x9.79.1) (:span 119 204))\n ((:id . :x9.79.2) (:span 98 109)) ((:id . :x9.79.3) (:span 0 96)))\n (:identifiers (:sid . :s9.79) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102652@unknown@formal@none@1@S@Finally, matDCC might be further stabilized by the addition of roX1 RNA, which could interact with several of the MSLs and perhaps roX2 RNA as well.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "matdcc") (:form . "matDCC") (:end . 15) (:start . 9)\n (:id . 44))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 21) (:start . 16)\n (:id . 45))\n ((:tag . "VB") (:stem . 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"MD") (:stem . "could") (:form . "could") (:end . 84) (:start . 79)\n (:id . 57))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 93)\n (:start . 85) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 98) (:start . 94)\n (:id . 59))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 106)\n (:start . 99) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 109) (:start . 107)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n (:id . 62))\n ((:tag . "NNPS") (:stem . "MSL") (:form . "MSLs") (:end . 118) (:start . 114)\n (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n (:id . 64))\n ((:tag . "RB") (:stem . "perhaps") (:form . "perhaps") (:end . 130)\n (:start . 123) (:id . 65))\n ((:tag . "NN") (:stem . "rox2") (:form . "roX2") (:end . 135) (:start . 131)\n (:id . 66))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 139) (:start . 136)\n (:id . 67))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 142) (:start . 140)\n (:id . 68))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 147) (:start . 143)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x9.80.1) (:span 79 84)) ((:id . :x9.80.2) (:span 16 21)))\n (:hscopes ((:id . :x9.80.1) (:span 79 147)) ((:id . :x9.80.2) (:span 9 147)))\n (:identifiers (:sid . :s9.80) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102653@unknown@formal@none@1@S@Significantly, assembly and disassembly of the complex might not necessarily follow the same order.@(((:tag . "RB") (:stem . "significantly") (:form . "Significantly")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 43))\n ((:tag . "NN") (:stem . "assembly") (:form . 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"the") (:end . 87) (:start . 84)\n (:id . 54))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 92) (:start . 88)\n (:id . 55))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 98) (:start . 93)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 57)))@@@1@16@((:hcues ((:id . :x9.81.2) (:span 55 60)))\n (:ncues ((:id . :x9.81.1) (:span 61 64)))\n (:hscopes ((:id . :x9.81.2) (:span 55 98)))\n (:nscopes ((:id . :x9.81.1) (:span 61 98)))\n (:identifiers (:sid . :s9.81) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102654@unknown@formal@none@1@S@For example, once the complex is formed, removal (for example, by high ionic strength) of a single component brought in relatively early (such as MLE) might be possible without affecting the rest of the complex.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . 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(:end . 211) (:start . 210)\n (:id . 84)))@@@1@43@((:hcues ((:id . :x9.82.2) (:span 151 156 160 168)))\n (:ncues ((:id . :x9.82.1) (:span 169 176)))\n (:hscopes ((:id . :x9.82.2) (:span 41 210)))\n (:nscopes ((:id . :x9.82.1) (:span 169 210)))\n (:identifiers (:sid . :s9.82) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102655@unknown@formal@none@1@S@One major task at hand now will be to resolve the specificities of the proposed interactions between the various MSL proteins and the roX RNAs.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "task") (:form . "task") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 17) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "hand") (:form . 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(:end . 143) (:start . 142)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s9.83) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102656@unknown@formal@none@1@S@This could be done by carrying out detailed in vitro studies, which might not be easy to perform; many MSL proteins are difficult to express stably in bacteria or eukaryotic expression systems.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "VBN") (:stem . "do") (:form . "done") (:end . 18) (:start . 14)\n (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 21) (:start . 19)\n (:id . 46))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 30)\n (:start . 22) (:id . 47))\n ((:tag . "RP") (:stem . 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(:end . 193) (:start . 192)\n (:id . 76)))@@@1@35@((:hcues ((:id . :x9.84.2) (:span 68 73)) ((:id . :x9.84.3) (:span 5 10)))\n (:ncues ((:id . :x9.84.1) (:span 74 77)))\n (:hscopes ((:id . :x9.84.2) (:span 68 96)) ((:id . :x9.84.3) (:span 0 96)))\n (:nscopes ((:id . :x9.84.1) (:span 74 96)))\n (:identifiers (:sid . :s9.84) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102657@unknown@formal@none@1@S@An alternative might be to establish a heterologous in vivo system such as yeast, where protein-protein and RNA-protein interactions can be readily detected using sensitive reporter assays.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "alternative") (:form . "alternative") (:end . 14)\n (:start . 3) (:id . 43))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 20) (:start . 15)\n (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . 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",") (:form . ",") (:end . 81) (:start . 80)\n (:id . 56))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 87) (:start . 82)\n (:id . 57))\n ((:tag . "JJ") (:stem . "protein-protein") (:form . "protein-protein")\n (:end . 103) (:start . 88) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n (:id . 59))\n ((:tag . "JJ") (:stem . "rna-protein") (:form . "RNA-protein") (:end . 119)\n (:start . 108) (:id . 60))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 132)\n (:start . 120) (:id . 61))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 136) (:start . 133)\n (:id . 62))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 139) (:start . 137)\n (:id . 63))\n ((:tag . "RB") (:stem . "readily") (:form . "readily") (:end . 147)\n (:start . 140) (:id . 64))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 156)\n (:start . 148) (:id . 65))\n ((:tag . "VBG") (:stem . "use") (:form . 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(:end . 107) (:start . 106)\n (:id . 59)))@@@1@18@((:hcues ((:id . :x9.86.1) (:span 31 38)))\n (:hscopes ((:id . :x9.86.1) (:span 31 106)))\n (:identifiers (:sid . :s9.86) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102660@unknown@formal@none@1@S@Unfortunately, no roX2 mutations have been recovered yet; they would be important tools for validating the significance of the roX RNAs in vivo.@(((:tag . "RB") (:stem . "unfortunately") (:form . "Unfortunately")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 43))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 17) (:start . 15)\n (:id . 44))\n ((:tag . "NN") (:stem . "rox2") (:form . "roX2") (:end . 22) (:start . 18)\n (:id . 45))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 32)\n (:start . 23) (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . 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"validate") (:form . "validating") (:end . 102)\n (:start . 92) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n (:id . 59))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 119)\n (:start . 107) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n (:id . 62))\n ((:tag . "NNP") (:stem . "roX") (:form . "roX") (:end . 130) (:start . 127)\n (:id . 63))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNAs") (:end . 135) (:start . 131)\n (:id . 64))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 138) (:start . 136)\n (:id . 65))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 143) (:start . 139)\n (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n (:id . 67)))@@@1@26@((:hcues ((:id . :x9.88.1) (:span 63 68)))\n (:ncues ((:id . :x9.88.2) (:span 15 17)))\n (:hscopes ((:id . :x9.88.1) (:span 63 143)))\n (:nscopes ((:id . :x9.88.2) (:span 15 52)))\n (:identifiers (:sid . :s9.88) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102661@unknown@formal@none@1@S@Furthermore, roX1 and roX2 are only the first two of about 35 chromatin entry sites, although perhaps they are the most important ones.@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 43))\n ((:tag . "NN") (:stem . "rox1") (:form . "roX1") (:end . 17) (:start . 13)\n (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n (:id . 45))\n ((:tag . "NN") (:stem . "rox2") (:form . "roX2") (:end . 26) (:start . 22)\n (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 30) (:start . 27)\n (:id . 47))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 35) (:start . 31)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 49))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 45) (:start . 40)\n (:id . 50))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 49) (:start . 46)\n (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n (:id . 52))\n ((:tag . "RB") (:stem . "about") (:form . "about") (:end . 58) (:start . 53)\n (:id . 53))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 61) (:start . 59)\n (:id . 54))\n ((:tag . "NN") (:stem . "chromatin") (:form . "chromatin") (:end . 71)\n (:start . 62) (:id . 55))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 77) (:start . 72)\n (:id . 56))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 83) (:start . 78)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n (:id . 58))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 93)\n (:start . 85) (:id . 59))\n ((:tag . "RB") (:stem . "perhaps") (:form . "perhaps") (:end . 101)\n (:start . 94) (:id . 60))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 106) (:start . 102)\n (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 110) (:start . 107)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n (:id . 63))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 119) (:start . 115)\n (:id . 64))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 129)\n (:start . 120) (:id . 65))\n ((:tag . "NNS") (:stem . "one") (:form . "ones") (:end . 134) (:start . 130)\n (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n (:id . 67)))@@@1@26@((:hcues ((:id . :x9.89.1) (:span 94 101)))\n (:hscopes ((:id . :x9.89.1) (:span 94 134)))\n (:identifiers (:sid . :s9.89) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102662@unknown@formal@none@1@S@The nature of the remaining 33 sites is entirely unclear and there is, as yet, no evidence that they contain other roX-like RNAs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "nature") (:form . "nature") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 45))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 27)\n (:start . 18) (:id . 46))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 30) (:start . 28)\n (:id . 47))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 36) (:start . 31)\n (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 39) (:start . 37)\n (:id . 49))\n ((:tag . "RB") (:stem . "entirely") (:form . "entirely") (:end . 48)\n (:start . 40) (:id . 50))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 56)\n (:start . 49) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n (:id . 52))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 66) (:start . 61)\n (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 69) (:start . 67)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 73) (:start . 71)\n (:id . 56))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 77) (:start . 74)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n (:id . 58))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 81) (:start . 79)\n (:id . 59))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 90)\n (:start . 82) (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 95) (:start . 91)\n (:id . 61))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 100) (:start . 96)\n (:id . 62))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 108)\n (:start . 101) (:id . 63))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 114)\n (:start . 109) (:id . 64))\n ((:tag . "JJ") (:stem . "rox-like") (:form . "roX-like") (:end . 123)\n (:start . 115) (:id . 65))\n ((:tag . "NNS") (:stem . "rna") (:form . "RNAs") (:end . 128) (:start . 124)\n (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n (:id . 67)))@@@1@26@((:hcues ((:id . :x9.90.1) (:span 79 90)) ((:id . :x9.90.2) (:span 49 56)))\n (:hscopes ((:id . :x9.90.1) (:span 79 128)) ((:id . :x9.90.2) (:span 0 56)))\n (:identifiers (:sid . :s9.90) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102663@unknown@formal@none@1@S@This brings us to the largest of all mysteries, namely how the DCC is spread along the X chromosome.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "bring") (:form . "brings") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 17) (:start . 15)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "JJS") (:stem . "large") (:form . "largest") (:end . 29)\n (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n (:id . 48))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 36) (:start . 33)\n (:id . 49))\n ((:tag . "NNS") (:stem . "mystery") (:form . "mysteries") (:end . 46)\n (:start . 37) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n (:id . 51))\n ((:tag . "RB") (:stem . "namely") (:form . "namely") (:end . 54)\n (:start . 48) (:id . 52))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 58) (:start . 55)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n (:id . 54))\n ((:tag . "NNP") (:stem . "DCC") (:form . "DCC") (:end . 66) (:start . 63)\n (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 69) (:start . 67)\n (:id . 56))\n ((:tag . "VBN") (:stem . "spread") (:form . "spread") (:end . 76)\n (:start . 70) (:id . 57))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 82) (:start . 77)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n (:id . 59))\n ((:tag . "NNP") (:stem . "X") (:form . "X") (:end . 88) (:start . 87)\n (:id . 60))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 99)\n (:start . 89) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.91) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102664@unknown@formal@none@1@S@One possibility is that the remaining 33 or so sites are ''stations' that serve as spreading facilitators in the form of DNA elements.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n (:id . 46))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 37)\n (:start . 28) (:id . 47))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 40) (:start . 38)\n (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 43) (:start . 41)\n (:id . 49))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 46) (:start . 44)\n (:id . 50))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 52) (:start . 47)\n (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 56) (:start . 53)\n (:id . 52))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 56) (:start . 56)\n (:id . 53))\n ((:tag . "NNS") (:stem . "stations") (:form . "stations") (:end . 67)\n (:start . 59) (:id . 54))\n ((:tag . "POS") (:stem . "'") (:form . "’") (:end . 68) (:start . 67)\n (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 73) (:start . 69)\n (:id . 56))\n ((:tag . "VBP") (:stem . "serve") (:form . "serve") (:end . 79) (:start . 74)\n (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 82) (:start . 80)\n (:id . 58))\n ((:tag . "VBG") (:stem . "spread") (:form . "spreading") (:end . 92)\n (:start . 83) (:id . 59))\n ((:tag . "NNS") (:stem . "facilitator") (:form . "facilitators") (:end . 105)\n (:start . 93) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n (:id . 62))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 117) (:start . 113)\n (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 120) (:start . 118)\n (:id . 64))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 124) (:start . 121)\n (:id . 65))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 133)\n (:start . 125) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n (:id . 67)))@@@1@26@((:hcues ((:id . :x9.92.1) (:span 41 43)) ((:id . :x9.92.2) (:span 4 15)))\n (:hscopes ((:id . :x9.92.1) (:span 28 46)) ((:id . :x9.92.2) (:span 4 133)))\n (:identifiers (:sid . :s9.92) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102665@unknown@formal@none@1@S@Thus, primDCCs and/or mature (mat) DCCs, originating from the roX entry sites, might hop from one ''station'' to the next and eventually reach all the entry sites distributed along the entire X chromosome [1].@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "primdcc") (:form . "primDCCs") (:end . 14)\n (:start . 6) (:id . 44))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 21)\n (:start . 15) (:id . 45))\n ((:tag . "JJ") (:stem . "mature") (:form . "mature") (:end . 28)\n (:start . 22) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n (:id . 47))\n ((:tag . "NN") (:stem . "mat") (:form . "mat") (:end . 33) (:start . 30)\n (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 34) (:start . 33)\n (:id . 49))\n ((:tag . "NNS") (:stem . "dcc") (:form . "DCCs") (:end . 39) (:start . 35)\n (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n (:id . 51))\n ((:tag . "VBG") (:stem . "originate") (:form . "originating") (:end . 52)\n (:start . 41) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 57) (:start . 53)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n (:id . 54))\n ((:tag . "NNP") (:stem . "roX") (:form . "roX") (:end . 65) (:start . 62)\n (:id . 55))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 71) (:start . 66)\n (:id . 56))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 77) (:start . 72)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n (:id . 58))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 84) (:start . 79)\n (:id . 59))\n ((:tag . "VB") (:stem . "hop") (:form . "hop") (:end . 88) (:start . 85)\n (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 93) (:start . 89)\n (:id . 61))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 97) (:start . 94)\n (:id . 62))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 97) (:start . 97)\n (:id . 63))\n ((:tag . "NN") (:stem . "station") (:form . "station") (:end . 107)\n (:start . 100) (:id . 64))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 107) (:start . 107)\n (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 112) (:start . 110)\n (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n (:id . 67))\n ((:tag . "JJ") (:stem . "next") (:form . "next") (:end . 121) (:start . 117)\n (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n (:id . 69))\n ((:tag . "RB") (:stem . "eventually") (:form . "eventually") (:end . 136)\n (:start . 126) (:id . 70))\n ((:tag . "VB") (:stem . "reach") (:form . "reach") (:end . 142)\n (:start . 137) (:id . 71))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 146) (:start . 143)\n (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 150) (:start . 147)\n (:id . 73))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 156)\n (:start . 151) (:id . 74))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 162)\n (:start . 157) (:id . 75))\n ((:tag . "VBN") (:stem . "distribute") (:form . "distributed") (:end . 174)\n (:start . 163) (:id . 76))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 180)\n (:start . 175) (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 184) (:start . 181)\n (:id . 78))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 191)\n (:start . 185) (:id . 79))\n ((:tag . "NNP") (:stem . "X") (:form . "X") (:end . 193) (:start . 192)\n (:id . 80))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 204)\n (:start . 194) (:id . 81))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 206) (:start . 205)\n (:id . 82))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 207) (:start . 206)\n (:id . 83))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 208) (:start . 207)\n (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n (:id . 85)))@@@1@44@((:hcues ((:id . :x9.93.1) (:span 79 84)))\n (:hscopes ((:id . :x9.93.1) (:span 79 204)))\n (:identifiers (:sid . :s9.93) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102666@unknown@formal@none@1@S@From these sites, they then reach into the neighboring chromatin regions by yet another mechanism.@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 16) (:start . 11)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 22) (:start . 18)\n (:id . 46))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 27) (:start . 23)\n (:id . 47))\n ((:tag . "VBP") (:stem . "reach") (:form . "reach") (:end . 33) (:start . 28)\n (:id . 48))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 38) (:start . 34)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n (:id . 50))\n ((:tag . "VBG") (:stem . "neighbor") (:form . "neighboring") (:end . 54)\n (:start . 43) (:id . 51))\n ((:tag . "NN") (:stem . "chromatin") (:form . "chromatin") (:end . 64)\n (:start . 55) (:id . 52))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 72)\n (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 75) (:start . 73)\n (:id . 54))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 79) (:start . 76)\n (:id . 55))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 87)\n (:start . 80) (:id . 56))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 97)\n (:start . 88) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s9.94) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102667@unknown@formal@none@1@S@One final thought: the dosage compensation machinery in C. elegans acts on the two X chromosomes in the hermaphrodite by twofold down-regulation of gene expression.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "thought") (:form . "thought") (:end . 17)\n (:start . 10) (:id . 44))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 18) (:start . 17)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 46))\n ((:tag . "NN") (:stem . "dosage") (:form . "dosage") (:end . 29)\n (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "compensation") (:form . "compensation") (:end . 42)\n (:start . 30) (:id . 48))\n ((:tag . "NN") (:stem . "machinery") (:form . "machinery") (:end . 52)\n (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n (:id . 50))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 58) (:start . 56)\n (:id . 51))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 66)\n (:start . 59) (:id . 52))\n ((:tag . "VBZ") (:stem . "act") (:form . "acts") (:end . 71) (:start . 67)\n (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 74) (:start . 72)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n (:id . 55))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 82) (:start . 79)\n (:id . 56))\n ((:tag . "NNP") (:stem . "X") (:form . "X") (:end . 84) (:start . 83)\n (:id . 57))\n ((:tag . "NNS") (:stem . "chromosome") (:form . "chromosomes") (:end . 96)\n (:start . 85) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n (:id . 60))\n ((:tag . "NN") (:stem . "hermaphrodite") (:form . "hermaphrodite")\n (:end . 117) (:start . 104) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 120) (:start . 118)\n (:id . 62))\n ((:tag . "JJ") (:stem . "twofold") (:form . "twofold") (:end . 128)\n (:start . 121) (:id . 63))\n ((:tag . "NN") (:stem . "down-regulation") (:form . "down-regulation")\n (:end . 144) (:start . 129) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 147) (:start . 145)\n (:id . 65))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 152) (:start . 148)\n (:id . 66))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 163)\n (:start . 153) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s9.95) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102668@unknown@formal@none@1@S@Six proteins are essential for this process and they associate with the X chromosomes; four of them are related to factors involved in chromosome condensation during mitosis in other systems.@(((:tag . "CD") (:stem . "six") (:form . "Six") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 26)\n (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 35) (:start . 31)\n (:id . 47))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 43)\n (:start . 36) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n (:id . 49))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 52) (:start . 48)\n (:id . 50))\n ((:tag . "VBP") (:stem . "associate") (:form . "associate") (:end . 62)\n (:start . 53) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 67) (:start . 63)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n (:id . 53))\n ((:tag . "NNP") (:stem . "X") (:form . "X") (:end . 73) (:start . 72)\n (:id . 54))\n ((:tag . "NNS") (:stem . "chromosome") (:form . "chromosomes") (:end . 85)\n (:start . 74) (:id . 55))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 86) (:start . 85)\n (:id . 56))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 91) (:start . 87)\n (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n (:id . 58))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 99) (:start . 95)\n (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 103) (:start . 100)\n (:id . 60))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 111)\n (:start . 104) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 114) (:start . 112)\n (:id . 62))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 122)\n (:start . 115) (:id . 63))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 131)\n (:start . 123) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 134) (:start . 132)\n (:id . 65))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 145)\n (:start . 135) (:id . 66))\n ((:tag . "NN") (:stem . "condensation") (:form . "condensation") (:end . 158)\n (:start . 146) (:id . 67))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 165)\n (:start . 159) (:id . 68))\n ((:tag . "NN") (:stem . "mitosis") (:form . "mitosis") (:end . 173)\n (:start . 166) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 176) (:start . 174)\n (:id . 70))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 182)\n (:start . 177) (:id . 71))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 190)\n (:start . 183) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s9.96) (:did . :pmc138894) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100009@unknown@formal@none@1@S@Assuming that the 23rd amino acid is also encoded by a stop codon, we systematically predicted proteins that contain stop-codon-encoded amino acids from 191 prokaryotic genomes.@(((:tag . "VBG") (:stem . "assume") (:form . "Assuming") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "that") (:form . 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"codon") (:end . 65) (:start . 60)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n (:id . 55))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 69) (:start . 67)\n (:id . 56))\n ((:tag . "RB") (:stem . "systematically") (:form . "systematically")\n (:end . 84) (:start . 70) (:id . 57))\n ((:tag . "VBD") (:stem . "predict") (:form . "predicted") (:end . 94)\n (:start . 85) (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 103)\n (:start . 95) (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 108) (:start . 104)\n (:id . 60))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 116)\n (:start . 109) (:id . 61))\n ((:tag . "JJ") (:stem . "stop-codon-encoded") (:form . "stop-codon-encoded")\n (:end . 135) (:start . 117) (:id . 62))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 141)\n (:start . 136) (:id . 63))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 147)\n (:start . 142) (:id . 64))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 152) (:start . 148)\n (:id . 65))\n ((:tag . "CD") (:stem . "191") (:form . "191") (:end . 156) (:start . 153)\n (:id . 66))\n ((:tag . "JJ") (:stem . "prokaryotic") (:form . "prokaryotic") (:end . 168)\n (:start . 157) (:id . 67))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 176)\n (:start . 169) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n (:id . 69)))@@@1@28@((:hcues ((:id . :x1.10.1) (:span 0 8)))\n (:hscopes ((:id . :x1.10.1) (:span 0 65)))\n (:identifiers (:sid . :s1.10) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100019@unknown@formal@none@1@S@Two such amino acids have been discovered to date: selenocysteine 34 and pyrrolysine 56.@(((:tag . "CD") (:stem . "two") (:form . "Two") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 20) (:start . 15)\n (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 25) (:start . 21)\n (:id . 46))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 30) (:start . 26)\n (:id . 47))\n ((:tag . "VBN") (:stem . "discover") (:form . "discovered") (:end . 41)\n (:start . 31) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n (:id . 49))\n ((:tag . "NN") (:stem . "date") (:form . "date") (:end . 49) (:start . 45)\n (:id . 50))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 50) (:start . 49)\n (:id . 51))\n ((:tag . "NN") (:stem . "selenocysteine") (:form . "selenocysteine")\n (:end . 65) (:start . 51) (:id . 52))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 68) (:start . 66)\n (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n (:id . 54))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 84)\n (:start . 73) (:id . 55))\n ((:tag . "CD") (:stem . "56") (:form . "56") (:end . 87) (:start . 85)\n (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.20) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100029@unknown@formal@none@1@S@Because genome sequences of various prokaryotes are available today, there will be a chance to discover the novel amino acid via analysis of these genomes.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 14) (:start . 8)\n (:id . 43))\n ((:tag . "NNS") (:stem . "sequence") (:form . 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"DT") (:stem . "a") (:form . "a") (:end . 84) (:start . 83)\n (:id . 55))\n ((:tag . "NN") (:stem . "chance") (:form . "chance") (:end . 91)\n (:start . 85) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n (:id . 57))\n ((:tag . "VB") (:stem . "discover") (:form . "discover") (:end . 103)\n (:start . 95) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n (:id . 59))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 113)\n (:start . 108) (:id . 60))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 119)\n (:start . 114) (:id . 61))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 124) (:start . 120)\n (:id . 62))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 128) (:start . 125)\n (:id . 63))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 137)\n (:start . 129) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 140) (:start . 138)\n (:id . 65))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 146)\n (:start . 141) (:id . 66))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 154)\n (:start . 147) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.30) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100039@unknown@formal@none@1@S@By enumerating ORFs that have an inframe stop codon from genomes and examining their evolutionary conservation, candidate proteins can be predicted.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBG") (:stem . "enumerate") (:form . "enumerating") (:end . 14)\n (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "orf") (:form . "ORFs") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 29) (:start . 25)\n (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 32) (:start . 30)\n (:id . 47))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 40)\n (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 45) (:start . 41)\n (:id . 49))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 51) (:start . 46)\n (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 56) (:start . 52)\n (:id . 51))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 64)\n (:start . 57) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n (:id . 53))\n ((:tag . "VBG") (:stem . "examine") (:form . "examining") (:end . 78)\n (:start . 69) (:id . 54))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 84)\n (:start . 79) (:id . 55))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 97)\n (:start . 85) (:id . 56))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 110)\n (:start . 98) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n (:id . 58))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 121)\n (:start . 112) (:id . 59))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 130)\n (:start . 122) (:id . 60))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 134) (:start . 131)\n (:id . 61))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 137) (:start . 135)\n (:id . 62))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 147)\n (:start . 138) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s1.40) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100049@unknown@formal@none@1@S@If we enumerate all iORFs from microbial genomes, most of the readthrough genes will be included in them.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "VBP") (:stem . "enumerate") (:form . "enumerate") (:end . 15)\n (:start . 6) (:id . 44))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 25) (:start . 20)\n (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 30) (:start . 26)\n (:id . 47))\n ((:tag . "JJ") (:stem . "microbial") (:form . "microbial") (:end . 40)\n (:start . 31) (:id . 48))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 48)\n (:start . 41) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n (:id . 50))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 54) (:start . 50)\n (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n (:id . 53))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 73)\n (:start . 62) (:id . 54))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 79) (:start . 74)\n (:id . 55))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 84) (:start . 80)\n (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 87) (:start . 85)\n (:id . 57))\n ((:tag . "VBN") (:stem . "include") (:form . "included") (:end . 96)\n (:start . 88) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n (:id . 59))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 104) (:start . 100)\n (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.50) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100059@unknown@formal@none@1@S@(a) Schematic illustration of an interrupted ORF (iORF).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "schematic") (:form . "Schematic") (:end . 13)\n (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "illustration") (:form . "illustration") (:end . 26)\n (:start . 14) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 47))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 32) (:start . 30)\n (:id . 48))\n ((:tag . "JJ") (:stem . "interrupted") (:form . "interrupted") (:end . 44)\n (:start . 33) (:id . 49))\n ((:tag . "NNP") (:stem . "ORF") (:form . "ORF") (:end . 48) (:start . 45)\n (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n (:id . 51))\n ((:tag . "NNP") (:stem . "iORF") (:form . "iORF") (:end . 54) (:start . 50)\n (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s1.60) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100069@unknown@formal@none@1@S@In this way, they can be eliminated as candidates.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 11) (:start . 8)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 45))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 17) (:start . 13)\n (:id . 46))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 21) (:start . 18)\n (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 24) (:start . 22)\n (:id . 48))\n ((:tag . "VBN") (:stem . "eliminate") (:form . "eliminated") (:end . 35)\n (:start . 25) (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 38) (:start . 36)\n (:id . 50))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 49)\n (:start . 39) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 50) (:start . 49)\n (:id . 52)))@@@1@11@((:identifiers (:sid . :s1.70) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100079@unknown@formal@none@1@S@The prediction schema is shown in Figure 2.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "schema") (:form . "schema") (:end . 21)\n (:start . 15) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 24) (:start . 22)\n (:id . 45))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 30) (:start . 25)\n (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 40)\n (:start . 34) (:id . 48))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 42) (:start . 41)\n (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 43) (:start . 42)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s1.80) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100089@unknown@formal@none@1@S@A flowchart of the prediction procedure@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "flowchart") (:form . "flowchart") (:end . 11)\n (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 29)\n (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 39)\n (:start . 30) (:id . 47)))@@@1@6@((:identifiers (:sid . :s1.90) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011 5100099@unknown@formal@none@1@S@There were 94,690 iORFs that have interspecific hits.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "CD") (:stem . "94,690") (:form . "94,690") (:end . 17)\n (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 23) (:start . 18)\n (:id . 45))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "JJ") (:stem . "interspecific") (:form . "interspecific")\n (:end . 47) (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 52) (:start . 48)\n (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 53) (:start . 52)\n (:id . 50)))@@@1@9@((:identifiers (:sid . :s1.100) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100109@unknown@formal@none@1@S@Hence, three-step filtering procedures were applied to remove the false positives.@(((:tag . "RB") (:stem . "hence") (:form . "Hence") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "JJ") (:stem . "three-step") (:form . "three-step") (:end . 17)\n (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "filtering") (:form . "filtering") (:end . 27)\n (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "procedure") (:form . "procedures") (:end . 38)\n (:start . 28) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 43) (:start . 39)\n (:id . 47))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 51)\n (:start . 44) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 54) (:start . 52)\n (:id . 49))\n ((:tag . "VB") (:stem . "remove") (:form . "remove") (:end . 61)\n (:start . 55) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n (:id . 51))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 71) (:start . 66)\n (:id . 52))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 81)\n (:start . 72) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s1.110) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100119@unknown@formal@none@1@S@Of the 14 families, 11 were found in our prediction result.@(((:tag . "IN") (:stem . "of") (:form . "Of") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 9) (:start . 7)\n (:id . 44))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 18)\n (:start . 10) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n (:id . 46))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 22) (:start . 20)\n (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 27) (:start . 23)\n (:id . 48))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 33) (:start . 28)\n (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n (:id . 50))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 40) (:start . 37)\n (:id . 51))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 51)\n (:start . 41) (:id . 52))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 58)\n (:start . 52) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 59) (:start . 58)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s1.120) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100129@unknown@formal@none@1@S@For example, "GSU2293 + downstream" means that the iORF consists of the gene GSU2293 and its downstream sequence.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 14) (:start . 13)\n (:id . 45))\n ((:tag . "NNP") (:stem . "GSU2293") (:form . "GSU2293") (:end . 21)\n (:start . 14) (:id . 46))\n ((:tag . "SYM") (:stem . "+") (:form . "+") (:end . 23) (:start . 22)\n (:id . 47))\n ((:tag . "NN") (:stem . "downstream") (:form . "downstream") (:end . 34)\n (:start . 24) (:id . 48))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 35) (:start . 34)\n (:id . 49))\n ((:tag . "VBZ") (:stem . "mean") (:form . "means") (:end . 41) (:start . 36)\n (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 46) (:start . 42)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n (:id . 52))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 55) (:start . 51)\n (:id . 53))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 64)\n (:start . 56) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n (:id . 56))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 76) (:start . 72)\n (:id . 57))\n ((:tag . "NN") (:stem . "gsu2293") (:form . "GSU2293") (:end . 84)\n (:start . 77) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n (:id . 59))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 92) (:start . 89)\n (:id . 60))\n ((:tag . "JJ") (:stem . "downstream") (:form . "downstream") (:end . 103)\n (:start . 93) (:id . 61))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 112)\n (:start . 104) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.130) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100139@unknown@formal@none@1@S@The rest is a cluster of TetR-like transcriptional regulators from Methanosarcina acetivorans and M. barkeri.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "rest") (:form . "rest") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n (:id . 45))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 21)\n (:start . 14) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n (:id . 47))\n ((:tag . "JJ") (:stem . "tetr-like") (:form . "TetR-like") (:end . 34)\n (:start . 25) (:id . 48))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n (:end . 50) (:start . 35) (:id . 49))\n ((:tag . "NNS") (:stem . "regulator") (:form . "regulators") (:end . 61)\n (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 66) (:start . 62)\n (:id . 51))\n ((:tag . "NNP") (:stem . "Methanosarcina") (:form . "Methanosarcina")\n (:end . 81) (:start . 67) (:id . 52))\n ((:tag . "NNP") (:stem . "acetivorans") (:form . "acetivorans") (:end . 93)\n (:start . 82) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n (:id . 54))\n ((:tag . "NNP") (:stem . "M.") (:form . "M.") (:end . 100) (:start . 98)\n (:id . 55))\n ((:tag . "NNP") (:stem . "barkeri") (:form . "barkeri") (:end . 108)\n (:start . 101) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.140) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100149@unknown@formal@none@1@S@There were two such clusters (Table 1).@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 19) (:start . 15)\n (:id . 45))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 28)\n (:start . 20) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n (:id . 47))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 35) (:start . 30)\n (:id . 48))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 37) (:start . 36)\n (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 38) (:start . 37)\n (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 39) (:start . 38)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s1.150) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100159@unknown@formal@none@1@S@A protein Dpro_2 contains yet another inframe stop codon (TAG) at the column 189.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 9)\n (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "dpro_2") (:form . "Dpro_2") (:end . 16)\n (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 25)\n (:start . 17) (:id . 45))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 29) (:start . 26)\n (:id . 46))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 37)\n (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 45)\n (:start . 38) (:id . 48))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 50) (:start . 46)\n (:id . 49))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 56) (:start . 51)\n (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n (:id . 51))\n ((:tag . "NNP") (:stem . "TAG") (:form . "TAG") (:end . 61) (:start . 58)\n (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 65) (:start . 63)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n (:id . 55))\n ((:tag . "NN") (:stem . "column") (:form . "column") (:end . 76)\n (:start . 70) (:id . 56))\n ((:tag . "CD") (:stem . "189") (:form . "189") (:end . 80) (:start . 77)\n (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.160) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100169@unknown@formal@none@1@S@However, computational analysis of sequences immediately downstream of the inframe stop codons failed to identify SECIS elements, which is a hallmark of selenocysteine-containing genes.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "computational") (:form . "computational")\n (:end . 22) (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 31)\n (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n (:id . 46))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 44)\n (:start . 35) (:id . 47))\n ((:tag . "RB") (:stem . "immediately") (:form . "immediately") (:end . 56)\n (:start . 45) (:id . 48))\n ((:tag . "RB") (:stem . "downstream") (:form . "downstream") (:end . 67)\n (:start . 57) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n (:id . 51))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 82)\n (:start . 75) (:id . 52))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 87) (:start . 83)\n (:id . 53))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 94)\n (:start . 88) (:id . 54))\n ((:tag . "VBD") (:stem . "fail") (:form . "failed") (:end . 101)\n (:start . 95) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 104) (:start . 102)\n (:id . 56))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 113)\n (:start . 105) (:id . 57))\n ((:tag . "NN") (:stem . "secis") (:form . "SECIS") (:end . 119)\n (:start . 114) (:id . 58))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 128)\n (:start . 120) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n (:id . 60))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 135)\n (:start . 130) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 138) (:start . 136)\n (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 140) (:start . 139)\n (:id . 63))\n ((:tag . "NN") (:stem . "hallmark") (:form . "hallmark") (:end . 149)\n (:start . 141) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 152) (:start . 150)\n (:id . 65))\n ((:tag . "JJ") (:stem . "selenocysteine-containing")\n (:form . "selenocysteine-containing") (:end . 178) (:start . 153)\n (:id . 66))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 184)\n (:start . 179) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n (:id . 68)))@@@1@27@((:ncues ((:id . :x1.170.1) (:span 95 101)))\n (:nscopes ((:id . :x1.170.1) (:span 95 128)))\n (:identifiers (:sid . :s1.170) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100179@unknown@formal@none@1@S@Stop codon usage in the pre-filtering clusters@(((:tag . "NNP") (:stem . "Stop") (:form . "Stop") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "usage") (:form . "usage") (:end . 16) (:start . 11)\n (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n (:id . 46))\n ((:tag . "JJ") (:stem . "pre-filtering") (:form . "pre-filtering")\n (:end . 37) (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 46)\n (:start . 38) (:id . 48)))@@@1@7@((:identifiers (:sid . :s1.180) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5100189@unknown@formal@none@1@S@Discrepancies of stop codon usages between the inframe and C-terminal stop codons@(((:tag . "NNS") (:stem . "discrepancy") (:form . "Discrepancies") (:end . 13)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 43))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 21) (:start . 17)\n (:id . 44))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 27) (:start . 22)\n (:id . 45))\n ((:tag . "NNS") (:stem . "usage") (:form . "usages") (:end . 34)\n (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 42)\n (:start . 35) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n (:id . 48))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 54)\n (:start . 47) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n (:id . 50))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 69)\n (:start . 59) (:id . 51))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 74) (:start . 70)\n (:id . 52))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 81)\n (:start . 75) (:id . 53)))@@@1@12@((:identifiers (:sid . :s1.190) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|FigureLegend|)))@oe@9-2-2011 5100199@unknown@formal@none@1@S@Sensitivity of this test is not high because many organisms that utilize selenocysteine were below the defined threshold.@(((:tag . "NN") (:stem . "sensitivity") (:form . "Sensitivity") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 19) (:start . 15)\n (:id . 44))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 24) (:start . 20)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 31) (:start . 28)\n (:id . 47))\n ((:tag . "JJ") (:stem . "high") (:form . 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"defined") (:end . 110)\n (:start . 103) (:id . 58))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 120)\n (:start . 111) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.200) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100209@unknown@formal@none@1@S@Perrodou et al. 19 constructed a database of predicted recoding events in microbes.@(((:tag . "NNP") (:stem . "Perrodou") (:form . "Perrodou") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 11) (:start . 9)\n (:id . 43))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "CD") (:stem . "19") (:form . "19") (:end . 18) (:start . 16)\n (:id . 45))\n ((:tag . "VBD") (:stem . "construct") (:form . "constructed") (:end . 30)\n (:start . 19) (:id . 46))\n ((:tag . 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(:end . 83) (:start . 82)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s1.210) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100219@unknown@formal@none@1@S@Dimethylamine methyltransferases also lack non-readthrough homologs.@(((:tag . "NNP") (:stem . "Dimethylamine") (:form . "Dimethylamine")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "methyltransferas") (:form . "methyltransferases")\n (:end . 32) (:start . 14) (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 37) (:start . 33)\n (:id . 44))\n ((:tag . "VBP") (:stem . "lack") (:form . "lack") (:end . 42) (:start . 38)\n (:id . 45))\n ((:tag . "JJ") (:stem . "non-readthrough") (:form . "non-readthrough")\n (:end . 58) (:start . 43) (:id . 46))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 67)\n (:start . 59) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n (:id . 48)))@@@1@7@((:ncues ((:id . :x1.220.1) (:span 38 42)))\n (:nscopes ((:id . :x1.220.1) (:span 38 67)))\n (:identifiers (:sid . :s1.220) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100229@unknown@formal@none@1@S@However, almost no novel candidates for readthrough genes were predicted.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 15) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 18) (:start . 16)\n (:id . 45))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 24) (:start . 19)\n (:id . 46))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 35)\n (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 39) (:start . 36)\n (:id . 48))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 51)\n (:start . 40) (:id . 49))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 57) (:start . 52)\n (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 62) (:start . 58)\n (:id . 51))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 72)\n (:start . 63) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s1.230) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100239@unknown@formal@none@1@S@Yet another possibility is that the 23rd amino acid exists but is not encoded by stop codons.@(((:tag . "RB") (:stem . "yet") (:form . "Yet") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "another") (:form . 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"not") (:form . "not") (:end . 69) (:start . 66)\n (:id . 54))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 77)\n (:start . 70) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 80) (:start . 78)\n (:id . 56))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 85) (:start . 81)\n (:id . 57))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 92)\n (:start . 86) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n (:id . 59)))@@@1@18@((:hcues ((:id . :x1.240.2) (:span 12 23)))\n (:ncues ((:id . :x1.240.1) (:span 66 69)))\n (:hscopes ((:id . :x1.240.2) (:span 12 92)))\n (:nscopes ((:id . :x1.240.1) (:span 66 92)))\n (:identifiers (:sid . :s1.240) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100249@unknown@formal@none@1@S@Such selenoproteins identified through our screening of nearly 200 microbial genomes were selenoprotein A and only one uncertain candidate.@(((:tag . "JJ") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "selenoprotein") (:form . "selenoproteins")\n (:end . 19) (:start . 5) (:id . 43))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 30)\n (:start . 20) (:id . 44))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 38)\n (:start . 31) (:id . 45))\n ((:tag . "PRP$") (:stem . "our") (:form . 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"many") (:form . "many") (:end . 13) (:start . 9)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 30)\n (:start . 21) (:id . 46))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 36) (:start . 31)\n (:id . 47))\n ((:tag . "NNS") (:stem . "selenoprotein") (:form . "selenoproteins")\n (:end . 51) (:start . 37) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n (:id . 49))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 67)\n (:start . 56) (:id . 50))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 76)\n (:start . 68) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 81) (:start . 77)\n (:id . 52))\n ((:tag . "RB") (:stem . "successfully") (:form . "successfully") (:end . 94)\n (:start . 82) (:id . 53))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 103)\n (:start . 95) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n (:id . 55))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 107) (:start . 105)\n (:id . 56))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 117)\n (:start . 108) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 121) (:start . 118)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n (:id . 59))\n ((:tag . "JJ") (:stem . "23rd") (:form . "23rd") (:end . 130) (:start . 126)\n (:id . 60))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 136)\n (:start . 131) (:id . 61))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 141) (:start . 137)\n (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 145) (:start . 142)\n (:id . 63))\n ((:tag . "VBN") (:stem . "discover") (:form . "discovered") (:end . 156)\n (:start . 146) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n (:id . 65)))@@@1@24@((:ncues ((:id . :x1.260.1) (:span 105 107)))\n (:nscopes ((:id . :x1.260.1) (:span 105 156)))\n (:identifiers (:sid . :s1.260) (:did . :1471-2105-8-225)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100269@unknown@formal@none@1@S@A total of 328 complete genome sequences of prokaryotes were downloaded from the KEGG FTP site 25 in April 2006.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "total") (:form . "total") (:end . 7) (:start . 2)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n (:id . 44))\n ((:tag . "CD") (:stem . "328") (:form . "328") (:end . 14) (:start . 11)\n (:id . 45))\n ((:tag . "JJ") (:stem . "complete") (:form . 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"functional") (:form . "functional") (:end . 33)\n (:start . 23) (:id . 47))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 42)\n (:start . 34) (:id . 48))\n ((:tag . "VBP") (:stem . "exploit") (:form . "exploit") (:end . 50)\n (:start . 43) (:id . 49))\n ((:tag . "JJ") (:stem . "non-sequence") (:form . "non-sequence") (:end . 63)\n (:start . 51) (:id . 50))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 75)\n (:start . 64) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n (:id . 52))\n ((:tag . "VB") (:stem . "infer") (:form . "infer") (:end . 84) (:start . 79)\n (:id . 53))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 97)\n (:start . 85) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.43) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100379@unknown@formal@none@1@S@Although, many computational methods have investigated the prediction of protein-protein interactions, few have so far been applied to the human proteome.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "JJ") (:stem . "computational") (:form . "computational")\n (:end . 28) (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 36)\n (:start . 29) (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 41) (:start . 37)\n (:id . 47))\n ((:tag . "VBN") (:stem . "investigate") (:form . "investigated") (:end . 54)\n (:start . 42) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n (:id . 49))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 69)\n (:start . 59) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n (:id . 51))\n ((:tag . "JJ") (:stem . "protein-protein") (:form . "protein-protein")\n (:end . 88) (:start . 73) (:id . 52))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 101)\n (:start . 89) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n (:id . 54))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 106) (:start . 103)\n (:id . 55))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 111) (:start . 107)\n (:id . 56))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 114) (:start . 112)\n (:id . 57))\n ((:tag . "RB") (:stem . "far") (:form . "far") (:end . 118) (:start . 115)\n (:id . 58))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 123) (:start . 119)\n (:id . 59))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 131)\n (:start . 124) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 134) (:start . 132)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n (:id . 62))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 144)\n (:start . 139) (:id . 63))\n ((:tag . "NN") (:stem . "proteome") (:form . "proteome") (:end . 153)\n (:start . 145) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.53) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100389@unknown@formal@none@1@S@Results and discussion@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n (:id . 43))\n ((:tag . "NN") (:stem . "discussion") (:form . "discussion") (:end . 22)\n (:start . 12) (:id . 44)))@@@1@3@((:identifiers (:sid . :s2.63) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011 5100399@unknown@formal@none@1@S@In the absence of the Transitive module, the Preliminary Score is used as the final likelihood ratio output by the predictor.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 14)\n (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 32)\n (:start . 22) (:id . 47))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 39)\n (:start . 33) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n (:id . 50))\n ((:tag . "JJ") (:stem . "preliminary") (:form . "Preliminary") (:end . 56)\n (:start . 45) (:id . 51))\n ((:tag . "NN") (:stem . "score") (:form . "Score") (:end . 62) (:start . 57)\n (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 65) (:start . 63)\n (:id . 53))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 70) (:start . 66)\n (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 73) (:start . 71)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n (:id . 56))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 83) (:start . 78)\n (:id . 57))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 94)\n (:start . 84) (:id . 58))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 100) (:start . 95)\n (:id . 59))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 107)\n (:start . 101) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 110) (:start . 108)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n (:id . 62))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 124)\n (:start . 115) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n (:id . 64)))@@@1@23@((:ncues ((:id . :x2.73.1) (:span 7 14)))\n (:nscopes ((:id . :x2.73.1) (:span 7 39)))\n (:identifiers (:sid . :s2.73) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100409@unknown@formal@none@1@S@The final likelihood ratio is then the product of the preliminary score calculated in panel A and the likelihood ratio output by the transitive module in panel B.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 20)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 26) (:start . 21)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 34) (:start . 30)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n (:id . 48))\n ((:tag . "NN") (:stem . "product") (:form . "product") (:end . 46)\n (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n (:id . 51))\n ((:tag . "JJ") (:stem . "preliminary") (:form . "preliminary") (:end . 65)\n (:start . 54) (:id . 52))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 71) (:start . 66)\n (:id . 53))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 82)\n (:start . 72) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 85) (:start . 83)\n (:id . 55))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 91) (:start . 86)\n (:id . 56))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 93) (:start . 92)\n (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n (:id . 59))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 112)\n (:start . 102) (:id . 60))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 118)\n (:start . 113) (:id . 61))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 125)\n (:start . 119) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 128) (:start . 126)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n (:id . 64))\n ((:tag . "JJ") (:stem . "transitive") (:form . "transitive") (:end . 143)\n (:start . 133) (:id . 65))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 150)\n (:start . 144) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 153) (:start . 151)\n (:id . 67))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 159)\n (:start . 154) (:id . 68))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 161) (:start . 160)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s2.83) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100419@unknown@formal@none@1@S@The evaluation of this ratio is difficult because not all true interactions are known.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 22) (:start . 18)\n (:id . 45))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 28) (:start . 23)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 31) (:start . 29)\n (:id . 47))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 41)\n (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 49)\n (:start . 42) (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 53) (:start . 50)\n (:id . 50))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 57) (:start . 54)\n (:id . 51))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 62) (:start . 58)\n (:id . 52))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 75)\n (:start . 63) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 79) (:start . 76)\n (:id . 54))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 85) (:start . 80)\n (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.93) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100429@unknown@formal@none@1@S@However, since the highest likelihood ratio for the expression datasets that we consider is 33, they are not sufficient on their own to predict interacting protein pairs with a posterior odds ratio above 1.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 26)\n (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 37)\n (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 43) (:start . 38)\n (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 47) (:start . 44)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n (:id . 50))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 62)\n (:start . 52) (:id . 51))\n ((:tag . "VBZ") (:stem . "dataset") (:form . "datasets") (:end . 71)\n (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 76) (:start . 72)\n (:id . 53))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 79) (:start . 77)\n (:id . 54))\n ((:tag . "VBP") (:stem . "consider") (:form . "consider") (:end . 88)\n (:start . 80) (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 91) (:start . 89)\n (:id . 56))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 94) (:start . 92)\n (:id . 57))\n ((:tag . 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"interacting") (:end . 155)\n (:start . 144) (:id . 68))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 163)\n (:start . 156) (:id . 69))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 169)\n (:start . 164) (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 174) (:start . 170)\n (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 176) (:start . 175)\n (:id . 72))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 186)\n (:start . 177) (:id . 73))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 191) (:start . 187)\n (:id . 74))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 197)\n (:start . 192) (:id . 75))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 203)\n (:start . 198) (:id . 76))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 205) (:start . 204)\n (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n (:id . 78)))@@@1@37@((:ncues ((:id . :x2.103.1) (:span 105 108)))\n (:nscopes ((:id . :x2.103.1) (:span 105 205)))\n (:identifiers (:sid . :s2.103) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100439@unknown@formal@none@1@S@Additionally, this combination circumvents possible problems of dependence between these features.@(((:tag . "RB") (:stem . "additionally") (:form . "Additionally") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 30)\n (:start . 19) (:id . 45))\n ((:tag . "VBZ") (:stem . "circumvent") (:form . "circumvents") (:end . 42)\n (:start . 31) (:id . 46))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 51)\n (:start . 43) (:id . 47))\n ((:tag . "NNS") (:stem . "problem") (:form . "problems") (:end . 60)\n (:start . 52) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n (:id . 49))\n ((:tag . "NN") (:stem . "dependence") (:form . "dependence") (:end . 74)\n (:start . 64) (:id . 50))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 82)\n (:start . 75) (:id . 51))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 88) (:start . 83)\n (:id . 52))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 97)\n (:start . 89) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n (:id . 54)))@@@1@13@((:hcues ((:id . :x2.113.1) (:span 43 51)))\n (:hscopes ((:id . :x2.113.1) (:span 43 97)))\n (:identifiers (:sid . :s2.113) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100449@unknown@formal@none@1@S@When investigated as a separate feature, the chi-square score of co-occurrence of domain pairs correlates well with the likelihood of interaction of protein pairs that contain these domains, with the highest chi-square score bin obtaining a likelihood ratio of 14, as shown in Figure 3A.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "investigate") (:form . "investigated") (:end . 17)\n (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 20) (:start . 18)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n (:id . 45))\n ((:tag . 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(:end . 258) (:start . 257)\n (:id . 84)))@@@1@43@((:identifiers (:sid . :s2.133) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100469@unknown@formal@none@1@S@Independence of all modules used in our predictor was verified by calculating Pearson correlation coefficients for all pairs of modules.@(((:tag . "NN") (:stem . "independence") (:form . "Independence") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 43))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 19) (:start . 16)\n (:id . 44))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 27)\n (:start . 20) (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 32) (:start . 28)\n (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n (:id . 47))\n ((:tag . "PRP$") (:stem . "our") (:form . 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(:end . 94) (:start . 93)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.153) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100489@unknown@formal@none@1@S@As the scores of the predictors increase, so do the number of interactions predicted above different posterior odds ratio thresholds (see lower portion of Table 3).@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 13) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 46))\n ((:tag . "NNS") (:stem . "predictor") (:form . "predictors") (:end . 31)\n (:start . 21) (:id . 47))\n ((:tag . "VBP") (:stem . "increase") (:form . 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(:end . 67) (:start . 66)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s2.173) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100509@unknown@formal@none@1@S@As shown in Table 4, the predictors trained on datasets containing 100 times more negatives than positives perform significantly better than those trained on datasets containing equal numbers of positives and negatives.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 17) (:start . 12)\n (:id . 45))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 19) (:start . 18)\n (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n (:id . 47))\n ((:tag . 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"containing") (:end . 177)\n (:start . 167) (:id . 68))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 183)\n (:start . 178) (:id . 69))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 191)\n (:start . 184) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 194) (:start . 192)\n (:id . 71))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 204)\n (:start . 195) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 208) (:start . 205)\n (:id . 73))\n ((:tag . "NNS") (:stem . "negative") (:form . "negatives") (:end . 218)\n (:start . 209) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s2.183) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100519@unknown@formal@none@1@S@A criticism of randomly chosen negatives is that they will contain some true interactors.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "criticism") (:form . "criticism") (:end . 11)\n (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n (:id . 44))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 30)\n (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "negative") (:form . "negatives") (:end . 40)\n (:start . 31) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 43) (:start . 41)\n (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 48) (:start . 44)\n (:id . 49))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 53) (:start . 49)\n (:id . 50))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 58) (:start . 54)\n (:id . 51))\n ((:tag . "VB") (:stem . "contain") (:form . "contain") (:end . 66)\n (:start . 59) (:id . 52))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 71) (:start . 67)\n (:id . 53))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 76) (:start . 72)\n (:id . 54))\n ((:tag . "NNS") (:stem . "interactor") (:form . "interactors") (:end . 88)\n (:start . 77) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.193) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100529@unknown@formal@none@1@S@The localization-derived negative trained predictor tested on sets containing localization-derived negatives achieves a lower accuracy than that of the random negative trained predictor tested on a test set containing randomly-generated negatives (0.0686 +/- 0.0010 vs 0.0747 +/- 0.0022).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "localization-derived")\n (:form . "localization-derived") (:end . 24) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 33)\n (:start . 25) (:id . 44))\n ((:tag . "JJ") (:stem . "trained") (:form . "trained") (:end . 41)\n (:start . 34) (:id . 45))\n ((:tag . "NN") (:stem . "predictor") (:form . 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"0.0010") (:end . 265)\n (:start . 259) (:id . 76))\n ((:tag . "IN") (:stem . "vs") (:form . "vs") (:end . 268) (:start . 266)\n (:id . 77))\n ((:tag . "CD") (:stem . "0.0747") (:form . "0.0747") (:end . 275)\n (:start . 269) (:id . 78))\n ((:tag . "SYM") (:stem . "+/-") (:form . "+/-") (:end . 279) (:start . 276)\n (:id . 79))\n ((:tag . "CD") (:stem . "0.0022") (:form . "0.0022") (:end . 286)\n (:start . 280) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 287) (:start . 286)\n (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 288) (:start . 287)\n (:id . 82)))@@@1@41@((:identifiers (:sid . :s2.203) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100539@unknown@formal@none@1@S@As shown in Figure 4A, all modules contribute positively (i.e. contribute a likelihood ratio greater than 1.0) to the prediction of a certain proportion of the interactions in the LR400 dataset.@(((:tag . 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"(") (:end . 58) (:start . 57)\n (:id . 52))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 62) (:start . 58)\n (:id . 53))\n ((:tag . "VBP") (:stem . "contribute") (:form . "contribute") (:end . 73)\n (:start . 63) (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 75) (:start . 74)\n (:id . 55))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 86)\n (:start . 76) (:id . 56))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 92) (:start . 87)\n (:id . 57))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 100)\n (:start . 93) (:id . 58))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 105) (:start . 101)\n (:id . 59))\n ((:tag . "CD") (:stem . "1.0") (:form . "1.0") (:end . 109) (:start . 106)\n (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 113) (:start . 111)\n (:id . 62))\n ((:tag . 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"the") (:end . 179) (:start . 176)\n (:id . 73))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 185)\n (:start . 180) (:id . 74))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 193)\n (:start . 186) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n (:id . 76)))@@@1@35@((:identifiers (:sid . :s2.213) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100549@unknown@formal@none@1@S@Few interactions in the LR400 dataset are predicted on the basis of having interacting orthologs in worm or fly alone.@(((:tag . "JJ") (:stem . "few") (:form . "Few") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 16)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 19) (:start . 17)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . 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"NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 96)\n (:start . 87) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n (:id . 57))\n ((:tag . "NN") (:stem . "worm") (:form . "worm") (:end . 104) (:start . 100)\n (:id . 58))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 107) (:start . 105)\n (:id . 59))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 111) (:start . 108)\n (:id . 60))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 117)\n (:start . 112) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.223) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100559@unknown@formal@none@1@S@The Combined and Transitive modules contribute the most to the prediction of interactions.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "combined") (:form . "Combined") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 27)\n (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 35)\n (:start . 28) (:id . 46))\n ((:tag . "VBP") (:stem . "contribute") (:form . "contribute") (:end . 46)\n (:start . 36) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n (:id . 48))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 55) (:start . 51)\n (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n (:id . 51))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 73)\n (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n (:id . 53))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 89)\n (:start . 77) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.233) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100569@unknown@formal@none@1@S@The right side of the curve illustrates the number of interactions that are predicted above likelihood ratios of 400 and more.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . 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"predicted") (:end . 85)\n (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 91) (:start . 86)\n (:id . 56))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 102)\n (:start . 92) (:id . 57))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 109)\n (:start . 103) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n (:id . 59))\n ((:tag . "CD") (:stem . "400") (:form . "400") (:end . 116) (:start . 113)\n (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n (:id . 61))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 125) (:start . 121)\n (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s2.243) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100579@unknown@formal@none@1@S@As the posterior odds ratio increases, the false positive rate decreases and the ratio of the true positive rate divided by the false positive ratio increases.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 16)\n (:start . 7) (:id . 44))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 21) (:start . 17)\n (:id . 45))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 27) (:start . 22)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "increase") (:form . "increases") (:end . 37)\n (:start . 28) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . 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(:end . 159) (:start . 158)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s2.253) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100589@unknown@formal@none@1@S@We estimated false positive rates for each of the datasets by comparing them two by two to one of the reference datasets, thus generating 4 to 6 different estimates of false positive rates for each computational dataset, as shown in Figure 6A (the two Lehner datasets were not compared to each other, which is why they have fewer FPR estimates).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "estimate") (:form . "estimated") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 18) (:start . 13)\n (:id . 44))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 27)\n (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . 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(:end . 345) (:start . 344)\n (:id . 107)))@@@1@66@((:ncues ((:id . :x2.263.1) (:span 273 276)))\n (:nscopes ((:id . :x2.263.1) (:span 243 299)))\n (:identifiers (:sid . :s2.263) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100599@unknown@formal@none@1@S@The number and overlap of distinct proteins (shown in B) and distinct interactions (shown in C) are shown for the LR400 dataset, the Rhodes prediction dataset and the June 2006 version of the HPRD.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 14) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "overlap") (:form . "overlap") (:end . 22)\n (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n (:id . 46))\n ((:tag . 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"eukaryotic") (:end . 288)\n (:start . 278) (:id . 87))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 300)\n (:start . 289) (:id . 88))\n ((:tag . "NN") (:stem . "initiation") (:form . "initiation") (:end . 311)\n (:start . 301) (:id . 89))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 319)\n (:start . 312) (:id . 90))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 320) (:start . 319)\n (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 321) (:start . 320)\n (:id . 92)))@@@1@51@((:identifiers (:sid . :s2.293) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100629@unknown@formal@none@1@S@-TCPTP was predicted to interact with STAT6 at a posterior odds ratio of 4300.@(((:tag . "NNP") (:stem . "-TCPTP") (:form . "-TCPTP") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 10) (:start . 7)\n (:id . 43))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 20)\n (:start . 11) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n (:id . 45))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 32)\n (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 37) (:start . 33)\n (:id . 47))\n ((:tag . "NN") (:stem . "stat6") (:form . "STAT6") (:end . 43) (:start . 38)\n (:id . 48))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 46) (:start . 44)\n (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n (:id . 50))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 58)\n (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 63) (:start . 59)\n (:id . 52))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 69) (:start . 64)\n (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n (:id . 54))\n ((:tag . "CD") (:stem . "4300") (:form . "4300") (:end . 77) (:start . 73)\n (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.303) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100639@unknown@formal@none@1@S@-Sam68 and Smad2 achieve a predicted posterior odds ratio of 32.@(((:tag . "NNP") (:stem . "-Sam68") (:form . "-Sam68") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 10) (:start . 7)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Smad2") (:form . "Smad2") (:end . 16) (:start . 11)\n (:id . 44))\n ((:tag . "VBP") (:stem . "achieve") (:form . "achieve") (:end . 24)\n (:start . 17) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n (:id . 46))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 36)\n (:start . 27) (:id . 47))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 46)\n (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 51) (:start . 47)\n (:id . 49))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 57) (:start . 52)\n (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n (:id . 51))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 63) (:start . 61)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 64) (:start . 63)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.313) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100649@unknown@formal@none@1@S@A subset of our novel predictions have been independently validated by identifying recent reports that experimentally investigated and confirmed that these protein pairs do interact.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 8) (:start . 2)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 15) (:start . 12)\n (:id . 45))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 21) (:start . 16)\n (:id . 46))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 33)\n (:start . 22) (:id . 47))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 38) (:start . 34)\n (:id . 48))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 43) (:start . 39)\n (:id . 49))\n ((:tag . "RB") (:stem . "independently") (:form . "independently")\n (:end . 57) (:start . 44) (:id . 50))\n ((:tag . "VBN") (:stem . "validate") (:form . "validated") (:end . 67)\n (:start . 58) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 70) (:start . 68)\n (:id . 52))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 82)\n (:start . 71) (:id . 53))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 89)\n (:start . 83) (:id . 54))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 97)\n (:start . 90) (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 102) (:start . 98)\n (:id . 56))\n ((:tag . "RB") (:stem . "experimentally") (:form . "experimentally")\n (:end . 117) (:start . 103) (:id . 57))\n ((:tag . "VBN") (:stem . "investigate") (:form . "investigated") (:end . 130)\n (:start . 118) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n (:id . 59))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 144)\n (:start . 135) (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 149) (:start . 145)\n (:id . 61))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 155)\n (:start . 150) (:id . 62))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 163)\n (:start . 156) (:id . 63))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 169)\n (:start . 164) (:id . 64))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 172) (:start . 170)\n (:id . 65))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 181)\n (:start . 173) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.323) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100659@unknown@formal@none@1@S@Additionally, some proteins were not recovered in the conversion between different identifiers.@(((:tag . "RB") (:stem . "additionally") (:form . "Additionally") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 43))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 27)\n (:start . 19) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 32) (:start . 28)\n (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 36) (:start . 33)\n (:id . 47))\n ((:tag . "VBN") (:stem . "recover") (:form . "recovered") (:end . 46)\n (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n (:id . 50))\n ((:tag . "NN") (:stem . "conversion") (:form . "conversion") (:end . 64)\n (:start . 54) (:id . 51))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 72)\n (:start . 65) (:id . 52))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 82)\n (:start . 73) (:id . 53))\n ((:tag . "NNS") (:stem . "identifier") (:form . "identifiers") (:end . 94)\n (:start . 83) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n (:id . 55)))@@@1@14@((:ncues ((:id . :x2.333.1) (:span 33 36)))\n (:nscopes ((:id . :x2.333.1) (:span 14 94)))\n (:identifiers (:sid . :s2.333) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100669@unknown@formal@none@1@S@In addition, positive to negative ratios of 1:1 and 1:100 were considered.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 21)\n (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 24) (:start . 22)\n (:id . 46))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 33)\n (:start . 25) (:id . 47))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 40)\n (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n (:id . 49))\n ((:tag . "CD") (:stem . "1:1") (:form . "1:1") (:end . 47) (:start . 44)\n (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n (:id . 51))\n ((:tag . "CD") (:stem . "1:100") (:form . "1:100") (:end . 57) (:start . 52)\n (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 62) (:start . 58)\n (:id . 53))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 73)\n (:start . 63) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.343) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100679@unknown@formal@none@1@S@The transparency of the method allows the straightforward determination of which features are most predictive of interaction at the level of the whole proteome as well as for individual protein pairs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "transparency") (:form . "transparency") (:end . 16)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 30)\n (:start . 24) (:id . 46))\n ((:tag . "VBZ") (:stem . "allow") (:form . "allows") (:end . 37)\n (:start . 31) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n (:id . 48))\n ((:tag . "JJ") (:stem . "straightforward") (:form . "straightforward")\n (:end . 57) (:start . 42) (:id . 49))\n ((:tag . "NN") (:stem . "determination") (:form . "determination")\n (:end . 71) (:start . 58) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 80) (:start . 75)\n (:id . 52))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 89)\n (:start . 81) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 93) (:start . 90)\n (:id . 54))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 98) (:start . 94)\n (:id . 55))\n ((:tag . "JJ") (:stem . "predictive") (:form . "predictive") (:end . 109)\n (:start . 99) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n (:id . 57))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 124)\n (:start . 113) (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 127) (:start . 125)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n (:id . 60))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 137)\n (:start . 132) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 140) (:start . 138)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n (:id . 63))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 150)\n (:start . 145) (:id . 64))\n ((:tag . "NN") (:stem . "proteome") (:form . "proteome") (:end . 159)\n (:start . 151) (:id . 65))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 162) (:start . 160)\n (:id . 66))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 167) (:start . 163)\n (:id . 67))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 170) (:start . 168)\n (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 174) (:start . 171)\n (:id . 69))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 185)\n (:start . 175) (:id . 70))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 193)\n (:start . 186) (:id . 71))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 199)\n (:start . 194) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s2.353) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100689@unknown@formal@none@1@S@When a particular state of a feature occurs only in positive examples (known interacting proteins), the likelihoods are set to the highest non-infinite value of any state for that feature (to avoid infinite values).@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 6) (:start . 5)\n (:id . 43))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 17)\n (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 23) (:start . 18)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "feature") (:form . "feature") (:end . 36)\n (:start . 29) (:id . 48))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 43)\n (:start . 37) (:id . 49))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 48) (:start . 44)\n (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n (:id . 51))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 60)\n (:start . 52) (:id . 52))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 69)\n (:start . 61) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n (:id . 54))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 76) (:start . 71)\n (:id . 55))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 88)\n (:start . 77) (:id . 56))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 97)\n (:start . 89) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n (:id . 60))\n ((:tag . "NNS") (:stem . "likelihood") (:form . "likelihoods") (:end . 115)\n (:start . 104) (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 119) (:start . 116)\n (:id . 62))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 123) (:start . 120)\n (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 126) (:start . 124)\n (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n (:id . 65))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 138)\n (:start . 131) (:id . 66))\n ((:tag . "JJ") (:stem . "non-infinite") (:form . "non-infinite") (:end . 151)\n (:start . 139) (:id . 67))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 157)\n (:start . 152) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 160) (:start . 158)\n (:id . 69))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 164) (:start . 161)\n (:id . 70))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 170)\n (:start . 165) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 174) (:start . 171)\n (:id . 72))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 179) (:start . 175)\n (:id . 73))\n ((:tag . "NN") (:stem . "feature") (:form . "feature") (:end . 187)\n (:start . 180) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 189) (:start . 188)\n (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 191) (:start . 189)\n (:id . 76))\n ((:tag . "VB") (:stem . "avoid") (:form . "avoid") (:end . 197)\n (:start . 192) (:id . 77))\n ((:tag . "JJ") (:stem . "infinite") (:form . "infinite") (:end . 206)\n (:start . 198) (:id . 78))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 213)\n (:start . 207) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 214) (:start . 213)\n (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n (:id . 81)))@@@1@40@((:identifiers (:sid . :s2.363) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100699@unknown@formal@none@1@S@Thus, between the two releases of the HPRD, there was a large increase in the number of interactions for this subset of proteins and this is likely to continue for at least the next few releases.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 13)\n (:start . 6) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 45))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 21) (:start . 18)\n (:id . 46))\n ((:tag . "NNS") (:stem . "release") (:form . "releases") (:end . 30)\n (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n (:id . 49))\n ((:tag . "NNP") (:stem . "HPRD") (:form . "HPRD") (:end . 42) (:start . 38)\n (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n (:id . 51))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 49) (:start . 44)\n (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 53) (:start . 50)\n (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 55) (:start . 54)\n (:id . 54))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 61) (:start . 56)\n (:id . 55))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 70)\n (:start . 62) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n (:id . 58))\n ((:tag . "NN") (:stem . 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".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n (:id . 80)))@@@1@39@((:hcues ((:id . :x2.373.1) (:span 141 147)))\n (:hscopes ((:id . :x2.373.1) (:span 133 194)))\n (:identifiers (:sid . :s2.373) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100709@unknown@formal@none@1@S@Pearson correlations were calculated for all 56620761 transcript pairs and correlation values were grouped into 20 bins of increasing co-expression.@(((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "correlation") (:form . "correlations") (:end . 20)\n (:start . 8) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 25) (:start . 21)\n (:id . 44))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 36)\n (:start . 26) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . 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"into") (:end . 111) (:start . 107)\n (:id . 56))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 114) (:start . 112)\n (:id . 57))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 119) (:start . 115)\n (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n (:id . 59))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 133)\n (:start . 123) (:id . 60))\n ((:tag . "NN") (:stem . "co-expression") (:form . "co-expression")\n (:end . 147) (:start . 134) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.383) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100719@unknown@formal@none@1@S@The orthology module has four additional bins: two bin for human pairs that have interacting paralogs in human (a medium and a low confidence bin which use the same definition as above for the model organisms), one bin for human pairs that have interacting homologs in more than one organism (these can be orthologs in yeast, worm or fly, or paralogs in human) and one bin for human pairs that have only non-interacting orthologs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "orthology") (:form . "orthology") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 20)\n (:start . 14) (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . 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"or") (:form . "or") (:end . 341) (:start . 339)\n (:id . 108))\n ((:tag . "NNS") (:stem . "paralog") (:form . "paralogs") (:end . 350)\n (:start . 342) (:id . 109))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 353) (:start . 351)\n (:id . 110))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 359)\n (:start . 354) (:id . 111))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 360) (:start . 359)\n (:id . 112))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 364) (:start . 361)\n (:id . 113))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 368) (:start . 365)\n (:id . 114))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 372) (:start . 369)\n (:id . 115))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 376) (:start . 373)\n (:id . 116))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 382)\n (:start . 377) (:id . 117))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 388)\n (:start . 383) (:id . 118))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 393) (:start . 389)\n (:id . 119))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 398) (:start . 394)\n (:id . 120))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 403) (:start . 399)\n (:id . 121))\n ((:tag . "JJ") (:stem . "non-interacting") (:form . "non-interacting")\n (:end . 419) (:start . 404) (:id . 122))\n ((:tag . "NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 429)\n (:start . 420) (:id . 123))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 430) (:start . 429)\n (:id . 124)))@@@1@83@((:identifiers (:sid . :s2.393) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100729@unknown@formal@none@1@S@Additionally, Pfam 74 domain pairs known to interact from three-dimensional structures 75 were included in the highest Chi-square score bin.@(((:tag . "RB") (:stem . "additionally") (:form . "Additionally") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 18) (:start . 14)\n (:id . 44))\n ((:tag . "CD") (:stem . "74") (:form . "74") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 28)\n (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 34) (:start . 29)\n (:id . 47))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 40) (:start . 35)\n (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 43) (:start . 41)\n (:id . 49))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 52)\n (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 57) (:start . 53)\n (:id . 51))\n ((:tag . "JJ") (:stem . "three-dimensional") (:form . "three-dimensional")\n (:end . 75) (:start . 58) (:id . 52))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 86)\n (:start . 76) (:id . 53))\n ((:tag . "CD") (:stem . "75") (:form . "75") (:end . 89) (:start . 87)\n (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 94) (:start . 90)\n (:id . 55))\n ((:tag . "VBN") (:stem . "include") (:form . "included") (:end . 103)\n (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n (:id . 58))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 118)\n (:start . 111) (:id . 59))\n ((:tag . "JJ") (:stem . "chi-square") (:form . "Chi-square") (:end . 129)\n (:start . 119) (:id . 60))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 135)\n (:start . 130) (:id . 61))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 139) (:start . 136)\n (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s2.403) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100739@unknown@formal@none@1@S@Disorder module@(((:tag . "NN") (:stem . "disorder") (:form . "Disorder") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 15) (:start . 9)\n (:id . 43)))@@@1@2@((:identifiers (:sid . :s2.413) (:did . :1471-2105-8-239)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100749@unknown@formal@none@1@S@It does this by considering the local topology of the network predicted by the integration of the Group A modules as depicted in Figure 2.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "do") (:form . 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(:end . 245) (:start . 244)\n (:id . 81)))@@@1@40@((:hcues ((:id . :x3.29.1) (:span 5 13)))\n (:hscopes ((:id . :x3.29.1) (:span 5 107)))\n (:identifiers (:sid . :s3.29) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100819@unknown@formal@none@1@S@Ensemble methods, well known in the machine learning community 9, are typically composed of multiple methods comprising different search strategies (or the same search strategies with different initiation settings or random restarts) with a unified objective function.@(((:tag . "JJ") (:stem . "ensemble") (:form . "Ensemble") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 16)\n (:start . 9) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 44))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 22) (:start . 18)\n (:id . 45))\n ((:tag . "VBN") (:stem . 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(:end . 268) (:start . 267)\n (:id . 83)))@@@1@42@((:identifiers (:sid . :s3.39) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100829@unknown@formal@none@1@S@Rather than randomly restarting the same search algorithm or comparing multiple search strategies that all search for the same global optimum (and are potentially vulnerable to the same local optima), our algorithm assumes that the ""biological significance surface"" primarily consists of three local optima, and that one of these peaks represents the global optimum.@(((:tag . "RB") (:stem . "rather") (:form . "Rather") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 11) (:start . 7)\n (:id . 43))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 20)\n (:start . 12) (:id . 44))\n ((:tag . "VBG") (:stem . "restart") (:form . "restarting") (:end . 31)\n (:start . 21) (:id . 45))\n ((:tag . 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"algorithm") (:end . 214)\n (:start . 205) (:id . 76))\n ((:tag . "VBZ") (:stem . "assume") (:form . "assumes") (:end . 222)\n (:start . 215) (:id . 77))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 227) (:start . 223)\n (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 231) (:start . 228)\n (:id . 79))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 233) (:start . 232)\n (:id . 80))\n ((:tag . "JJ") (:stem . "”biological") (:form . "”biological") (:end . 244)\n (:start . 233) (:id . 81))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 257)\n (:start . 245) (:id . 82))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 265)\n (:start . 258) (:id . 83))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 266) (:start . 265)\n (:id . 84))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 267) (:start . 266)\n (:id . 85))\n ((:tag . "RB") (:stem . "primarily") (:form . "primarily") (:end . 277)\n (:start . 268) (:id . 86))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 286)\n (:start . 278) (:id . 87))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 289) (:start . 287)\n (:id . 88))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 295)\n (:start . 290) (:id . 89))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 301)\n (:start . 296) (:id . 90))\n ((:tag . "NNS") (:stem . "optimum") (:form . "optima") (:end . 308)\n (:start . 302) (:id . 91))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 309) (:start . 308)\n (:id . 92))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 313) (:start . 310)\n (:id . 93))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 318) (:start . 314)\n (:id . 94))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 322) (:start . 319)\n (:id . 95))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 325) (:start . 323)\n (:id . 96))\n ((:tag . 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(:end . 368) (:start . 367)\n (:id . 103)))@@@1@62@((:hcues ((:id . :x3.49.1) (:span 215 222)) ((:id . :x3.49.2) (:span 151 162))\n ((:id . :x3.49.3) (:span 58 60)))\n (:ncues ((:id . :x3.49.4) (:span 0 11)))\n (:hscopes ((:id . :x3.49.1) (:span 215 367))\n ((:id . :x3.49.2) (:span 151 173)) ((:id . :x3.49.3) (:span 12 199)))\n (:nscopes ((:id . :x3.49.4) (:span 0 199)))\n (:identifiers (:sid . :s3.49) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100839@unknown@formal@none@1@S@The ultimate goal of a motif finder is to identify the specific subsequences Û in U that act as binding sites for the transcription factor(s) that regulate G.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "ultimate") (:form . "ultimate") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "goal") (:form . 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"transcription")\n (:end . 131) (:start . 118) (:id . 65))\n ((:tag . "NN") (:stem . "factor(s)") (:form . "factor(s)") (:end . 141)\n (:start . 132) (:id . 66))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 146) (:start . 142)\n (:id . 67))\n ((:tag . "VBP") (:stem . "regulate") (:form . "regulate") (:end . 155)\n (:start . 147) (:id . 68))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 157) (:start . 156)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s3.59) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100849@unknown@formal@none@1@S@BEAM and SPACER are run independently; PRISM runs on the top 100 motifs output by BEAM.@(((:tag . "NN") (:stem . "beam") (:form . "BEAM") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "NNP") (:stem . "SPACER") (:form . "SPACER") (:end . 15)\n (:start . 9) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "VBN") (:stem . "run") (:form . "run") (:end . 23) (:start . 20)\n (:id . 46))\n ((:tag . "RB") (:stem . "independently") (:form . "independently")\n (:end . 37) (:start . 24) (:id . 47))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 38) (:start . 37)\n (:id . 48))\n ((:tag . "NN") (:stem . "prism") (:form . "PRISM") (:end . 44) (:start . 39)\n (:id . 49))\n ((:tag . "VBZ") (:stem . "run") (:form . "runs") (:end . 49) (:start . 45)\n (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 52) (:start . 50)\n (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n (:id . 52))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 60) (:start . 57)\n (:id . 53))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 64) (:start . 61)\n (:id . 54))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 71)\n (:start . 65) (:id . 55))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 78)\n (:start . 72) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 81) (:start . 79)\n (:id . 57))\n ((:tag . "NNP") (:stem . "BEAM") (:form . "BEAM") (:end . 86) (:start . 82)\n (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.69) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100859@unknown@formal@none@1@S@In general, we seek to maximize -log(p(M = m)).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 14) (:start . 12)\n (:id . 45))\n ((:tag . "VBP") (:stem . "seek") (:form . "seek") (:end . 19) (:start . 15)\n (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 22) (:start . 20)\n (:id . 47))\n ((:tag . "VB") (:stem . "maximize") (:form . "maximize") (:end . 31)\n (:start . 23) (:id . 48))\n ((:tag . "JJ") (:stem . "-log(p(M") (:form . "-log(p(M") (:end . 40)\n (:start . 32) (:id . 49))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 42) (:start . 41)\n (:id . 50))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 44) (:start . 43)\n (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 46) (:start . 45)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 47) (:start . 46)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.79) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100869@unknown@formal@none@1@S@In contrast, we have proposed that all characters should not be treated equally, but should be penalized in proportion to the information provided by them 1112.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 20) (:start . 16)\n (:id . 46))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 29)\n (:start . 21) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . 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"be") (:form . "be") (:end . 94) (:start . 92)\n (:id . 59))\n ((:tag . "VBN") (:stem . "penalize") (:form . "penalized") (:end . 104)\n (:start . 95) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n (:id . 61))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 118)\n (:start . 108) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 121) (:start . 119)\n (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n (:id . 64))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 137)\n (:start . 126) (:id . 65))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 146)\n (:start . 138) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 149) (:start . 147)\n (:id . 67))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 154) (:start . 150)\n (:id . 68))\n ((:tag . "CD") (:stem . "1112") (:form . "1112") (:end . 159) (:start . 155)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x3.89.1) (:span 85 91)) ((:id . :x3.89.2) (:span 50 56))\n ((:id . :x3.89.4) (:span 21 29)))\n (:ncues ((:id . :x3.89.3) (:span 57 60)))\n (:hscopes ((:id . :x3.89.1) (:span 85 154)) ((:id . :x3.89.2) (:span 35 79))\n ((:id . :x3.89.4) (:span 21 154)))\n (:nscopes ((:id . :x3.89.3) (:span 35 79)))\n (:identifiers (:sid . :s3.89) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5100879@unknown@formal@none@1@S@These objective functions were as follows: position bias (based on the Kolmogorov-Smirnov, or KS, statistic), overrepresentation (a Poisson-based measure based on how often a motif occurs in U) and coverage (a Poisson-based measure based on how many upstream sequences contain the motif).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 15)\n (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 25)\n (:start . 16) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 30) (:start . 26)\n (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 33) (:start . 31)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 41)\n (:start . 34) (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 42) (:start . 41)\n (:id . 48))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 51)\n (:start . 43) (:id . 49))\n ((:tag . "NN") (:stem . "bias") (:form . "bias") (:end . 56) (:start . 52)\n (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n (:id . 51))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 63) (:start . 58)\n (:id . 52))\n ((:tag . "IN") (:stem . 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(:end . 197) (:start . 196)\n (:id . 78)))@@@1@37@((:identifiers (:sid . :s3.109) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100899@unknown@formal@none@1@S@We used the overrepresentation objective function for the other species, as our upstream definitions for those species were of variable length due to the available annotations.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n (:id . 44))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n (:end . 30) (:start . 12) (:id . 45))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 40)\n (:start . 31) (:id . 46))\n ((:tag . "NN") (:stem . "function") (:form . 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(:end . 342) (:start . 341)\n (:id . 104)))@@@1@63@((:hcues ((:id . :x3.159.1) (:span 14 17)))\n (:hscopes ((:id . :x3.159.1) (:span 14 33)))\n (:identifiers (:sid . :s3.159) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100949@unknown@formal@none@1@S@Motif model abbreviations: cons = consensus; PWM = position weight matrix; mis = consensus with predefined number of allowed non-position-specific mismatches.@(((:tag . "NN") (:stem . "motif") (:form . "Motif") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "NNS") (:stem . "abbreviation") (:form . "abbreviations")\n (:end . 25) (:start . 12) (:id . 44))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 26) (:start . 25)\n (:id . 45))\n ((:tag . "NNS") (:stem . "con") (:form . "cons") (:end . 31) (:start . 27)\n (:id . 46))\n ((:tag . "SYM") (:stem . "=") (:form . 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(:end . 158) (:start . 157)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.169) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100959@unknown@formal@none@1@S@Performance comparisons@(((:tag . "NNP") (:stem . "Performance") (:form . "Performance") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 23)\n (:start . 12) (:id . 43)))@@@1@2@((:identifiers (:sid . :s3.179) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|FigureLegend|)))@oe@9-2-2011 5100969@unknown@formal@none@1@S@By these measures, SCOPE was the only program that scored highly in both sensitivity and PPV (ranking first and second respectively).@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . 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"respectively") (:end . 131)\n (:start . 119) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 132) (:start . 131)\n (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.189) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100979@unknown@formal@none@1@S@Therefore, sets of genes identified from co-expression data may often contain multiple extraneous upstream sequences.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n (:id . 43))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n (:id . 45))\n ((:tag . "NNS") (:stem . "gene") (:form . 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"upstream") (:end . 106)\n (:start . 98) (:id . 56))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 116)\n (:start . 107) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n (:id . 58)))@@@1@17@((:hcues ((:id . :x3.199.1) (:span 60 63)))\n (:hscopes ((:id . :x3.199.1) (:span 60 116)))\n (:identifiers (:sid . :s3.199) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100989@unknown@formal@none@1@S@Increasing quantities of randomly selected upstream regions were added to each regulon.@(((:tag . "VBG") (:stem . "increase") (:form . "Increasing") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "quantity") (:form . "quantities") (:end . 21)\n (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n (:id . 44))\n ((:tag . "RB") (:stem . "randomly") (:form . 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(:end . 87) (:start . 86)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.209) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5100999@unknown@formal@none@1@S@Conversely, the PWM-based methods have an apparently more powerful motif model 17, but their search strategies cannot guarantee optimality and often terminate at local optima.@(((:tag . "RB") (:stem . "conversely") (:form . "Conversely") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "JJ") (:stem . "pwm-based") (:form . "PWM-based") (:end . 25)\n (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 33)\n (:start . 26) (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 38) (:start . 34)\n (:id . 47))\n ((:tag . 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"search") (:end . 99)\n (:start . 93) (:id . 58))\n ((:tag . "NNS") (:stem . "strategy") (:form . "strategies") (:end . 110)\n (:start . 100) (:id . 59))\n ((:tag . "JJ") (:stem . "cannot") (:form . "cannot") (:end . 117)\n (:start . 111) (:id . 60))\n ((:tag . "VB") (:stem . "guarantee") (:form . "guarantee") (:end . 127)\n (:start . 118) (:id . 61))\n ((:tag . "NN") (:stem . "optimality") (:form . "optimality") (:end . 138)\n (:start . 128) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n (:id . 63))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 148)\n (:start . 143) (:id . 64))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 158)\n (:start . 149) (:id . 65))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 161) (:start . 159)\n (:id . 66))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 167)\n (:start . 162) (:id . 67))\n ((:tag . "NNS") (:stem . "optimum") (:form . "optima") (:end . 174)\n (:start . 168) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n (:id . 69)))@@@1@28@((:ncues ((:id . :x3.219.1) (:span 111 117)))\n (:nscopes ((:id . :x3.219.1) (:span 111 138)))\n (:identifiers (:sid . :s3.219) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101009@unknown@formal@none@1@S@In this light, SCOPE can be seen as leveraging the second key observation by embracing the No Free Lunch Theorem:: rather than boost average performance by taking the average results of three general purpose algorithms, SCOPE uses highly specialized algorithms and assumes each will perform strongly on some regulons and weakly on others (and that the unified scoring metric can tell the difference).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . 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(:end . 400) (:start . 399)\n (:id . 111)))@@@1@70@((:hcues ((:id . :x3.229.1) (:span 265 272))\n ((:id . :x3.229.3) (:span 21 24)))\n (:ncues ((:id . :x3.229.2) (:span 115 126)))\n (:hscopes ((:id . :x3.229.1) (:span 265 399))\n ((:id . :x3.229.3) (:span 15 112)))\n (:nscopes ((:id . :x3.229.2) (:span 115 218)))\n (:identifiers (:sid . :s3.229) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101019@unknown@formal@none@1@S@This observation could be leveraged by a search algorithm that explicitly searches for motifs matching this unique structure.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 16)\n (:start . 5) (:id . 43))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 22) (:start . 17)\n (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . 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"motifs") (:end . 93)\n (:start . 87) (:id . 55))\n ((:tag . "VBG") (:stem . "match") (:form . "matching") (:end . 102)\n (:start . 94) (:id . 56))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 107) (:start . 103)\n (:id . 57))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 114)\n (:start . 108) (:id . 58))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 124)\n (:start . 115) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n (:id . 60)))@@@1@19@((:hcues ((:id . :x3.239.1) (:span 17 22)))\n (:hscopes ((:id . :x3.239.1) (:span 17 124)))\n (:identifiers (:sid . :s3.239) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101029@unknown@formal@none@1@S@An important factor to consider when taking the best of multiple runs is the relative size of the search space.@(((:tag . "DT") (:stem . "an") (:form . 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"NNS") (:stem . "run") (:form . "runs") (:end . 69) (:start . 65)\n (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 72) (:start . 70)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n (:id . 55))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 85)\n (:start . 77) (:id . 56))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 90) (:start . 86)\n (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n (:id . 59))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 104)\n (:start . 98) (:id . 60))\n ((:tag . "NN") (:stem . "space") (:form . "space") (:end . 110)\n (:start . 105) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.249) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101039@unknown@formal@none@1@S@Whereas previous performance comparisons attempt to optimize the parameters of the programs in question 467 or allow expert users to tune their own programs and manually filter both the input and output 5 we intentionally made our comparisons between programs without manually optimizing any parameters for any species so as to emulate typical use conditions.@(((:tag . "IN") (:stem . "whereas") (:form . "Whereas") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 16)\n (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 28)\n (:start . 17) (:id . 44))\n ((:tag . "NNS") (:stem . "comparison") (:form . 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"RB") (:stem . "intentionally") (:form . "intentionally")\n (:end . 221) (:start . 208) (:id . 76))\n ((:tag . "VBD") (:stem . "make") (:form . "made") (:end . 226) (:start . 222)\n (:id . 77))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 230) (:start . 227)\n (:id . 78))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 242)\n (:start . 231) (:id . 79))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 250)\n (:start . 243) (:id . 80))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 259)\n (:start . 251) (:id . 81))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 267)\n (:start . 260) (:id . 82))\n ((:tag . "RB") (:stem . "manually") (:form . "manually") (:end . 276)\n (:start . 268) (:id . 83))\n ((:tag . "VBG") (:stem . "optimize") (:form . "optimizing") (:end . 287)\n (:start . 277) (:id . 84))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 291) (:start . 288)\n (:id . 85))\n ((:tag . 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"conditions") (:end . 358)\n (:start . 348) (:id . 96))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 359) (:start . 358)\n (:id . 97)))@@@1@56@((:ncues ((:id . :x3.259.1) (:span 260 267)))\n (:nscopes ((:id . :x3.259.1) (:span 260 358)))\n (:identifiers (:sid . :s3.259) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101049@unknown@formal@none@1@S@Whereas a background set of promoter regions is easy to identify, it is not clear how to define a reasonable genomic sample of enhancers.@(((:tag . "IN") (:stem . "whereas") (:form . "Whereas") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 9) (:start . 8)\n (:id . 43))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 20)\n (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 24) (:start . 21)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n (:id . 46))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 36)\n (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 44)\n (:start . 37) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 47) (:start . 45)\n (:id . 49))\n ((:tag . "JJ") (:stem . "easy") (:form . "easy") (:end . 52) (:start . 48)\n (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 55) (:start . 53)\n (:id . 51))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 64)\n (:start . 56) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n (:id . 53))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 68) (:start . 66)\n (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 71) (:start . 69)\n (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 75) (:start . 72)\n (:id . 56))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 81) (:start . 76)\n (:id . 57))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 85) (:start . 82)\n (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n (:id . 59))\n ((:tag . "VB") (:stem . "define") (:form . "define") (:end . 95)\n (:start . 89) (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 97) (:start . 96)\n (:id . 61))\n ((:tag . "JJ") (:stem . "reasonable") (:form . "reasonable") (:end . 108)\n (:start . 98) (:id . 62))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 116)\n (:start . 109) (:id . 63))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 123)\n (:start . 117) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n (:id . 65))\n ((:tag . "NNS") (:stem . "enhancer") (:form . "enhancers") (:end . 136)\n (:start . 127) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n (:id . 67)))@@@1@26@((:hcues ((:id . :x3.269.1) (:span 72 81)))\n (:hscopes ((:id . :x3.269.1) (:span 72 136)))\n (:identifiers (:sid . :s3.269) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101059@unknown@formal@none@1@S@By dividing the search space into tractable domains, SCOPE mitigates the potential liabilities associated with ensemble methods, resulting in a program that is capable of finding cis-regulatory elements of arbitrary length, degree of degeneracy, motif orientation and frequency of occurrence.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBG") (:stem . "divide") (:form . "dividing") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 22)\n (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "space") (:form . "space") (:end . 28) (:start . 23)\n (:id . 46))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 33) (:start . 29)\n (:id . 47))\n ((:tag . "JJ") (:stem . "tractable") (:form . "tractable") (:end . 43)\n (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 51)\n (:start . 44) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n (:id . 50))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 58) (:start . 53)\n (:id . 51))\n ((:tag . "VBZ") (:stem . "mitigate") (:form . "mitigates") (:end . 68)\n (:start . 59) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n (:id . 53))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 82)\n (:start . 73) (:id . 54))\n ((:tag . "NNS") (:stem . "liability") (:form . "liabilities") (:end . 94)\n (:start . 83) (:id . 55))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 105)\n (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 110) (:start . 106)\n (:id . 57))\n ((:tag . "JJ") (:stem . "ensemble") (:form . "ensemble") (:end . 119)\n (:start . 111) (:id . 58))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 127)\n (:start . 120) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n (:id . 60))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 138)\n (:start . 129) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 141) (:start . 139)\n (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 143) (:start . 142)\n (:id . 63))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 151)\n (:start . 144) (:id . 64))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 156) (:start . 152)\n (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 159) (:start . 157)\n (:id . 66))\n ((:tag . "JJ") (:stem . "capable") (:form . "capable") (:end . 167)\n (:start . 160) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 170) (:start . 168)\n (:id . 68))\n ((:tag . "VBG") (:stem . "find") (:form . "finding") (:end . 178)\n (:start . 171) (:id . 69))\n ((:tag . "JJ") (:stem . "cis-regulatory") (:form . "cis-regulatory")\n (:end . 193) (:start . 179) (:id . 70))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 202)\n (:start . 194) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 205) (:start . 203)\n (:id . 72))\n ((:tag . "JJ") (:stem . "arbitrary") (:form . "arbitrary") (:end . 215)\n (:start . 206) (:id . 73))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 222)\n (:start . 216) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 223) (:start . 222)\n (:id . 75))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 230)\n (:start . 224) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 233) (:start . 231)\n (:id . 77))\n ((:tag . "NN") (:stem . "degeneracy") (:form . "degeneracy") (:end . 244)\n (:start . 234) (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 245) (:start . 244)\n (:id . 79))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 251)\n (:start . 246) (:id . 80))\n ((:tag . "NN") (:stem . "orientation") (:form . "orientation") (:end . 263)\n (:start . 252) (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 267) (:start . 264)\n (:id . 82))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 277)\n (:start . 268) (:id . 83))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 280) (:start . 278)\n (:id . 84))\n ((:tag . "NN") (:stem . "occurrence") (:form . "occurrence") (:end . 291)\n (:start . 281) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 292) (:start . 291)\n (:id . 86)))@@@1@45@((:identifiers (:sid . :s3.279) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101069@unknown@formal@none@1@S@As in Hu et al. 4, we define accuracy to be the Phi score between the known and predicted binding sites.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 5) (:start . 3)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Hu") (:form . "Hu") (:end . 8) (:start . 6)\n (:id . 44))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 11) (:start . 9)\n (:id . 45))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 15) (:start . 12)\n (:id . 46))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 17) (:start . 16)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 21) (:start . 19)\n (:id . 49))\n ((:tag . "VBP") (:stem . "define") (:form . "define") (:end . 28)\n (:start . 22) (:id . 50))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 37)\n (:start . 29) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 43) (:start . 41)\n (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n (:id . 54))\n ((:tag . "NNP") (:stem . "Phi") (:form . "Phi") (:end . 51) (:start . 48)\n (:id . 55))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 57) (:start . 52)\n (:id . 56))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 65)\n (:start . 58) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n (:id . 58))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 75) (:start . 70)\n (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 79) (:start . 76)\n (:id . 60))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 89)\n (:start . 80) (:id . 61))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 97)\n (:start . 90) (:id . 62))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 103) (:start . 98)\n (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.289) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101079@unknown@formal@none@1@S@The most common statistical test in motif finding is based on overrepresentation, which can be roughly defined as the probability that a motif m that is observed C(m) times in the regulon would occur at least C(m) times in a random collection of the same number of genes.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 15) (:start . 9)\n (:id . 44))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 27)\n (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 32) (:start . 28)\n (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n (:id . 47))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 41) (:start . 36)\n (:id . 48))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 49)\n (:start . 42) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 52) (:start . 50)\n (:id . 50))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 58) (:start . 53)\n (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 61) (:start . 59)\n (:id . 52))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n (:end . 80) (:start . 62) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n (:id . 54))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 87) (:start . 82)\n (:id . 55))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 91) (:start . 88)\n (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 94) (:start . 92)\n (:id . 57))\n ((:tag . "RB") (:stem . "roughly") (:form . "roughly") (:end . 102)\n (:start . 95) (:id . 58))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 110)\n (:start . 103) (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 113) (:start . 111)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n (:id . 61))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 129)\n (:start . 118) (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 134) (:start . 130)\n (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 136) (:start . 135)\n (:id . 64))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 142)\n (:start . 137) (:id . 65))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 144) (:start . 143)\n (:id . 66))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 149) (:start . 145)\n (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 152) (:start . 150)\n (:id . 68))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 161)\n (:start . 153) (:id . 69))\n ((:tag . "JJ") (:stem . "C(m)") (:form . "C(m)") (:end . 166) (:start . 162)\n (:id . 70))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 172)\n (:start . 167) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 175) (:start . 173)\n (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n (:id . 73))\n ((:tag . "NN") (:stem . "regulon") (:form . "regulon") (:end . 187)\n (:start . 180) (:id . 74))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 193)\n (:start . 188) (:id . 75))\n ((:tag . "VB") (:stem . "occur") (:form . "occur") (:end . 199)\n (:start . 194) (:id . 76))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 202) (:start . 200)\n (:id . 77))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 208)\n (:start . 203) (:id . 78))\n ((:tag . "CD") (:stem . "C(m)") (:form . "C(m)") (:end . 213) (:start . 209)\n (:id . 79))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 219)\n (:start . 214) (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 222) (:start . 220)\n (:id . 81))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 224) (:start . 223)\n (:id . 82))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 231)\n (:start . 225) (:id . 83))\n ((:tag . "NN") (:stem . "collection") (:form . "collection") (:end . 242)\n (:start . 232) (:id . 84))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 245) (:start . 243)\n (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 249) (:start . 246)\n (:id . 86))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 254) (:start . 250)\n (:id . 87))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 261)\n (:start . 255) (:id . 88))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 264) (:start . 262)\n (:id . 89))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 270)\n (:start . 265) (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 271) (:start . 270)\n (:id . 91)))@@@1@50@((:identifiers (:sid . :s3.299) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101089@unknown@formal@none@1@S@Transcription factors often require their binding sites to be located in a restricted range relative to the start of transcription.@(((:tag . "NNP") (:stem . "Transcription") (:form . "Transcription")\n (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 21)\n (:start . 14) (:id . 43))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 27) (:start . 22)\n (:id . 44))\n ((:tag . "VBP") (:stem . "require") (:form . "require") (:end . 35)\n (:start . 28) (:id . 45))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 41)\n (:start . 36) (:id . 46))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 49)\n (:start . 42) (:id . 47))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 55) (:start . 50)\n (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 61) (:start . 59)\n (:id . 50))\n ((:tag . "VBN") (:stem . "locate") (:form . "located") (:end . 69)\n (:start . 62) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 74) (:start . 73)\n (:id . 53))\n ((:tag . "JJ") (:stem . "restricted") (:form . "restricted") (:end . 85)\n (:start . 75) (:id . 54))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 91) (:start . 86)\n (:id . 55))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 100)\n (:start . 92) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 103) (:start . 101)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n (:id . 58))\n ((:tag . "NN") (:stem . "start") (:form . "start") (:end . 113)\n (:start . 108) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n (:id . 60))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n (:end . 130) (:start . 117) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.309) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101099@unknown@formal@none@1@S@The reference sample Y is defined as the set of starting positions of m in all upstream regions in the genome.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 20)\n (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "y") (:form . "Y") (:end . 22) (:start . 21)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n (:id . 46))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 33)\n (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 36) (:start . 34)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n (:id . 49))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 44) (:start . 41)\n (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n (:id . 51))\n ((:tag . "VBG") (:stem . "start") (:form . "starting") (:end . 56)\n (:start . 48) (:id . 52))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 66)\n (:start . 57) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n (:id . 54))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 71) (:start . 70)\n (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 78) (:start . 75)\n (:id . 57))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 87)\n (:start . 79) (:id . 58))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 95)\n (:start . 88) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n (:id . 61))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 109)\n (:start . 103) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.319) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101109@unknown@formal@none@1@S@Such an assumption may be overly generous – as the TBP example above makes clear, the transcriptional machinery of a cell is clearly able to differentiate between the two strands.@(((:tag . "PDT") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "assumption") (:form . "assumption") (:end . 18)\n (:start . 8) (:id . 44))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 22) (:start . 19)\n (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 25) (:start . 23)\n (:id . 46))\n ((:tag . "RB") (:stem . "overly") (:form . "overly") (:end . 32)\n (:start . 26) (:id . 47))\n ((:tag . "JJ") (:stem . "generous") (:form . "generous") (:end . 41)\n (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "–") (:form . "–") (:end . 43) (:start . 42)\n (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 46) (:start . 44)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n (:id . 51))\n ((:tag . "NNP") (:stem . "TBP") (:form . "TBP") (:end . 54) (:start . 51)\n (:id . 52))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 62)\n (:start . 55) (:id . 53))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 68) (:start . 63)\n (:id . 54))\n ((:tag . "VBZ") (:stem . "make") (:form . "makes") (:end . 74) (:start . 69)\n (:id . 55))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 80) (:start . 75)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n (:id . 58))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n (:end . 101) (:start . 86) (:id . 59))\n ((:tag . "NN") (:stem . "machinery") (:form . "machinery") (:end . 111)\n (:start . 102) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 116) (:start . 115)\n (:id . 62))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 121) (:start . 117)\n (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 124) (:start . 122)\n (:id . 64))\n ((:tag . "RB") (:stem . "clearly") (:form . "clearly") (:end . 132)\n (:start . 125) (:id . 65))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 137) (:start . 133)\n (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 140) (:start . 138)\n (:id . 67))\n ((:tag . "VB") (:stem . "differentiate") (:form . "differentiate")\n (:end . 154) (:start . 141) (:id . 68))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 162)\n (:start . 155) (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n (:id . 70))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 170) (:start . 167)\n (:id . 71))\n ((:tag . "NNS") (:stem . "strand") (:form . "strands") (:end . 178)\n (:start . 171) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n (:id . 73)))@@@1@32@((:hcues ((:id . :x3.329.1) (:span 19 22)))\n (:hscopes ((:id . :x3.329.1) (:span 19 41)))\n (:identifiers (:sid . :s3.329) (:did . :1471-2105-8-249)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101119@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.7) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101129@unknown@formal@none@1@S@One way to understand a protein's function is to look at its composition of conserved domains.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 10) (:start . 8)\n (:id . 44))\n ((:tag . "VB") (:stem . "understand") (:form . "understand") (:end . 21)\n (:start . 11) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 31)\n (:start . 24) (:id . 47))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 33) (:start . 31)\n (:id . 48))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 42)\n (:start . 34) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 45) (:start . 43)\n (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n (:id . 51))\n ((:tag . "VB") (:stem . "look") (:form . "look") (:end . 53) (:start . 49)\n (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 56) (:start . 54)\n (:id . 53))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 60) (:start . 57)\n (:id . 54))\n ((:tag . "NN") (:stem . "composition") (:form . "composition") (:end . 72)\n (:start . 61) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n (:id . 56))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 85)\n (:start . 76) (:id . 57))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 93)\n (:start . 86) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.17) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101139@unknown@formal@none@1@S@The structural evidence lends strong support to the inferred domain pair, resulting in a high confidence set of domain pairs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 23)\n (:start . 15) (:id . 44))\n ((:tag . "VBZ") (:stem . "lend") (:form . "lends") (:end . 29) (:start . 24)\n (:id . 45))\n ((:tag . "JJ") (:stem . "strong") (:form . "strong") (:end . 36)\n (:start . 30) (:id . 46))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 44)\n (:start . 37) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n (:id . 49))\n ((:tag . "JJ") (:stem . "inferred") (:form . "inferred") (:end . 60)\n (:start . 52) (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 67)\n (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 72) (:start . 68)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n (:id . 53))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 83)\n (:start . 74) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 88) (:start . 87)\n (:id . 56))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 93) (:start . 89)\n (:id . 57))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 104)\n (:start . 94) (:id . 58))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 108) (:start . 105)\n (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n (:id . 60))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 118)\n (:start . 112) (:id . 61))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 124)\n (:start . 119) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n (:id . 63)))@@@1@22@((:hcues ((:id . :x4.27.1) (:span 52 60)) ((:id . :x4.27.2) (:span 24 44)))\n (:hscopes ((:id . :x4.27.1) (:span 52 72)) ((:id . :x4.27.2) (:span 24 72)))\n (:identifiers (:sid . :s4.27) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101149@unknown@formal@none@1@S@How conserved are domain–domain pairs between species, and how many interacting domain pairs are still unknown?@(((:tag . "WRB") (:stem . "how") (:form . "How") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "JJ") (:stem . "domain–domain") (:form . "domain–domain")\n (:end . 31) (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 37) (:start . 32)\n (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 45)\n (:start . 38) (:id . 47))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 53)\n (:start . 46) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n (:id . 50))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 62) (:start . 59)\n (:id . 51))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 67) (:start . 63)\n (:id . 52))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 79)\n (:start . 68) (:id . 53))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 86)\n (:start . 80) (:id . 54))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 92) (:start . 87)\n (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 96) (:start . 93)\n (:id . 56))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 102) (:start . 97)\n (:id . 57))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 110)\n (:start . 103) (:id . 58))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 111) (:start . 110)\n (:id . 59)))@@@1@18@((:hcues ((:id . :x4.37.1) (:span 103 110)))\n (:hscopes ((:id . :x4.37.1) (:span 59 110)))\n (:identifiers (:sid . :s4.37) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101159@unknown@formal@none@1@S@Given that 74% of all UniProt proteins contain at least one Pfam match, this is not by itself surprising.@(((:tag . "VBN") (:stem . "give") (:form . "Given") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "CD") (:stem . "74") (:form . "74") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 14) (:start . 13)\n (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n (:id . 46))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 21) (:start . 18)\n (:id . 47))\n ((:tag . "NNP") (:stem . "UniProt") (:form . "UniProt") (:end . 29)\n (:start . 22) (:id . 48))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 38)\n (:start . 30) (:id . 49))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 46)\n (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 49) (:start . 47)\n (:id . 51))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 55) (:start . 50)\n (:id . 52))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 59) (:start . 56)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 64) (:start . 60)\n (:id . 54))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 70) (:start . 65)\n (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n (:id . 56))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 76) (:start . 72)\n (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 79) (:start . 77)\n (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 83) (:start . 80)\n (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 86) (:start . 84)\n (:id . 60))\n ((:tag . "PRP") (:stem . "itself") (:form . "itself") (:end . 93)\n (:start . 87) (:id . 61))\n ((:tag . "JJ") (:stem . "surprising") (:form . "surprising") (:end . 104)\n (:start . 94) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n (:id . 63)))@@@1@22@((:ncues ((:id . :x4.47.1) (:span 80 83)))\n (:nscopes ((:id . :x4.47.1) (:span 80 104)))\n (:identifiers (:sid . :s4.47) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101169@unknown@formal@none@1@S@The relatively low iPfam coverage is by itself a disappointing finding.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 14)\n (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 18) (:start . 15)\n (:id . 44))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 24) (:start . 19)\n (:id . 45))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 33)\n (:start . 25) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 36) (:start . 34)\n (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 39) (:start . 37)\n (:id . 48))\n ((:tag . "PRP") (:stem . "itself") (:form . "itself") (:end . 46)\n (:start . 40) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n (:id . 50))\n ((:tag . "JJ") (:stem . "disappointing") (:form . "disappointing")\n (:end . 62) (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 70)\n (:start . 63) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s4.57) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101179@unknown@formal@none@1@S@In the following paragraph, we will call the experimental interactions that contain an iPfam domain pair the covered experimental interactions.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 16)\n (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "paragraph") (:form . "paragraph") (:end . 26)\n (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 30) (:start . 28)\n (:id . 47))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 35) (:start . 31)\n (:id . 48))\n ((:tag . "VB") (:stem . "call") (:form . "call") (:end . 40) (:start . 36)\n (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n (:id . 50))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 57)\n (:start . 45) (:id . 51))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 70)\n (:start . 58) (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 75) (:start . 71)\n (:id . 53))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 83)\n (:start . 76) (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 86) (:start . 84)\n (:id . 55))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 92) (:start . 87)\n (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 99)\n (:start . 93) (:id . 57))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 104) (:start . 100)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n (:id . 59))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 116)\n (:start . 109) (:id . 60))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 129)\n (:start . 117) (:id . 61))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 142)\n (:start . 130) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s4.67) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101189@unknown@formal@none@1@S@In both H. sapiens (blue) and S. cerevisiae (green) a small number of iPfam domain pairs covers a large fraction of the interactome, whereas in E. coli, no iPfam domain occurs in more than 4 experimental interactions at a time.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 10) (:start . 8)\n (:id . 44))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 18)\n (:start . 11) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 20) (:start . 19)\n (:id . 46))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 24) (:start . 20)\n (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 25) (:start . 24)\n (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 29) (:start . 26)\n (:id . 49))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 32) (:start . 30)\n (:id . 50))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 43)\n (:start . 33) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n (:id . 52))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 50) (:start . 45)\n (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 51) (:start . 50)\n (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n (:id . 55))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 59) (:start . 54)\n (:id . 56))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 66)\n (:start . 60) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n (:id . 58))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 75) (:start . 70)\n (:id . 59))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 82)\n (:start . 76) (:id . 60))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 88) (:start . 83)\n (:id . 61))\n ((:tag . "VBZ") (:stem . "cover") (:form . "covers") (:end . 95)\n (:start . 89) (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 97) (:start . 96)\n (:id . 63))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 103) (:start . 98)\n (:id . 64))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 112)\n (:start . 104) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n (:id . 67))\n ((:tag . "NN") (:stem . "interactome") (:form . "interactome") (:end . 131)\n (:start . 120) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n (:id . 69))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 140)\n (:start . 133) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 143) (:start . 141)\n (:id . 71))\n ((:tag . "NNP") (:stem . "E.") (:form . "E.") (:end . 146) (:start . 144)\n (:id . 72))\n ((:tag . "NNP") (:stem . "coli") (:form . "coli") (:end . 151) (:start . 147)\n (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n (:id . 74))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 155) (:start . 153)\n (:id . 75))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 161)\n (:start . 156) (:id . 76))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 168)\n (:start . 162) (:id . 77))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 175)\n (:start . 169) (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 178) (:start . 176)\n (:id . 79))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 183) (:start . 179)\n (:id . 80))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 188) (:start . 184)\n (:id . 81))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 190) (:start . 189)\n (:id . 82))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 203)\n (:start . 191) (:id . 83))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 216)\n (:start . 204) (:id . 84))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 219) (:start . 217)\n (:id . 85))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 221) (:start . 220)\n (:id . 86))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 226) (:start . 222)\n (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n (:id . 88)))@@@1@47@((:ncues ((:id . :x4.77.1) (:span 153 155)))\n (:nscopes ((:id . :x4.77.1) (:span 153 226)))\n (:identifiers (:sid . :s4.77) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101199@unknown@formal@none@1@S@We reasoned that if there are iPfam domain pairs that act as reusable modules in protein interactions, then highly connected proteins should also be more likely to contain promiscuous iPfam domain pairs and vice-versa.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "reason") (:form . "reasoned") (:end . 11)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n (:id . 44))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 19) (:start . 17)\n (:id . 45))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 25) (:start . 20)\n (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n (:id . 47))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 35) (:start . 30)\n (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 42)\n (:start . 36) (:id . 49))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 48) (:start . 43)\n (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 53) (:start . 49)\n (:id . 51))\n ((:tag . "VBP") (:stem . "act") (:form . "act") (:end . 57) (:start . 54)\n (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 60) (:start . 58)\n (:id . 53))\n ((:tag . "JJ") (:stem . "reusable") (:form . "reusable") (:end . 69)\n (:start . 61) (:id . 54))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 77)\n (:start . 70) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 88)\n (:start . 81) (:id . 57))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 101)\n (:start . 89) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n (:id . 59))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 107) (:start . 103)\n (:id . 60))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 114)\n (:start . 108) (:id . 61))\n ((:tag . "JJ") (:stem . "connected") (:form . "connected") (:end . 124)\n (:start . 115) (:id . 62))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 133)\n (:start . 125) (:id . 63))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 140)\n (:start . 134) (:id . 64))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 145) (:start . 141)\n (:id . 65))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 148) (:start . 146)\n (:id . 66))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 153) (:start . 149)\n (:id . 67))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 160)\n (:start . 154) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 163) (:start . 161)\n (:id . 69))\n ((:tag . "VB") (:stem . "contain") (:form . "contain") (:end . 171)\n (:start . 164) (:id . 70))\n ((:tag . "JJ") (:stem . "promiscuous") (:form . "promiscuous") (:end . 183)\n (:start . 172) (:id . 71))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 189)\n (:start . 184) (:id . 72))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 196)\n (:start . 190) (:id . 73))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 202)\n (:start . 197) (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 206) (:start . 203)\n (:id . 75))\n ((:tag . "NN") (:stem . "vice-versa") (:form . "vice-versa") (:end . 217)\n (:start . 207) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n (:id . 77)))@@@1@36@((:hcues ((:id . :x4.87.1) (:span 134 140 154 160))\n ((:id . :x4.87.3) (:span 3 11)))\n (:hscopes ((:id . :x4.87.1) (:span 108 217))\n ((:id . :x4.87.3) (:span 3 217)))\n (:identifiers (:sid . :s4.87) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101209@unknown@formal@none@1@S@The correlation is outlined by dotted lines.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n (:id . 44))\n ((:tag . "VBN") (:stem . "outline") (:form . "outlined") (:end . 27)\n (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "VBN") (:stem . "dot") (:form . "dotted") (:end . 37) (:start . 31)\n (:id . 47))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 43) (:start . 38)\n (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 44) (:start . 43)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s4.97) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101219@unknown@formal@none@1@S@Looking for example at the covered experimental interactions in H. sapiens(Additional file 1), only 8 out of the 100 most frequent iPfam domain pairs are seen in intrachain interactions exclusively, while 61 are exclusive to interchain interactions and 31 are seen in both.@(((:tag . "VBG") (:stem . "look") (:form . "Looking") (:end . 7) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 11) (:start . 8)\n (:id . 43))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 19)\n (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 22) (:start . 20)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 34)\n (:start . 27) (:id . 47))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 47)\n (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 60)\n (:start . 48) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n (:id . 50))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 66) (:start . 64)\n (:id . 51))\n ((:tag . "JJ") (:stem . "sapiens(Additional") (:form . "sapiens(Additional")\n (:end . 85) (:start . 67) (:id . 52))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 90) (:start . 86)\n (:id . 53))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 92) (:start . 91)\n (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n (:id . 56))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 99) (:start . 95)\n (:id . 57))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 101) (:start . 100)\n (:id . 58))\n ((:tag . "IN") (:stem . "out") (:form . "out") (:end . 105) (:start . 102)\n (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 108) (:start . 106)\n (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n (:id . 61))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 116) (:start . 113)\n (:id . 62))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 121) (:start . 117)\n (:id . 63))\n ((:tag . "JJ") (:stem . "frequent") (:form . "frequent") (:end . 130)\n (:start . 122) (:id . 64))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 136)\n (:start . 131) (:id . 65))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 143)\n (:start . 137) (:id . 66))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 149)\n (:start . 144) (:id . 67))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 153) (:start . 150)\n (:id . 68))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 158) (:start . 154)\n (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 161) (:start . 159)\n (:id . 70))\n ((:tag . "JJ") (:stem . "intrachain") (:form . "intrachain") (:end . 172)\n (:start . 162) (:id . 71))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 185)\n (:start . 173) (:id . 72))\n ((:tag . "RB") (:stem . "exclusively") (:form . "exclusively") (:end . 197)\n (:start . 186) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 198) (:start . 197)\n (:id . 74))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 204)\n (:start . 199) (:id . 75))\n ((:tag . "CD") (:stem . "61") (:form . "61") (:end . 207) (:start . 205)\n (:id . 76))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 211) (:start . 208)\n (:id . 77))\n ((:tag . "JJ") (:stem . "exclusive") (:form . "exclusive") (:end . 221)\n (:start . 212) (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 224) (:start . 222)\n (:id . 79))\n ((:tag . "VB") (:stem . "interchain") (:form . "interchain") (:end . 235)\n (:start . 225) (:id . 80))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 248)\n (:start . 236) (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 252) (:start . 249)\n (:id . 82))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 255) (:start . 253)\n (:id . 83))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 259) (:start . 256)\n (:id . 84))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 264) (:start . 260)\n (:id . 85))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 267) (:start . 265)\n (:id . 86))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 272) (:start . 268)\n (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 273) (:start . 272)\n (:id . 88)))@@@1@47@((:identifiers (:sid . :s4.107) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101229@unknown@formal@none@1@S@3671 out of a total of 5380 interacting protein pairs from the PDB contain an iPfam domain pair that does not interact in one complex structure but does so in another.@(((:tag . "CD") (:stem . "3671") (:form . "3671") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "out") (:form . "out") (:end . 8) (:start . 5)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n (:id . 45))\n ((:tag . "NN") (:stem . "total") (:form . "total") (:end . 19) (:start . 14)\n (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n (:id . 47))\n ((:tag . "CD") (:stem . "5380") (:form . "5380") (:end . 27) (:start . 23)\n (:id . 48))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 39)\n (:start . 28) (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 47)\n (:start . 40) (:id . 50))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 53) (:start . 48)\n (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 58) (:start . 54)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n (:id . 53))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 66) (:start . 63)\n (:id . 54))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 74)\n (:start . 67) (:id . 55))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 77) (:start . 75)\n (:id . 56))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 83) (:start . 78)\n (:id . 57))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 90)\n (:start . 84) (:id . 58))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 95) (:start . 91)\n (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 100) (:start . 96)\n (:id . 60))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 105) (:start . 101)\n (:id . 61))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 109) (:start . 106)\n (:id . 62))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 118)\n (:start . 110) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n (:id . 64))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 125) (:start . 122)\n (:id . 65))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 133)\n (:start . 126) (:id . 66))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 143)\n (:start . 134) (:id . 67))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 147) (:start . 144)\n (:id . 68))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 152) (:start . 148)\n (:id . 69))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 155) (:start . 153)\n (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 158) (:start . 156)\n (:id . 71))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 166)\n (:start . 159) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n (:id . 73)))@@@1@32@((:ncues ((:id . :x4.117.1) (:span 106 109)))\n (:nscopes ((:id . :x4.117.1) (:span 106 143)))\n (:identifiers (:sid . :s4.117) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101239@unknown@formal@none@1@S@We also analysed the full dataset of protein complexes.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "analyse") (:form . "analysed") (:end . 16)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 25) (:start . 21)\n (:id . 46))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 33)\n (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 44)\n (:start . 37) (:id . 49))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 54)\n (:start . 45) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 55) (:start . 54)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s4.127) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101249@unknown@formal@none@1@S@Within the 3 to 19% of experimental interactions covered by iPfam, we analysed the conservation of iPfam domain pairs between species.@(((:tag . "IN") (:stem . "within") (:form . "Within") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n (:id . 43))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 12) (:start . 11)\n (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "CD") (:stem . "19") (:form . "19") (:end . 18) (:start . 16)\n (:id . 46))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 19) (:start . 18)\n (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n (:id . 48))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 35)\n (:start . 23) (:id . 49))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 48)\n (:start . 36) (:id . 50))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 56)\n (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 59) (:start . 57)\n (:id . 52))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 65) (:start . 60)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n (:id . 54))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 69) (:start . 67)\n (:id . 55))\n ((:tag . "VBD") (:stem . "analyse") (:form . "analysed") (:end . 78)\n (:start . 70) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n (:id . 57))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 95)\n (:start . 83) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n (:id . 59))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 104) (:start . 99)\n (:id . 60))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 111)\n (:start . 105) (:id . 61))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 117)\n (:start . 112) (:id . 62))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 125)\n (:start . 118) (:id . 63))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 133)\n (:start . 126) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.137) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101259@unknown@formal@none@1@S@The iPfam domains in these pairs are related to housekeeping activities such as translation, replication or ATP synthesis.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 9) (:start . 4)\n (:id . 43))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 17)\n (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 20) (:start . 18)\n (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 26) (:start . 21)\n (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 32) (:start . 27)\n (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 36) (:start . 33)\n (:id . 48))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 44)\n (:start . 37) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n (:id . 50))\n ((:tag . "JJ") (:stem . "housekeeping") (:form . "housekeeping") (:end . 60)\n (:start . 48) (:id . 51))\n ((:tag . "NNS") (:stem . "activity") (:form . "activities") (:end . 71)\n (:start . 61) (:id . 52))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 76) (:start . 72)\n (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 79) (:start . 77)\n (:id . 54))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 91)\n (:start . 80) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n (:id . 56))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 104)\n (:start . 93) (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 107) (:start . 105)\n (:id . 58))\n ((:tag . "NNP") (:stem . "ATP") (:form . "ATP") (:end . 111) (:start . 108)\n (:id . 59))\n ((:tag . "NN") (:stem . "synthesis") (:form . "synthesis") (:end . 121)\n (:start . 112) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s4.147) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101269@unknown@formal@none@1@S@From these random results, we derive a P value of 3.6 · 10-30 that the observed correlation is random.@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 17)\n (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 25)\n (:start . 18) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 29) (:start . 27)\n (:id . 47))\n ((:tag . "VBP") (:stem . "derive") (:form . "derive") (:end . 36)\n (:start . 30) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n (:id . 49))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 40) (:start . 39)\n (:id . 50))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 46) (:start . 41)\n (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n (:id . 52))\n ((:tag . "CD") (:stem . "3.6") (:form . "3.6") (:end . 53) (:start . 50)\n (:id . 53))\n ((:tag . "NN") (:stem . "·") (:form . "·") (:end . 55) (:start . 54)\n (:id . 54))\n ((:tag . "CD") (:stem . "10-30") (:form . "10-30") (:end . 61) (:start . 56)\n (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 66) (:start . 62)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n (:id . 57))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 79)\n (:start . 71) (:id . 58))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 91)\n (:start . 80) (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 94) (:start . 92)\n (:id . 60))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 101)\n (:start . 95) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.157) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101279@unknown@formal@none@1@S@ΨS The proteome size for species S@(((:tag . "VBZ") (:stem . "ψs") (:form . "ΨS") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "proteome") (:form . "proteome") (:end . 15)\n (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 20) (:start . 16)\n (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 24) (:start . 21)\n (:id . 46))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 32)\n (:start . 25) (:id . 47))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 34) (:start . 33)\n (:id . 48)))@@@1@7@((:identifiers (:sid . :s4.167) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101289@unknown@formal@none@1@S@The estimates for the total number of iPfam domain pairs ranges from 33813 to 120511, with an average of 76918.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "estimate") (:form . "estimates") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n (:id . 45))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 27) (:start . 22)\n (:id . 46))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 34)\n (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n (:id . 48))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 43) (:start . 38)\n (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 50)\n (:start . 44) (:id . 50))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 56) (:start . 51)\n (:id . 51))\n ((:tag . "VBZ") (:stem . "range") (:form . "ranges") (:end . 63)\n (:start . 57) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 68) (:start . 64)\n (:id . 53))\n ((:tag . "CD") (:stem . "33813") (:form . "33813") (:end . 74) (:start . 69)\n (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 77) (:start . 75)\n (:id . 55))\n ((:tag . "CD") (:stem . "120511") (:form . "120511") (:end . 84)\n (:start . 78) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 90) (:start . 86)\n (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 93) (:start . 91)\n (:id . 59))\n ((:tag . "NN") (:stem . "average") (:form . "average") (:end . 101)\n (:start . 94) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n (:id . 61))\n ((:tag . "CD") (:stem . "76918") (:form . "76918") (:end . 110)\n (:start . 105) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s4.177) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101299@unknown@formal@none@1@S@The estimated total number of iPfam domains in all species@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 19) (:start . 14)\n (:id . 44))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 26)\n (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n (:id . 46))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 35) (:start . 30)\n (:id . 47))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 43)\n (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n (:id . 49))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 50) (:start . 47)\n (:id . 50))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 58)\n (:start . 51) (:id . 51)))@@@1@10@((:identifiers (:sid . :s4.187) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101309@unknown@formal@none@1@S@This in turn creates new targets for future structural genomics projects 30.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 7) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "turn") (:form . "turn") (:end . 12) (:start . 8)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "create") (:form . "creates") (:end . 20)\n (:start . 13) (:id . 45))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 24) (:start . 21)\n (:id . 46))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 32)\n (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 36) (:start . 33)\n (:id . 48))\n ((:tag . "JJ") (:stem . "future") (:form . "future") (:end . 43)\n (:start . 37) (:id . 49))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 54)\n (:start . 44) (:id . 50))\n ((:tag . "NNS") (:stem . "genomic") (:form . "genomics") (:end . 63)\n (:start . 55) (:id . 51))\n ((:tag . "NNS") (:stem . "project") (:form . "projects") (:end . 72)\n (:start . 64) (:id . 52))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 75) (:start . 73)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s4.197) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101319@unknown@formal@none@1@S@In fact, we find the most frequent iPfam domain pairs to be recognition domains in signal transduction.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n (:id . 45))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 16) (:start . 12)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 47))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 25) (:start . 21)\n (:id . 48))\n ((:tag . "JJ") (:stem . "frequent") (:form . "frequent") (:end . 34)\n (:start . 26) (:id . 49))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 40) (:start . 35)\n (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 47)\n (:start . 41) (:id . 51))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 53) (:start . 48)\n (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 59) (:start . 57)\n (:id . 54))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 71)\n (:start . 60) (:id . 55))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 79)\n (:start . 72) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n (:id . 57))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 89)\n (:start . 83) (:id . 58))\n ((:tag . "NN") (:stem . "transduction") (:form . "transduction") (:end . 102)\n (:start . 90) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.207) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101329@unknown@formal@none@1@S@While all such estimates should be taken with caution, our results show that at best 10% of all structural domain pairs are represented in iPfam.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 9) (:start . 6)\n (:id . 43))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 14) (:start . 10)\n (:id . 44))\n ((:tag . "NNS") (:stem . "estimate") (:form . "estimates") (:end . 24)\n (:start . 15) (:id . 45))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 31)\n (:start . 25) (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 34) (:start . 32)\n (:id . 47))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 40) (:start . 35)\n (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 45) (:start . 41)\n (:id . 49))\n ((:tag . "NN") (:stem . "caution") (:form . "caution") (:end . 53)\n (:start . 46) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n (:id . 51))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 58) (:start . 55)\n (:id . 52))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 66)\n (:start . 59) (:id . 53))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 71) (:start . 67)\n (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 76) (:start . 72)\n (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 79) (:start . 77)\n (:id . 56))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 84) (:start . 80)\n (:id . 57))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 87) (:start . 85)\n (:id . 58))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 88) (:start . 87)\n (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n (:id . 60))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 95) (:start . 92)\n (:id . 61))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 106)\n (:start . 96) (:id . 62))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 113)\n (:start . 107) (:id . 63))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 119)\n (:start . 114) (:id . 64))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 123) (:start . 120)\n (:id . 65))\n ((:tag . "VBN") (:stem . "represent") (:form . "represented") (:end . 135)\n (:start . 124) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 138) (:start . 136)\n (:id . 67))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 144)\n (:start . 139) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n (:id . 69)))@@@1@28@((:identifiers (:sid . :s4.217) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101339@unknown@formal@none@1@S@They found only 16 orthologous interacting protein pairs that were conserved in S. cerevisiae, C. elegans, D. melanogaster and H. sapiens.@(((:tag . "PRP") (:stem . "they") (:form . "They") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 18) (:start . 16)\n (:id . 45))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 30)\n (:start . 19) (:id . 46))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 42)\n (:start . 31) (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 50)\n (:start . 43) (:id . 48))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 56) (:start . 51)\n (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 61) (:start . 57)\n (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 66) (:start . 62)\n (:id . 51))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 76)\n (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n (:id . 53))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 82) (:start . 80)\n (:id . 54))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 93)\n (:start . 83) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n (:id . 56))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 97) (:start . 95)\n (:id . 57))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 105)\n (:start . 98) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n (:id . 59))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 109) (:start . 107)\n (:id . 60))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n (:end . 122) (:start . 110) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n (:id . 62))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 129) (:start . 127)\n (:id . 63))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 137)\n (:start . 130) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.227) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101349@unknown@formal@none@1@S@In this study, we addressed the utility of current knowledge about structural domain interactions in order to interpret experimental protein interactions.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 13) (:start . 8)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n (:id . 46))\n ((:tag . "VBD") (:stem . "address") (:form . "addressed") (:end . 27)\n (:start . 18) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n (:id . 48))\n ((:tag . "NN") (:stem . "utility") (:form . "utility") (:end . 39)\n (:start . 32) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n (:id . 50))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 50)\n (:start . 43) (:id . 51))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 60)\n (:start . 51) (:id . 52))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 66) (:start . 61)\n (:id . 53))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 77)\n (:start . 67) (:id . 54))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 84)\n (:start . 78) (:id . 55))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 97)\n (:start . 85) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 100) (:start . 98)\n (:id . 57))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 106)\n (:start . 101) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 109) (:start . 107)\n (:id . 59))\n ((:tag . "VB") (:stem . "interpret") (:form . "interpret") (:end . 119)\n (:start . 110) (:id . 60))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 132)\n (:start . 120) (:id . 61))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 140)\n (:start . 133) (:id . 62))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 153)\n (:start . 141) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s4.237) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101359@unknown@formal@none@1@S@A wide range of databases were used to cover as many distinct experimental data sets as possible.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "wide") (:form . "wide") (:end . 6) (:start . 2)\n (:id . 43))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 12) (:start . 7)\n (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n (:id . 45))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 25)\n (:start . 16) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 30) (:start . 26)\n (:id . 47))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 35) (:start . 31)\n (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n (:id . 49))\n ((:tag . "VB") (:stem . "cover") (:form . "cover") (:end . 44) (:start . 39)\n (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 47) (:start . 45)\n (:id . 51))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 52) (:start . 48)\n (:id . 52))\n ((:tag . "JJ") (:stem . "distinct") (:form . 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"domain") (:end . 36)\n (:start . 30) (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 42) (:start . 37)\n (:id . 47)))@@@1@6@((:identifiers (:sid . :s4.277) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|FigureLegend|)))@oe@9-2-2011 5101399@unknown@formal@none@1@S@Random networks@(((:tag . "NNP") (:stem . "Random") (:form . "Random") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "network") (:form . "networks") (:end . 15)\n (:start . 7) (:id . 43)))@@@1@2@((:identifiers (:sid . :s4.287) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|SectionTitle|)))@oe@9-2-2011 5101409@unknown@formal@none@1@S@Where appropriate, the inverse probability P(X > x) = 1 - f(x; μ, σ) was applied.@(((:tag . "WRB") (:stem . "where") (:form . "Where") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "appropriate") (:form . 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(:end . 81) (:start . 80)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s4.297) (:did . :1471-2105-8-259)\n (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n (:dpart . :|Text|)))@oe@9-2-2011 5101419@unknown@formal@none@1@S@Finally, ectopic expression of neur in D-mib mutant larvae rescues the wing D-mib phenotype, indicating that Neur can compensate for the lack of D-mib activity.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "ectopic") (:form . "ectopic") (:end . 16)\n (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 27)\n (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n (:id . 46))\n ((:tag . "NN") (:stem . "neur") (:form . "neur") (:end . 35) (:start . 31)\n (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . 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"activity") (:end . 159)\n (:start . 151) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n (:id . 69)))@@@1@28@((:hcues ((:id . :x5.10.2) (:span 93 108)))\n (:ncues ((:id . :x5.10.1) (:span 137 141)))\n (:hscopes ((:id . :x5.10.2) (:span 93 159)))\n (:nscopes ((:id . :x5.10.1) (:span 137 159)))\n (:identifiers (:sid . :s5.10) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101429@unknown@formal@none@1@S@Conversely, Ser (but not Dl) is specifically required for segmental patterning [5].@(((:tag . "RB") (:stem . "conversely") (:form . "Conversely") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 15) (:start . 12)\n (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 17) (:start . 16)\n (:id . 45))\n ((:tag . "CC") (:stem . "but") (:form . 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"rerio") (:end . 179)\n (:start . 174) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 180) (:start . 179)\n (:id . 77))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 193)\n (:start . 181) (:id . 78))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 195) (:start . 194)\n (:id . 79))\n ((:tag . "CD") (:stem . "18,19,20,21,22,23,24,25")\n (:form . "18,19,20,21,22,23,24,25") (:end . 218) (:start . 195) (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 219) (:start . 218)\n (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n (:id . 82)))@@@1@41@((:identifiers (:sid . :s5.30) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101449@unknown@formal@none@1@S@How endocytosis of Dl leads to the activation of N remains to be elucidated.@(((:tag . "WRB") (:stem . "how") (:form . "How") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 15)\n (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 21) (:start . 19)\n (:id . 45))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 27) (:start . 22)\n (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 48))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 45)\n (:start . 35) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n (:id . 50))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 50) (:start . 49)\n (:id . 51))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 58)\n (:start . 51) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . 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(:end . 167) (:start . 166)\n (:id . 73)))@@@1@32@((:hcues ((:id . :x5.50.1) (:span 46 53)))\n (:hscopes ((:id . :x5.50.1) (:span 20 166)))\n (:identifiers (:sid . :s5.50) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101469@unknown@formal@none@1@S@Insertion of this P-element confers late pupal lethality.@(((:tag . "NNP") (:stem . "Insertion") (:form . "Insertion") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 17) (:start . 13)\n (:id . 44))\n ((:tag . "NNP") (:stem . "P-element") (:form . "P-element") (:end . 27)\n (:start . 18) (:id . 45))\n ((:tag . "VBZ") (:stem . "confer") (:form . "confers") (:end . 35)\n (:start . 28) (:id . 46))\n ((:tag . "RB") (:stem . "late") (:form . "late") (:end . 40) (:start . 36)\n (:id . 47))\n ((:tag . "JJ") (:stem . "pupal") (:form . 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(:end . 126) (:start . 125)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s5.70) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101489@unknown@formal@none@1@S@Open reading frames are shown in black.@(((:tag . "JJ") (:stem . "open") (:form . "Open") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "reading") (:form . "reading") (:end . 12)\n (:start . 5) (:id . 43))\n ((:tag . "NNS") (:stem . "frame") (:form . "frames") (:end . 19)\n (:start . 13) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 23) (:start . 20)\n (:id . 45))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 29) (:start . 24)\n (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n (:id . 47))\n ((:tag . "NN") (:stem . "black") (:form . "black") (:end . 38) (:start . 33)\n (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 39) (:start . 38)\n (:id . 49)))@@@1@8@((:identifiers (:sid . :s5.80) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101499@unknown@formal@none@1@S@D-mib (E) and Ser (F) mutant flies showed similar wing loss phenotypes.@(((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 8) (:start . 7)\n (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 9) (:start . 8) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 13) (:start . 10)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 17) (:start . 14)\n (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 19) (:start . 18)\n (:id . 48))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 20) (:start . 19)\n (:id . 49))\n ((:tag . 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(:end . 71) (:start . 70)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s5.90) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101509@unknown@formal@none@1@S@D-mib Regulates Dl Signaling@(((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "regulate") (:form . "Regulates") (:end . 15)\n (:start . 6) (:id . 43))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 18) (:start . 16)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Signaling") (:form . "Signaling") (:end . 28)\n (:start . 19) (:id . 45)))@@@1@4@((:identifiers (:sid . :s5.100) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101519@unknown@formal@none@1@S@Finally, the vein phenotype seen in D-mib hypomorphic flies is similar to the one seen in Dlts mutant flies [39].@(((:tag . "RB") (:stem . "finally") (:form . 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"N") (:end . 58) (:start . 57)\n (:id . 52))\n ((:tag . "JJ") (:stem . "inductive") (:form . "inductive") (:end . 68)\n (:start . 59) (:id . 53))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 78)\n (:start . 69) (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 81) (:start . 79)\n (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n (:id . 56))\n ((:tag . "NNP") (:stem . "D-V") (:form . "D-V") (:end . 89) (:start . 86)\n (:id . 57))\n ((:tag . "NN") (:stem . "boundary") (:form . "boundary") (:end . 98)\n (:start . 90) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n (:id . 59)))@@@1@18@((:hcues ((:id . :x5.130.1) (:span 31 34)))\n (:hscopes ((:id . :x5.130.1) (:span 31 98)))\n (:identifiers (:sid . :s5.130) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101549@unknown@formal@none@1@S@D-mib co-localized with Ser, Dl, and N at the apical cortex (Figure 3B–3D???).@(((:tag . "JJ") (:stem . "d-mib") (:form . "D-mib") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "co-localized") (:form . "co-localized") (:end . 18)\n (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 23) (:start . 19)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 27) (:start . 24)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 31) (:start . 29)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . 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(:end . 75) (:start . 74)\n (:id . 59))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 76) (:start . 75)\n (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n (:id . 62)))@@@1@21@((:identifiers (:sid . :s5.140) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101559@unknown@formal@none@1@S@(E–E??) D-mib (green in [E and E?]) co-localized with Dl (red in [E and E??]) at the apical cortex of wing pouch cells.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E–E") (:form . "E–E") (:end . 4) (:start . 1)\n (:id . 43))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 6) (:start . 5) (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . 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"cells") (:end . 118)\n (:start . 113) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n (:id . 80)))@@@1@39@((:identifiers (:sid . :s5.150) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101569@unknown@formal@none@1@S@(B) and (D) show high-magnification views of the areas boxed in (A) and (C), respectively.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 7) (:start . 4)\n (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 9) (:start . 8) (:id . 46))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 10) (:start . 9)\n (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 11) (:start . 10)\n (:id . 48))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 16) (:start . 12)\n (:id . 49))\n ((:tag . "JJ") (:stem . "high-magnification") (:form . "high-magnification")\n (:end . 35) (:start . 17) (:id . 50))\n ((:tag . "NNS") (:stem . "view") (:form . "views") (:end . 41) (:start . 36)\n (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n (:id . 53))\n ((:tag . "NNS") (:stem . "area") (:form . "areas") (:end . 54) (:start . 49)\n (:id . 54))\n ((:tag . "VBN") (:stem . "box") (:form . "boxed") (:end . 60) (:start . 55)\n (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n (:id . 57))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 66) (:start . 65)\n (:id . 58))\n ((:tag . ")") (:stem . 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"PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 12)\n (:start . 3) (:id . 43))\n ((:tag . "VBP") (:stem . "conclude") (:form . "conclude") (:end . 21)\n (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n (:id . 46))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 36) (:start . 31)\n (:id . 47))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 41) (:start . 37)\n (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 44) (:start . 42)\n (:id . 49))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 53)\n (:start . 45) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n (:id . 51))\n ((:tag . "VB") (:stem . "regulate") (:form . 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(:end . 57) (:start . 56)\n (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 58) (:start . 57)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 59) (:start . 58)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s5.180) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101599@unknown@formal@none@1@S@The uptake of anti-Ser and anti-Dl antibodies was then assessed using secondary antibodies.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "uptake") (:form . "uptake") (:end . 10) (:start . 4)\n (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n (:id . 44))\n ((:tag . "JJ") (:stem . "anti-ser") (:form . "anti-Ser") (:end . 22)\n (:start . 14) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "JJ") (:stem . "anti-dl") (:form . 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(:end . 91) (:start . 90)\n (:id . 55)))@@@1@14@((:identifiers (:sid . :s5.190) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101609@unknown@formal@none@1@S@(C–C??) and (F–F??) show confocal z-sections.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C–C") (:form . "C–C") (:end . 4) (:start . 1)\n (:id . 43))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 6) (:start . 5) (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 7) (:start . 6) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 13) (:start . 12)\n (:id . 48))\n ((:tag . "NNP") (:stem . "F–F") (:form . "F–F") (:end . 16) (:start . 13)\n (:id . 49))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 17) (:start . 16)\n (:id . 50))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 18) (:start . 17)\n (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 19) (:start . 18)\n (:id . 52))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 24) (:start . 20)\n (:id . 53))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 33)\n (:start . 25) (:id . 54))\n ((:tag . "NNS") (:stem . "z-section") (:form . "z-sections") (:end . 44)\n (:start . 34) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 45) (:start . 44)\n (:id . 56)))@@@1@15@((:identifiers (:sid . :s5.200) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101619@unknown@formal@none@1@S@Loss of D-mib activity in large dorsal clones of D-mib2 mutant cells resulted in a loss of Cut expression at the D-V interface (Figure 6A and 6B).@(((:tag . "NN") (:stem . "loss") (:form . 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"functional") (:end . 116)\n (:start . 106) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n (:id . 60)))@@@1@19@((:hcues ((:id . :x5.220.1) (:span 76 91)))\n (:hscopes ((:id . :x5.220.1) (:span 76 116)))\n (:identifiers (:sid . :s5.220) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101639@unknown@formal@none@1@S@D-mib Acts Downstream of Ser and Upstream of Activated N@(((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "NNPS") (:stem . "Acts") (:form . "Acts") (:end . 10) (:start . 6)\n (:id . 43))\n ((:tag . "NNP") (:stem . "Downstream") (:form . "Downstream") (:end . 21)\n (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 28) (:start . 25)\n (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . 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(:end . 160) (:start . 159)\n (:id . 63)))@@@1@22@((:ncues ((:id . :x5.280.1) (:span 59 65)))\n (:nscopes ((:id . :x5.280.1) (:span 0 159)))\n (:identifiers (:sid . :s5.280) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101699@unknown@formal@none@1@S@Whether endogenous Neur binds and activates Ser remains to be tested.@(((:tag . "IN") (:stem . "whether") (:form . "Whether") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 18)\n (:start . 8) (:id . 43))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 23) (:start . 19)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "bind") (:form . "binds") (:end . 29) (:start . 24)\n (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n (:id . 46))\n ((:tag . "VBZ") (:stem . "activate") (:form . "activates") (:end . 43)\n (:start . 34) (:id . 47))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 47) (:start . 44)\n (:id . 48))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 55)\n (:start . 48) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 61) (:start . 59)\n (:id . 51))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 68) (:start . 62)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n (:id . 53)))@@@1@12@((:hcues ((:id . :x5.290.1) (:span 0 7)))\n (:hscopes ((:id . :x5.290.1) (:span 0 47)))\n (:identifiers (:sid . :s5.290) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101709@unknown@formal@none@1@S@In conclusion, Neur and D-mib appear to have similar molecular activities in the regulation of Dl and Ser endocytosis but distinct developmental functions in Drosophila.@(((:tag . "IN") (:stem . "in") (:form . 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"NNS") (:stem . "activity") (:form . "activities") (:end . 73)\n (:start . 63) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n (:id . 55))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 91)\n (:start . 81) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n (:id . 57))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 97) (:start . 95)\n (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n (:id . 59))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 105) (:start . 102)\n (:id . 60))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 117)\n (:start . 106) (:id . 61))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 121) (:start . 118)\n (:id . 62))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 130)\n (:start . 122) (:id . 63))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n (:end . 144) (:start . 131) (:id . 64))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 154)\n (:start . 145) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 157) (:start . 155)\n (:id . 66))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 168)\n (:start . 158) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n (:id . 68)))@@@1@27@((:hcues ((:id . :x5.300.1) (:span 30 36)))\n (:hscopes ((:id . :x5.300.1) (:span 15 168)))\n (:identifiers (:sid . :s5.300) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101719@unknown@formal@none@1@S@Sequence analysis of the D-mib3 and D-mib4 alleles was carried on PCR products prepared from genomic DNA prepared from D-mib3/D-mib2 and D-mib4/D-mib2 mutant pupae.@(((:tag . "NN") (:stem . "sequence") (:form . "Sequence") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 17)\n (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n (:id . 45))\n ((:tag . "NN") (:stem . "d-mib3") (:form . "D-mib3") (:end . 31)\n (:start . 25) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . 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"NN") (:stem . "dna") (:form . "DNA") (:end . 104) (:start . 101)\n (:id . 58))\n ((:tag . "VBN") (:stem . "prepare") (:form . "prepared") (:end . 113)\n (:start . 105) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 118) (:start . 114)\n (:id . 60))\n ((:tag . "NN") (:stem . "d-mib3/d-mib2") (:form . "D-mib3/D-mib2")\n (:end . 132) (:start . 119) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 136) (:start . 133)\n (:id . 62))\n ((:tag . "NN") (:stem . "d-mib4/d-mib2") (:form . "D-mib4/D-mib2")\n (:end . 150) (:start . 137) (:id . 63))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 157)\n (:start . 151) (:id . 64))\n ((:tag . "NNS") (:stem . "pupa") (:form . "pupae") (:end . 163)\n (:start . 158) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s5.310) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101729@unknown@formal@none@1@S@Rabbit polyclonal anti-D-mib antibodies were raised against the CYNERKTDDSELPGN peptide (CovalAb, Lyon, France).@(((:tag . "NN") (:stem . "rabbit") (:form . "Rabbit") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "polyclonal") (:form . "polyclonal") (:end . 17)\n (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "anti-d-mib") (:form . "anti-D-mib") (:end . 28)\n (:start . 18) (:id . 44))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 39)\n (:start . 29) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 44) (:start . 40)\n (:id . 46))\n ((:tag . "VBN") (:stem . "raise") (:form . "raised") (:end . 51)\n (:start . 45) (:id . 47))\n ((:tag . "IN") (:stem . "against") (:form . 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(:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s5.320) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101739@unknown@formal@none@1@S@Following three medium changes and a 45-min chase period, wing discs were fixed and incubated with secondary antibodies.@(((:tag . "VBG") (:stem . "follow") (:form . "Following") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 15) (:start . 10)\n (:id . 43))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 22)\n (:start . 16) (:id . 44))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 30)\n (:start . 23) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 34) (:start . 31)\n (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 36) (:start . 35)\n (:id . 47))\n ((:tag . "JJ") (:stem . "45-min") (:form . 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"secondary") (:form . "secondary") (:end . 108)\n (:start . 99) (:id . 59))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 119)\n (:start . 109) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n (:id . 61)))@@@1@20@((:identifiers (:sid . :s5.330) (:did . :pmc1064853) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101749@unknown@formal@none@1@S@We also studied several divergent proteins encoded by the sea urchin and lancelet genomes that are 25%-30% identical to the RAG1 N-terminal domain and the RAG1 core.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "VBD") (:stem . "study") (:form . "studied") (:end . 15)\n (:start . 8) (:id . 44))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 23)\n (:start . 16) (:id . 45))\n ((:tag . 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(:end . 151) (:start . 150)\n (:id . 64)))@@@1@23@((:identifiers (:sid . :s6.20) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101769@unknown@formal@none@1@S@In vertebrates, in vivo RAG-mediated transpositions are strongly suppressed, probably to minimize potential harm to genome function.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "vertebrate") (:form . "vertebrates") (:end . 14)\n (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n (:id . 44))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n (:id . 45))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 23) (:start . 19)\n (:id . 46))\n ((:tag . "JJ") (:stem . "rag-mediated") (:form . "RAG-mediated") (:end . 36)\n (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "transposition") (:form . "transpositions")\n (:end . 51) (:start . 37) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 55) (:start . 52)\n (:id . 49))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 64)\n (:start . 56) (:id . 50))\n ((:tag . "VBN") (:stem . "suppress") (:form . "suppressed") (:end . 75)\n (:start . 65) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n (:id . 52))\n ((:tag . "RB") (:stem . "probably") (:form . "probably") (:end . 85)\n (:start . 77) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n (:id . 54))\n ((:tag . "VB") (:stem . "minimize") (:form . "minimize") (:end . 97)\n (:start . 89) (:id . 55))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 107)\n (:start . 98) (:id . 56))\n ((:tag . "NN") (:stem . "harm") (:form . "harm") (:end . 112) (:start . 108)\n (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 115) (:start . 113)\n (:id . 58))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 122)\n (:start . 116) (:id . 59))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 131)\n (:start . 123) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n (:id . 61)))@@@1@20@((:hcues ((:id . :x6.30.1) (:span 77 85)))\n (:hscopes ((:id . :x6.30.1) (:span 77 131)))\n (:identifiers (:sid . :s6.30) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101779@unknown@formal@none@1@S@Genomes of plants and vertebrates seem to be free of any recognizable Transib transposons (Figure 1).@(((:tag . "NNS") (:stem . "genome") (:form . "Genomes") (:end . 7)\n (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n (:id . 43))\n ((:tag . "NNS") (:stem . "plant") (:form . "plants") (:end . 17)\n (:start . 11) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n (:id . 45))\n ((:tag . "NNS") (:stem . "vertebrate") (:form . "vertebrates") (:end . 33)\n (:start . 22) (:id . 46))\n ((:tag . "VBP") (:stem . "seem") (:form . "seem") (:end . 38) (:start . 34)\n (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 44) (:start . 42)\n (:id . 49))\n ((:tag . "JJ") (:stem . "free") (:form . "free") (:end . 49) (:start . 45)\n (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n (:id . 51))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 56) (:start . 53)\n (:id . 52))\n ((:tag . "JJ") (:stem . "recognizable") (:form . "recognizable") (:end . 69)\n (:start . 57) (:id . 53))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 77)\n (:start . 70) (:id . 54))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 89)\n (:start . 78) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n (:id . 56))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 97)\n (:start . 91) (:id . 57))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 99) (:start . 98)\n (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n (:id . 60)))@@@1@19@((:hcues ((:id . :x6.40.1) (:span 34 38)))\n (:hscopes ((:id . :x6.40.1) (:span 0 89)))\n (:identifiers (:sid . :s6.40) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101789@unknown@formal@none@1@S@In fungi, the Transib TPase was detected in soybean rust only.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "NNS") (:stem . "fungus") (:form . "fungi") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n (:id . 45))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 21)\n (:start . 14) (:id . 46))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 27) (:start . 22)\n (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 31) (:start . 28)\n (:id . 48))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 40)\n (:start . 32) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n (:id . 50))\n ((:tag . "NN") (:stem . "soybean") (:form . "soybean") (:end . 51)\n (:start . 44) (:id . 51))\n ((:tag . "NN") (:stem . "rust") (:form . "rust") (:end . 56) (:start . 52)\n (:id . 52))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 61) (:start . 57)\n (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 62) (:start . 61)\n (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.50) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101799@unknown@formal@none@1@S@To achieve that, we combined protein sequences of the seven known Transib TPases with the set of all GenBank proteins.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "achieve") (:form . "achieve") (:end . 10)\n (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 19) (:start . 17)\n (:id . 46))\n ((:tag . "VBD") (:stem . "combine") (:form . "combined") (:end . 28)\n (:start . 20) (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 36)\n (:start . 29) (:id . 48))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 46)\n (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n (:id . 51))\n ((:tag . "CD") (:stem . "seven") (:form . "seven") (:end . 59) (:start . 54)\n (:id . 52))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 65) (:start . 60)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 73)\n (:start . 66) (:id . 54))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 80) (:start . 74)\n (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 85) (:start . 81)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n (:id . 57))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 93) (:start . 90)\n (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n (:id . 59))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 100) (:start . 97)\n (:id . 60))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 108)\n (:start . 101) (:id . 61))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 117)\n (:start . 109) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.60) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101809@unknown@formal@none@1@S@The more diverse the TPases used in determining the PSSM, the more accurate is the approximation; some of the insect Transib TPases are less than 30% identical to each other, as shown in Figure 2.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 16)\n (:start . 9) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n (:id . 45))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 27) (:start . 21)\n (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 32) (:start . 28)\n (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n (:id . 48))\n ((:tag . "VBG") (:stem . "determine") (:form . "determining") (:end . 47)\n (:start . 36) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n (:id . 50))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 56) (:start . 52)\n (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n (:id . 53))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 66) (:start . 62)\n (:id . 54))\n ((:tag . "JJ") (:stem . "accurate") (:form . "accurate") (:end . 75)\n (:start . 67) (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 78) (:start . 76)\n (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n (:id . 57))\n ((:tag . "NN") (:stem . "approximation") (:form . "approximation")\n (:end . 96) (:start . 83) (:id . 58))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 97) (:start . 96)\n (:id . 59))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 102) (:start . 98)\n (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n (:id . 62))\n ((:tag . "NN") (:stem . "insect") (:form . "insect") (:end . 116)\n (:start . 110) (:id . 63))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 124)\n (:start . 117) (:id . 64))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 131)\n (:start . 125) (:id . 65))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 135) (:start . 132)\n (:id . 66))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 140) (:start . 136)\n (:id . 67))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 145) (:start . 141)\n (:id . 68))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 148) (:start . 146)\n (:id . 69))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 149) (:start . 148)\n (:id . 70))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 159)\n (:start . 150) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 162) (:start . 160)\n (:id . 72))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 167) (:start . 163)\n (:id . 73))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 173)\n (:start . 168) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 174) (:start . 173)\n (:id . 75))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 177) (:start . 175)\n (:id . 76))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 183)\n (:start . 178) (:id . 77))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 186) (:start . 184)\n (:id . 78))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 193)\n (:start . 187) (:id . 79))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 195) (:start . 194)\n (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n (:id . 81)))@@@1@40@((:identifiers (:sid . :s6.70) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101819@unknown@formal@none@1@S@At the same time, recently sequenced genomes of honeybee, roundworms, fish, frog, mammals, sea squirts, plants, and fungi (except soybean rust) do not contain any detectable Transib transposons (see Figure 1).@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 11) (:start . 7)\n (:id . 44))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 16) (:start . 12)\n (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n (:id . 46))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 26)\n (:start . 18) (:id . 47))\n ((:tag . "VBN") (:stem . "sequence") (:form . "sequenced") (:end . 36)\n (:start . 27) (:id . 48))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 44)\n (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n (:id . 50))\n ((:tag . "NN") (:stem . "honeybee") (:form . "honeybee") (:end . 56)\n (:start . 48) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n (:id . 52))\n ((:tag . "NNS") (:stem . "roundworm") (:form . "roundworms") (:end . 68)\n (:start . 58) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n (:id . 54))\n ((:tag . "NN") (:stem . "fish") (:form . "fish") (:end . 74) (:start . 70)\n (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n (:id . 56))\n ((:tag . "NN") (:stem . "frog") (:form . "frog") (:end . 80) (:start . 76)\n (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n (:id . 58))\n ((:tag . "NNS") (:stem . "mammal") (:form . "mammals") (:end . 89)\n (:start . 82) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n (:id . 60))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 94) (:start . 91)\n (:id . 61))\n ((:tag . "NNS") (:stem . "squirt") (:form . "squirts") (:end . 102)\n (:start . 95) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n (:id . 63))\n ((:tag . "NNS") (:stem . "plant") (:form . "plants") (:end . 110)\n (:start . 104) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n (:id . 66))\n ((:tag . "NNS") (:stem . "fungus") (:form . "fungi") (:end . 121)\n (:start . 116) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 123) (:start . 122)\n (:id . 68))\n ((:tag . "IN") (:stem . "except") (:form . "except") (:end . 129)\n (:start . 123) (:id . 69))\n ((:tag . "NN") (:stem . "soybean") (:form . "soybean") (:end . 137)\n (:start . 130) (:id . 70))\n ((:tag . "NN") (:stem . "rust") (:form . "rust") (:end . 142) (:start . 138)\n (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n (:id . 72))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 146) (:start . 144)\n (:id . 73))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 150) (:start . 147)\n (:id . 74))\n ((:tag . "VB") (:stem . "contain") (:form . "contain") (:end . 158)\n (:start . 151) (:id . 75))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 162) (:start . 159)\n (:id . 76))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 173)\n (:start . 163) (:id . 77))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 181)\n (:start . 174) (:id . 78))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 193)\n (:start . 182) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 195) (:start . 194)\n (:id . 80))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 198) (:start . 195)\n (:id . 81))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 205)\n (:start . 199) (:id . 82))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 207) (:start . 206)\n (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 208) (:start . 207)\n (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n (:id . 85)))@@@1@44@((:ncues ((:id . :x6.80.1) (:span 147 150)))\n (:nscopes ((:id . :x6.80.1) (:span 147 193)))\n (:identifiers (:sid . :s6.80) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101829@unknown@formal@none@1@S@Each empty cell indicates that the corresponding TPase query was not used at the particular stage of PSI-BLAST analysis.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "empty") (:form . "empty") (:end . 10) (:start . 5)\n (:id . 43))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 15) (:start . 11)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 25)\n (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n (:id . 47))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 48)\n (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "tpase") (:form . "TPase") (:end . 54) (:start . 49)\n (:id . 49))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 60) (:start . 55)\n (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 64) (:start . 61)\n (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 68) (:start . 65)\n (:id . 52))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 73) (:start . 69)\n (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 76) (:start . 74)\n (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n (:id . 55))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 91)\n (:start . 81) (:id . 56))\n ((:tag . "NN") (:stem . "stage") (:form . "stage") (:end . 97) (:start . 92)\n (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n (:id . 58))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 110)\n (:start . 101) (:id . 59))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 119)\n (:start . 111) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n (:id . 61)))@@@1@20@((:ncues ((:id . :x6.90.1) (:span 65 68)))\n (:nscopes ((:id . :x6.90.1) (:span 31 119)))\n (:identifiers (:sid . :s6.90) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101839@unknown@formal@none@1@S@This includes the distances between the second D and E residues, which are much longer in Transib transposons (206–214 aa) and RAG1 (253 aa) than in DDE TPases from other studied superfamilies (e.g., approximately 35-aa in Mariner/Tc1 [23], 2-aa in P [23], approximately 35-aa in Harbinger [24], with hAT as an exception (325-aa, [25]).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 13)\n (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n (:id . 44))\n ((:tag . "NNS") (:stem . "distance") (:form . "distances") (:end . 27)\n (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 35)\n (:start . 28) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n (:id . 47))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 46)\n (:start . 40) (:id . 48))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 48) (:start . 47)\n (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n (:id . 50))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 54) (:start . 53)\n (:id . 51))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 63)\n (:start . 55) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 70) (:start . 65)\n (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 74) (:start . 71)\n (:id . 55))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 79) (:start . 75)\n (:id . 56))\n ((:tag . "RBR") (:stem . "longer") (:form . "longer") (:end . 86)\n (:start . 80) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n (:id . 58))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 97)\n (:start . 90) (:id . 59))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 109)\n (:start . 98) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n (:id . 61))\n ((:tag . "CD") (:stem . "206–214") (:form . "206–214") (:end . 118)\n (:start . 111) (:id . 62))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 121) (:start . 119)\n (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 122) (:start . 121)\n (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n (:id . 65))\n ((:tag . "NNP") (:stem . "RAG1") (:form . 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(:end . 336) (:start . 335)\n (:id . 117)))@@@1@76@((:identifiers (:sid . :s6.100) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101849@unknown@formal@none@1@S@Based on this information, the function of these motifs in Transib TPases is expected to be similar to that in RAG1.@(((:tag . "VBN") (:stem . "base") (:form . "Based") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 8) (:start . 6)\n (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n (:id . 44))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 25)\n (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n (:id . 47))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 39)\n (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n (:id . 49))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 48) (:start . 43)\n (:id . 50))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 55)\n (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n (:id . 52))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 66)\n (:start . 59) (:id . 53))\n ((:tag . "NNP") (:stem . "TPases") (:form . "TPases") (:end . 73)\n (:start . 67) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 76) (:start . 74)\n (:id . 55))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 85)\n (:start . 77) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 91) (:start . 89)\n (:id . 58))\n ((:tag . "JJ") (:stem . "similar") (:form . 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"position") (:form . "positions") (:end . 18)\n (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 32)\n (:start . 26) (:id . 46))\n ((:tag . "RB") (:stem . "immediately") (:form . "immediately") (:end . 44)\n (:start . 33) (:id . 47))\n ((:tag . "VBP") (:stem . "follow") (:form . "follow") (:end . 51)\n (:start . 45) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n (:id . 49))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 69)\n (:start . 56) (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 77)\n (:start . 70) (:id . 51))\n ((:tag . "NNS") (:stem . "name") (:form . "names") (:end . 83) (:start . 78)\n (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n (:id . 53)))@@@1@12@((:identifiers (:sid . :s6.120) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101869@unknown@formal@none@1@S@(A) Frequencies of the most frequent nucleotides at each position of the consensus sequence of the 5? TIRs of transposons that belong to 20 families of Transib transposons identified in fruit flies and mosquitoes.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNS") (:stem . "frequency") (:form . "Frequencies") (:end . 15)\n (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n (:id . 47))\n ((:tag . "RBS") (:stem . 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"family") (:form . "families") (:end . 148)\n (:start . 140) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n (:id . 70))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 159)\n (:start . 152) (:id . 71))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 171)\n (:start . 160) (:id . 72))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 182)\n (:start . 172) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 185) (:start . 183)\n (:id . 74))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 191)\n (:start . 186) (:id . 75))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 197) (:start . 192)\n (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 201) (:start . 198)\n (:id . 77))\n ((:tag . "NNS") (:stem . "mosquito") (:form . "mosquitoes") (:end . 212)\n (:start . 202) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 213) (:start . 212)\n (:id . 79)))@@@1@38@((:identifiers (:sid . :s6.130) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101879@unknown@formal@none@1@S@In one study [12], 35 of 38 (92%) TSDs generated during RAG-mediated intermolecular transposition were 5 bp long, and the remaining 8% were either 4 or 3 bp long.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 12) (:start . 7)\n (:id . 44))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 14) (:start . 13)\n (:id . 45))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 16) (:start . 14)\n (:id . 46))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 17) (:start . 16)\n (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . 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"RAG-mediated") (:end . 68)\n (:start . 56) (:id . 59))\n ((:tag . "JJ") (:stem . "intermolecular") (:form . "intermolecular")\n (:end . 83) (:start . 69) (:id . 60))\n ((:tag . "NN") (:stem . "transposition") (:form . "transposition")\n (:end . 97) (:start . 84) (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 102) (:start . 98)\n (:id . 62))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 104) (:start . 103)\n (:id . 63))\n ((:tag . "NN") (:stem . "bp") (:form . "bp") (:end . 107) (:start . 105)\n (:id . 64))\n ((:tag . "RB") (:stem . "long") (:form . "long") (:end . 112) (:start . 108)\n (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n (:id . 68))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 131)\n (:start . 122) (:id . 69))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 133) (:start . 132)\n (:id . 70))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 134) (:start . 133)\n (:id . 71))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 139) (:start . 135)\n (:id . 72))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 146)\n (:start . 140) (:id . 73))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 148) (:start . 147)\n (:id . 74))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 151) (:start . 149)\n (:id . 75))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 153) (:start . 152)\n (:id . 76))\n ((:tag . "NN") (:stem . "bp") (:form . "bp") (:end . 156) (:start . 154)\n (:id . 77))\n ((:tag . "RB") (:stem . "long") (:form . "long") (:end . 161) (:start . 157)\n (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n (:id . 79)))@@@1@38@((:identifiers (:sid . :s6.140) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101889@unknown@formal@none@1@S@Both RAG1/2-mediated and Transib transpositions show strong preference for GC-rich target sites [12–14,32], even though genomes hosting Transib transposons are AT-rich (Figure S4; Table 2).@(((:tag . "CC") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "rag1/2-mediated") (:form . "RAG1/2-mediated")\n (:end . 20) (:start . 5) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n (:id . 44))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 32)\n (:start . 25) (:id . 45))\n ((:tag . "NNS") (:stem . "transposition") (:form . "transpositions")\n (:end . 47) (:start . 33) (:id . 46))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 52) (:start . 48)\n (:id . 47))\n ((:tag . "JJ") (:stem . "strong") (:form . "strong") (:end . 59)\n (:start . 53) (:id . 48))\n ((:tag . "NN") (:stem . "preference") (:form . "preference") (:end . 70)\n (:start . 60) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 74) (:start . 71)\n (:id . 50))\n ((:tag . "JJ") (:stem . "gc-rich") (:form . "GC-rich") (:end . 82)\n (:start . 75) (:id . 51))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 89)\n (:start . 83) (:id . 52))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 95) (:start . 90)\n (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 97) (:start . 96)\n (:id . 54))\n ((:tag . "CD") (:stem . "12–14,32") (:form . "12–14,32") (:end . 105)\n (:start . 97) (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 106) (:start . 105)\n (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n (:id . 57))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 112) (:start . 108)\n (:id . 58))\n ((:tag . "IN") (:stem . "though") (:form . "though") (:end . 119)\n (:start . 113) (:id . 59))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 127)\n (:start . 120) (:id . 60))\n ((:tag . "VBG") (:stem . "host") (:form . "hosting") (:end . 135)\n (:start . 128) (:id . 61))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 143)\n (:start . 136) (:id . 62))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 155)\n (:start . 144) (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 159) (:start . 156)\n (:id . 64))\n ((:tag . "JJ") (:stem . "at-rich") (:form . "AT-rich") (:end . 167)\n (:start . 160) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 169) (:start . 168)\n (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 175)\n (:start . 169) (:id . 67))\n ((:tag . "NNP") (:stem . "S4") (:form . "S4") (:end . 178) (:start . 176)\n (:id . 68))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 179) (:start . 178)\n (:id . 69))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 185)\n (:start . 180) (:id . 70))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 187) (:start . 186)\n (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n (:id . 73)))@@@1@32@((:identifiers (:sid . :s6.150) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101899@unknown@formal@none@1@S@RAG1 Core–Like Sequences in the Sea Urchin, Lancelet, Starlet Sea Anemone, and Hydra Genomes@(((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NNP") (:stem . "Core–Like") (:form . "Core–Like") (:end . 14)\n (:start . 5) (:id . 43))\n ((:tag . "NNP") (:stem . "Sequence") (:form . "Sequences") (:end . 24)\n (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n (:id . 46))\n ((:tag . "NNP") (:stem . "Sea") (:form . "Sea") (:end . 35) (:start . 32)\n (:id . 47))\n ((:tag . "NNP") (:stem . "Urchin") (:form . "Urchin") (:end . 42)\n (:start . 36) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n (:id . 49))\n ((:tag . "NNP") (:stem . "Lancelet") (:form . "Lancelet") (:end . 52)\n (:start . 44) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n (:id . 51))\n ((:tag . "NNP") (:stem . "Starlet") (:form . "Starlet") (:end . 61)\n (:start . 54) (:id . 52))\n ((:tag . "NNP") (:stem . "Sea") (:form . "Sea") (:end . 65) (:start . 62)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Anemone") (:form . "Anemone") (:end . 73)\n (:start . 66) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n (:id . 56))\n ((:tag . "NNP") (:stem . "Hydra") (:form . "Hydra") (:end . 84) (:start . 79)\n (:id . 57))\n ((:tag . "NNPS") (:stem . "Genome") (:form . "Genomes") (:end . 92)\n (:start . 85) (:id . 58)))@@@1@17@((:identifiers (:sid . :s6.160) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5101909@unknown@formal@none@1@S@Although the two proteins are only 38% identical to each other, they share common features: (1) their N-terminal portions are missing and the RAG1-like sequences start at positions 17 or 18; (2) in both proteins the first aa residue overlaps with the acceptor splice site; and (3) their similarity to RAG1 starts at positions corresponding to position 470 of the human RAG1.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n (:id . 43))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 16) (:start . 13)\n (:id . 44))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 25)\n (:start . 17) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n (:id . 46))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 34) (:start . 30)\n (:id . 47))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 37) (:start . 35)\n (:id . 48))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 38) (:start . 37)\n (:id . 49))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 48)\n (:start . 39) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n (:id . 51))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 56) (:start . 52)\n (:id . 52))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 62) (:start . 57)\n (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n (:id . 54))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 68) (:start . 64)\n (:id . 55))\n ((:tag . "VBP") (:stem . "share") (:form . "share") (:end . 74) (:start . 69)\n (:id . 56))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 81)\n (:start . 75) (:id . 57))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 90)\n (:start . 82) (:id . 58))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 91) (:start . 90)\n (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 93) (:start . 92)\n (:id . 60))\n ((:tag . "LS") (:stem . "1") (:form . "1") (:end . 94) (:start . 93)\n (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 95) (:start . 94)\n (:id . 62))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 101)\n (:start . 96) (:id . 63))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 112)\n (:start . 102) (:id . 64))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 121)\n (:start . 113) (:id . 65))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 125) (:start . 122)\n (:id . 66))\n ((:tag . "VBG") (:stem . "miss") (:form . "missing") (:end . 133)\n (:start . 126) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n (:id . 69))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 151)\n (:start . 142) (:id . 70))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 161)\n (:start . 152) (:id . 71))\n ((:tag . "VBP") (:stem . "start") (:form . "start") (:end . 167)\n (:start . 162) (:id . 72))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 170) (:start . 168)\n (:id . 73))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 180)\n (:start . 171) (:id . 74))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 183) (:start . 181)\n (:id . 75))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 186) (:start . 184)\n (:id . 76))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 189) (:start . 187)\n (:id . 77))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 190) (:start . 189)\n (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 192) (:start . 191)\n (:id . 79))\n ((:tag . "LS") (:stem . "2") (:form . "2") (:end . 193) (:start . 192)\n (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 194) (:start . 193)\n (:id . 81))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 197) (:start . 195)\n (:id . 82))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 202) (:start . 198)\n (:id . 83))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 211)\n (:start . 203) (:id . 84))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 215) (:start . 212)\n (:id . 85))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 221)\n (:start . 216) (:id . 86))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 224) (:start . 222)\n (:id . 87))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 232)\n (:start . 225) (:id . 88))\n ((:tag . "VBZ") (:stem . "overlap") (:form . "overlaps") (:end . 241)\n (:start . 233) (:id . 89))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 246) (:start . 242)\n (:id . 90))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 250) (:start . 247)\n (:id . 91))\n ((:tag . "NN") (:stem . "acceptor") (:form . "acceptor") (:end . 259)\n (:start . 251) (:id . 92))\n ((:tag . "NN") (:stem . "splice") (:form . "splice") (:end . 266)\n (:start . 260) (:id . 93))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 271) (:start . 267)\n (:id . 94))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 272) (:start . 271)\n (:id . 95))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 276) (:start . 273)\n (:id . 96))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 278) (:start . 277)\n (:id . 97))\n ((:tag . "LS") (:stem . "3") (:form . "3") (:end . 279) (:start . 278)\n (:id . 98))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 280) (:start . 279)\n (:id . 99))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 286)\n (:start . 281) (:id . 100))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 297)\n (:start . 287) (:id . 101))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 300) (:start . 298)\n (:id . 102))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 305) (:start . 301)\n (:id . 103))\n ((:tag . "VBZ") (:stem . "start") (:form . "starts") (:end . 312)\n (:start . 306) (:id . 104))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 315) (:start . 313)\n (:id . 105))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 325)\n (:start . 316) (:id . 106))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 339)\n (:start . 326) (:id . 107))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 342) (:start . 340)\n (:id . 108))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 351)\n (:start . 343) (:id . 109))\n ((:tag . "CD") (:stem . "470") (:form . "470") (:end . 355) (:start . 352)\n (:id . 110))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 358) (:start . 356)\n (:id . 111))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 362) (:start . 359)\n (:id . 112))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 368)\n (:start . 363) (:id . 113))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 373) (:start . 369)\n (:id . 114))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 374) (:start . 373)\n (:id . 115)))@@@1@74@((:ncues ((:id . :x6.170.1) (:span 126 133)))\n (:nscopes ((:id . :x6.170.1) (:span 96 133)))\n (:identifiers (:sid . :s6.170) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101919@unknown@formal@none@1@S@Using these trace sequences, we partially assembled a hydra gene, called RAG1L_NM, which encodes the RAG1 core–like protein.@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 11) (:start . 6)\n (:id . 43))\n ((:tag . "NN") (:stem . "trace") (:form . "trace") (:end . 17) (:start . 12)\n (:id . 44))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 27)\n (:start . 18) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 31) (:start . 29)\n (:id . 47))\n ((:tag . "RB") (:stem . "partially") (:form . "partially") (:end . 41)\n (:start . 32) (:id . 48))\n ((:tag . "VBD") (:stem . "assemble") (:form . "assembled") (:end . 51)\n (:start . 42) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n (:id . 50))\n ((:tag . "NN") (:stem . "hydra") (:form . "hydra") (:end . 59) (:start . 54)\n (:id . 51))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 64) (:start . 60)\n (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n (:id . 53))\n ((:tag . "VBN") (:stem . "call") (:form . "called") (:end . 72) (:start . 66)\n (:id . 54))\n ((:tag . "NNP") (:stem . "RAG1L_NM") (:form . "RAG1L_NM") (:end . 81)\n (:start . 73) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 88) (:start . 83)\n (:id . 57))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 96)\n (:start . 89) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n (:id . 59))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 105) (:start . 101)\n (:id . 60))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 115)\n (:start . 106) (:id . 61))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 123)\n (:start . 116) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.180) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101929@unknown@formal@none@1@S@Names of these elements are shown above the rectangles.@(((:tag . "NNS") (:stem . "name") (:form . "Names") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 8) (:start . 6)\n (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 14) (:start . 9)\n (:id . 44))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 23)\n (:start . 15) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 27) (:start . 24)\n (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 33) (:start . 28)\n (:id . 47))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 39) (:start . 34)\n (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n (:id . 49))\n ((:tag . "NNS") (:stem . "rectangle") (:form . "rectangles") (:end . 54)\n (:start . 44) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 55) (:start . 54)\n (:id . 51)))@@@1@10@((:identifiers (:sid . :s6.190) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101939@unknown@formal@none@1@S@Furthermore, we found that unassembled WGS trace sequences encode two other proteins, P4_SP and P5_SP, similar to the N-terminal RAG1 domain (Figure 6).@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n (:id . 44))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 21) (:start . 16)\n (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n (:id . 46))\n ((:tag . "JJ") (:stem . "unassembled") (:form . "unassembled") (:end . 38)\n (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "wgs") (:form . "WGS") (:end . 42) (:start . 39)\n (:id . 48))\n ((:tag . "NN") (:stem . "trace") (:form . "trace") (:end . 48) (:start . 43)\n (:id . 49))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 58)\n (:start . 49) (:id . 50))\n ((:tag . "VBP") (:stem . "encode") (:form . "encode") (:end . 65)\n (:start . 59) (:id . 51))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 69) (:start . 66)\n (:id . 52))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 75) (:start . 70)\n (:id . 53))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 84)\n (:start . 76) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n (:id . 55))\n ((:tag . "NNP") (:stem . "P4_SP") (:form . "P4_SP") (:end . 91) (:start . 86)\n (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n (:id . 57))\n ((:tag . "NNP") (:stem . "P5_SP") (:form . "P5_SP") (:end . 101)\n (:start . 96) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n (:id . 59))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 110)\n (:start . 103) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 113) (:start . 111)\n (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n (:id . 62))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 128)\n (:start . 118) (:id . 63))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 133) (:start . 129)\n (:id . 64))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 140)\n (:start . 134) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 148)\n (:start . 142) (:id . 67))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 150) (:start . 149)\n (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s6.200) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101949@unknown@formal@none@1@S@To test whether the reported sea urchin sequences represent a true RAG1-like match, we cut off the ring finger motif and repeated the BLASTP search against all GenBank proteins.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 7) (:start . 3)\n (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 15)\n (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n (:id . 45))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 28)\n (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 32) (:start . 29)\n (:id . 47))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 39)\n (:start . 33) (:id . 48))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 49)\n (:start . 40) (:id . 49))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 59)\n (:start . 50) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 61) (:start . 60)\n (:id . 51))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 66) (:start . 62)\n (:id . 52))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 76)\n (:start . 67) (:id . 53))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 82) (:start . 77)\n (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n (:id . 55))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 86) (:start . 84)\n (:id . 56))\n ((:tag . "VBD") (:stem . "cut") (:form . "cut") (:end . 90) (:start . 87)\n (:id . 57))\n ((:tag . "RP") (:stem . "off") (:form . "off") (:end . 94) (:start . 91)\n (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n (:id . 59))\n ((:tag . "NN") (:stem . "ring") (:form . "ring") (:end . 103) (:start . 99)\n (:id . 60))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 110)\n (:start . 104) (:id . 61))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 116)\n (:start . 111) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n (:id . 63))\n ((:tag . "VBD") (:stem . "repeat") (:form . "repeated") (:end . 129)\n (:start . 121) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n (:id . 65))\n ((:tag . "NNP") (:stem . "BLASTP") (:form . "BLASTP") (:end . 140)\n (:start . 134) (:id . 66))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 147)\n (:start . 141) (:id . 67))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 155)\n (:start . 148) (:id . 68))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 159) (:start . 156)\n (:id . 69))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 167)\n (:start . 160) (:id . 70))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 176)\n (:start . 168) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n (:id . 72)))@@@1@31@((:hcues ((:id . :x6.210.1) (:span 8 15)))\n (:hscopes ((:id . :x6.210.1) (:span 8 82)))\n (:identifiers (:sid . :s6.210) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101959@unknown@formal@none@1@S@The sea urchin and lancelet proteins are marked by “_SP” and “_BF” following the identification numbers of the corresponding contigs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 7) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 14) (:start . 8)\n (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 18) (:start . 15)\n (:id . 45))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 27)\n (:start . 19) (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 36)\n (:start . 28) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 40) (:start . 37)\n (:id . 48))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 47) (:start . 41)\n (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 50) (:start . 48)\n (:id . 50))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 52) (:start . 51)\n (:id . 51))\n ((:tag . "NNP") (:stem . "_SP") (:form . "_SP") (:end . 55) (:start . 52)\n (:id . 52))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 56) (:start . 55)\n (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n (:id . 54))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 62) (:start . 61)\n (:id . 55))\n ((:tag . "NNP") (:stem . "_BF") (:form . "_BF") (:end . 65) (:start . 62)\n (:id . 56))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 66) (:start . 65)\n (:id . 57))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 76)\n (:start . 67) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n (:id . 59))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n (:end . 95) (:start . 81) (:id . 60))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 103)\n (:start . 96) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n (:id . 63))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 124)\n (:start . 111) (:id . 64))\n ((:tag . "NNS") (:stem . "contig") (:form . "contigs") (:end . 132)\n (:start . 125) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s6.220) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101969@unknown@formal@none@1@S@As shown in this paper, the RAG1 core was derived from a Transib TPase, but given the low identity between the Transib TPase and the RAG1 core (14%–17%) it is not clear whether the ancestral transposon was a member of the group of canonical Transib transposons preserved in modern genomes of insects, hydra, and sea urchin (see Figure 1), or a member of an unknown group of Transib transposons that encoded a TPase that was more similar to RAG1 core than to the canonical TPase from the currently known Transib transposons.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 16) (:start . 12)\n (:id . 45))\n ((:tag . "NN") (:stem . "paper") (:form . "paper") (:end . 22) (:start . 17)\n (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n (:id . 48))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 32) (:start . 28)\n (:id . 49))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 37) (:start . 33)\n (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 41) (:start . 38)\n (:id . 51))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 49)\n (:start . 42) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . 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"was") (:end . 423) (:start . 420)\n (:id . 126))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 428) (:start . 424)\n (:id . 127))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 436)\n (:start . 429) (:id . 128))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 439) (:start . 437)\n (:id . 129))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 444) (:start . 440)\n (:id . 130))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 449) (:start . 445)\n (:id . 131))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 454) (:start . 450)\n (:id . 132))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 457) (:start . 455)\n (:id . 133))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 461) (:start . 458)\n (:id . 134))\n ((:tag . "JJ") (:stem . "canonical") (:form . "canonical") (:end . 471)\n (:start . 462) (:id . 135))\n ((:tag . "NN") (:stem . "tpase") (:form . "TPase") (:end . 477)\n (:start . 472) (:id . 136))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 482) (:start . 478)\n (:id . 137))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 486) (:start . 483)\n (:id . 138))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 496)\n (:start . 487) (:id . 139))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 502)\n (:start . 497) (:id . 140))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 510)\n (:start . 503) (:id . 141))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 522)\n (:start . 511) (:id . 142))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 523) (:start . 522)\n (:id . 143)))@@@1@102@((:hcues ((:id . :x6.230.1) (:span 339 341))\n ((:id . :x6.230.2) (:span 169 176)) ((:id . :x6.230.3) (:span 159 168)))\n (:hscopes ((:id . :x6.230.1) (:span 206 522))\n ((:id . :x6.230.2) (:span 169 522)) ((:id . :x6.230.3) (:span 159 522)))\n (:identifiers (:sid . :s6.230) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101979@unknown@formal@none@1@S@Nevertheless, based on the orientations and relative positions of these transposons, none of them appears to be associated with the RAG1-like sequences (see Figure 5).@(((:tag . "RB") (:stem . "nevertheless") (:form . "Nevertheless") (:end . 12)\n (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n (:id . 43))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 19) (:start . 14)\n (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 22) (:start . 20)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n (:id . 46))\n ((:tag . "NNS") (:stem . "orientation") (:form . "orientations") (:end . 39)\n (:start . 27) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n (:id . 48))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 52)\n (:start . 44) (:id . 49))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 62)\n (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n (:id . 51))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 71) (:start . 66)\n (:id . 52))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 83)\n (:start . 72) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n (:id . 54))\n ((:tag . "NN") (:stem . "none") (:form . 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(:end . 167) (:start . 166)\n (:id . 71)))@@@1@30@((:hcues ((:id . :x6.240.2) (:span 98 105)))\n (:ncues ((:id . :x6.240.1) (:span 85 89)))\n (:hscopes ((:id . :x6.240.2) (:span 85 151)))\n (:nscopes ((:id . :x6.240.1) (:span 85 151)))\n (:identifiers (:sid . :s6.240) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101989@unknown@formal@none@1@S@In the sea urchin, lancelet, hydra, and starlet sea anemone genomes, the RAG1 core–like sequences and the N-terminal domain–like sequences do not appear to be linked to each other or to any other proteins.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 10) (:start . 7)\n (:id . 44))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 17)\n (:start . 11) (:id . 45))\n ((:tag . 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"not") (:end . 145) (:start . 142)\n (:id . 67))\n ((:tag . "VB") (:stem . "appear") (:form . "appear") (:end . 152)\n (:start . 146) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 155) (:start . 153)\n (:id . 69))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 158) (:start . 156)\n (:id . 70))\n ((:tag . "VBN") (:stem . "link") (:form . "linked") (:end . 165)\n (:start . 159) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 168) (:start . 166)\n (:id . 72))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 173) (:start . 169)\n (:id . 73))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 179)\n (:start . 174) (:id . 74))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 182) (:start . 180)\n (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 185) (:start . 183)\n (:id . 76))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 189) (:start . 186)\n (:id . 77))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 195)\n (:start . 190) (:id . 78))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 204)\n (:start . 196) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n (:id . 80)))@@@1@39@((:hcues ((:id . :x6.250.2) (:span 146 152)))\n (:ncues ((:id . :x6.250.1) (:span 142 145)))\n (:hscopes ((:id . :x6.250.2) (:span 69 204)))\n (:nscopes ((:id . :x6.250.1) (:span 69 204)))\n (:identifiers (:sid . :s6.250) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5101999@unknown@formal@none@1@S@Again, it is unclear if this part is not present in sea urchins or simply undetectable due to its small size and the high sequence divergence.@(((:tag . "RB") (:stem . "again") (:form . "Again") (:end . 5) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . 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(:end . 142) (:start . 141)\n (:id . 69)))@@@1@28@((:hcues ((:id . :x6.260.2) (:span 64 66)) ((:id . :x6.260.3) (:span 21 23))\n ((:id . :x6.260.4) (:span 13 20)))\n (:ncues ((:id . :x6.260.1) (:span 37 40)))\n (:hscopes ((:id . :x6.260.2) (:span 37 63))\n ((:id . :x6.260.3) (:span 21 141)) ((:id . :x6.260.4) (:span 13 141)))\n (:nscopes ((:id . :x6.260.1) (:span 37 86)))\n (:identifiers (:sid . :s6.260) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102009@unknown@formal@none@1@S@The observed sequence similarity between the RAG1 and Transib TPase protein can help to identify aa residues in the TPase that are crucial for transposition of Transib transposons.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 12)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "sequence") (:form . 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"IN") (:stem . "for") (:form . "for") (:end . 142) (:start . 139)\n (:id . 65))\n ((:tag . "NN") (:stem . "transposition") (:form . "transposition")\n (:end . 156) (:start . 143) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 159) (:start . 157)\n (:id . 67))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 167)\n (:start . 160) (:id . 68))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 179)\n (:start . 168) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n (:id . 70)))@@@1@29@((:hcues ((:id . :x6.270.1) (:span 76 79)))\n (:hscopes ((:id . :x6.270.1) (:span 76 179)))\n (:identifiers (:sid . :s6.270) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102019@unknown@formal@none@1@S@Second, although RAG1/2-mediated transpositions are characterized by 5-bp (sometimes 4-bp) TSDs, all known hAT transposons are characterized by 8-bp TSDs.@(((:tag . "RB") (:stem . "second") (:form . "Second") (:end . 6) (:start . 0)\n (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 16)\n (:start . 8) (:id . 44))\n ((:tag . "JJ") (:stem . "rag1/2-mediated") (:form . "RAG1/2-mediated")\n (:end . 32) (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "transposition") (:form . "transpositions")\n (:end . 47) (:start . 33) (:id . 46))\n ((:tag . "VBP") (:stem . 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(:end . 154) (:start . 153)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s6.280) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102029@unknown@formal@none@1@S@Partially assembled S. purpuratus contig sequences were downloaded on 12 August 2004 from the Baylor College of Medicine through the Web site at ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Spurpuratus/blast/Spur20030922-genome.@(((:tag . "RB") (:stem . "partially") (:form . "Partially") (:end . 9)\n (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "assemble") (:form . "assembled") (:end . 19)\n (:start . 10) (:id . 43))\n ((:tag . "NNP") (:stem . "S.") (:form . "S.") (:end . 22) (:start . 20)\n (:id . 44))\n ((:tag . "NN") (:stem . "purpuratus") (:form . "purpuratus") (:end . 33)\n (:start . 23) (:id . 45))\n ((:tag . "NN") (:stem . "contig") (:form . "contig") (:end . 40)\n (:start . 34) (:id . 46))\n ((:tag . "NNS") (:stem . "sequence") (:form . 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(:end . 219) (:start . 218)\n (:id . 66)))@@@1@25@((:identifiers (:sid . :s6.290) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102039@unknown@formal@none@1@S@To avoid background noise introduced by mutations, Transib relics, whose TPase-coding regions contained numerous stop codons and indels, were ignored unless several copies were available.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n (:id . 42))\n ((:tag . "VB") (:stem . "avoid") (:form . "avoid") (:end . 8) (:start . 3)\n (:id . 43))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 19)\n (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 25) (:start . 20)\n (:id . 45))\n ((:tag . "VBN") (:stem . "introduce") (:form . "introduced") (:end . 36)\n (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 39) (:start . 37)\n (:id . 47))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 49)\n (:start . 40) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n (:id . 49))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 58)\n (:start . 51) (:id . 50))\n ((:tag . "NNS") (:stem . "relic") (:form . "relics") (:end . 65)\n (:start . 59) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n (:id . 52))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 72) (:start . 67)\n (:id . 53))\n ((:tag . "NN") (:stem . "tpase-coding") (:form . "TPase-coding") (:end . 85)\n (:start . 73) (:id . 54))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 93)\n (:start . 86) (:id . 55))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 103)\n (:start . 94) (:id . 56))\n ((:tag . "JJ") (:stem . "numerous") (:form . "numerous") (:end . 112)\n (:start . 104) (:id . 57))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 117) (:start . 113)\n (:id . 58))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 124)\n (:start . 118) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n (:id . 60))\n ((:tag . "NNS") (:stem . "indel") (:form . "indels") (:end . 135)\n (:start . 129) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 141) (:start . 137)\n (:id . 63))\n ((:tag . "VBN") (:stem . "ignore") (:form . "ignored") (:end . 149)\n (:start . 142) (:id . 64))\n ((:tag . "IN") (:stem . "unless") (:form . "unless") (:end . 156)\n (:start . 150) (:id . 65))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 164)\n (:start . 157) (:id . 66))\n ((:tag . "NNS") (:stem . "copy") (:form . "copies") (:end . 171)\n (:start . 165) (:id . 67))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 176) (:start . 172)\n (:id . 68))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 186)\n (:start . 177) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n (:id . 70)))@@@1@29@((:identifiers (:sid . :s6.300) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102049@unknown@formal@none@1@S@A standalone 2001 version of PSI (Position-Specific Iterating)-BLAST [18,45] was used for detection of proteins that were significantly similar to TPases encoded by Transib and other superfamilies of DNA transposons.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n (:id . 42))\n ((:tag . "JJ") (:stem . "standalone") (:form . "standalone") (:end . 12)\n (:start . 2) (:id . 43))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 17) (:start . 13)\n (:id . 44))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 25)\n (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n (:id . 46))\n ((:tag . "NNP") (:stem . "PSI") (:form . "PSI") (:end . 32) (:start . 29)\n (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 34) (:start . 33)\n (:id . 48))\n ((:tag . "JJ") (:stem . "position-specific") (:form . "Position-Specific")\n (:end . 51) (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "Iterating)-BLAST") (:form . "Iterating)-BLAST")\n (:end . 68) (:start . 52) (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 70) (:start . 69)\n (:id . 51))\n ((:tag . "CD") (:stem . "18,45") (:form . "18,45") (:end . 75) (:start . 70)\n (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 76) (:start . 75)\n (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 80) (:start . 77)\n (:id . 54))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 85) (:start . 81)\n (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 89) (:start . 86)\n (:id . 56))\n ((:tag . "NN") (:stem . "detection") (:form . "detection") (:end . 99)\n (:start . 90) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 111)\n (:start . 103) (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 116) (:start . 112)\n (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 121) (:start . 117)\n (:id . 61))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n (:end . 135) (:start . 122) (:id . 62))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 143)\n (:start . 136) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 146) (:start . 144)\n (:id . 64))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 153)\n (:start . 147) (:id . 65))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 161)\n (:start . 154) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 164) (:start . 162)\n (:id . 67))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 172)\n (:start . 165) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 176) (:start . 173)\n (:id . 69))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 182)\n (:start . 177) (:id . 70))\n ((:tag . "NNS") (:stem . "superfamily") (:form . "superfamilies")\n (:end . 196) (:start . 183) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 199) (:start . 197)\n (:id . 72))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 203) (:start . 200)\n (:id . 73))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 215)\n (:start . 204) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n (:id . 75)))@@@1@34@((:identifiers (:sid . :s6.310) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102059@unknown@formal@none@1@S@The following protocol describes the procedure: (1) Use a GenBank set combined with N number of Transib TPases (in our studies, N was equal to 7, 13, and 18), (2) run PSI-BLAST against GenBank combined with TPases using each TPase as a query or seed, (3) select only Transib TPase sequences with E-values less than 10-5 to define the PSSM, (4) take the best E-value (Ei) obtained by PSI-BLAST for RAG1s when PSSM is constructed without RAG1, then (5) repeat these operations for different numbers (N) of TPases.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 13)\n (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 22)\n (:start . 14) (:id . 44))\n ((:tag . "VBZ") (:stem . "describe") (:form . "describes") (:end . 32)\n (:start . 23) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n (:id . 46))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 46)\n (:start . 37) (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 47) (:start . 46)\n (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 49) (:start . 48)\n (:id . 49))\n ((:tag . "LS") (:stem . "1") (:form . "1") (:end . 50) (:start . 49)\n (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 51) (:start . 50)\n (:id . 51))\n ((:tag . "VB") (:stem . "use") (:form . "Use") (:end . 55) (:start . 52)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n (:id . 53))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 65)\n (:start . 58) (:id . 54))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 69) (:start . 66)\n (:id . 55))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 78)\n (:start . 70) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 83) (:start . 79)\n (:id . 57))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 85) (:start . 84)\n (:id . 58))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 92)\n (:start . 86) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n (:id . 60))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 103)\n (:start . 96) (:id . 61))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 110)\n (:start . 104) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n (:id . 64))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 118) (:start . 115)\n (:id . 65))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 126)\n (:start . 119) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n (:id . 67))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 129) (:start . 128)\n (:id . 68))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 133) (:start . 130)\n (:id . 69))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 139)\n (:start . 134) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n (:id . 71))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 144) (:start . 143)\n (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n (:id . 73))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 148) (:start . 146)\n (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 153) (:start . 150)\n (:id . 76))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 156) (:start . 154)\n (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 157) (:start . 156)\n (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 160) (:start . 159)\n (:id . 80))\n ((:tag . "LS") (:stem . "2") (:form . "2") (:end . 161) (:start . 160)\n (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n (:id . 82))\n ((:tag . "VB") (:stem . "run") (:form . "run") (:end . 166) (:start . 163)\n (:id . 83))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 176)\n (:start . 167) (:id . 84))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 184)\n (:start . 177) (:id . 85))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 192)\n (:start . 185) (:id . 86))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 201)\n (:start . 193) (:id . 87))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 206) (:start . 202)\n (:id . 88))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 213)\n (:start . 207) (:id . 89))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 219) (:start . 214)\n (:id . 90))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 224) (:start . 220)\n (:id . 91))\n ((:tag . "NN") (:stem . "tpase") (:form . "TPase") (:end . 230)\n (:start . 225) (:id . 92))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 233) (:start . 231)\n (:id . 93))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 235) (:start . 234)\n (:id . 94))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 241)\n (:start . 236) (:id . 95))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 244) (:start . 242)\n (:id . 96))\n ((:tag . "NN") (:stem . "seed") (:form . "seed") (:end . 249) (:start . 245)\n (:id . 97))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 250) (:start . 249)\n (:id . 98))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 252) (:start . 251)\n (:id . 99))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 253) (:start . 252)\n (:id . 100))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 254) (:start . 253)\n (:id . 101))\n ((:tag . "VBP") (:stem . "select") (:form . "select") (:end . 261)\n (:start . 255) (:id . 102))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 266) (:start . 262)\n (:id . 103))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 274)\n (:start . 267) (:id . 104))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 280)\n (:start . 275) (:id . 105))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 290)\n (:start . 281) (:id . 106))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 295) (:start . 291)\n (:id . 107))\n ((:tag . "NNS") (:stem . "e-value") (:form . "E-values") (:end . 304)\n (:start . 296) (:id . 108))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 309) (:start . 305)\n (:id . 109))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 314) (:start . 310)\n (:id . 110))\n ((:tag . "CD") (:stem . "10-5") (:form . "10-5") (:end . 319) (:start . 315)\n (:id . 111))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 322) (:start . 320)\n (:id . 112))\n ((:tag . "VB") (:stem . "define") (:form . "define") (:end . 329)\n (:start . 323) (:id . 113))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 333) (:start . 330)\n (:id . 114))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 338) (:start . 334)\n (:id . 115))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 339) (:start . 338)\n (:id . 116))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 341) (:start . 340)\n (:id . 117))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 342) (:start . 341)\n (:id . 118))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 343) (:start . 342)\n (:id . 119))\n ((:tag . "VBP") (:stem . "take") (:form . "take") (:end . 348) (:start . 344)\n (:id . 120))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 352) (:start . 349)\n (:id . 121))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 357) (:start . 353)\n (:id . 122))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-value") (:end . 365)\n (:start . 358) (:id . 123))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 367) (:start . 366)\n (:id . 124))\n ((:tag . "NNP") (:stem . "Ei") (:form . "Ei") (:end . 369) (:start . 367)\n (:id . 125))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 370) (:start . 369)\n (:id . 126))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 379)\n (:start . 371) (:id . 127))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 382) (:start . 380)\n (:id . 128))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 392)\n (:start . 383) (:id . 129))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 396) (:start . 393)\n (:id . 130))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1s") (:end . 402)\n (:start . 397) (:id . 131))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 407) (:start . 403)\n (:id . 132))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 412) (:start . 408)\n (:id . 133))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 415) (:start . 413)\n (:id . 134))\n ((:tag . "VBN") (:stem . "construct") (:form . "constructed") (:end . 427)\n (:start . 416) (:id . 135))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 435)\n (:start . 428) (:id . 136))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 440) (:start . 436)\n (:id . 137))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 441) (:start . 440)\n (:id . 138))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 446) (:start . 442)\n (:id . 139))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 448) (:start . 447)\n (:id . 140))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 449) (:start . 448)\n (:id . 141))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 450) (:start . 449)\n (:id . 142))\n ((:tag . "VBP") (:stem . "repeat") (:form . "repeat") (:end . 457)\n (:start . 451) (:id . 143))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 463)\n (:start . 458) (:id . 144))\n ((:tag . "NNS") (:stem . "operation") (:form . "operations") (:end . 474)\n (:start . 464) (:id . 145))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 478) (:start . 475)\n (:id . 146))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 488)\n (:start . 479) (:id . 147))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 496)\n (:start . 489) (:id . 148))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 498) (:start . 497)\n (:id . 149))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 499) (:start . 498)\n (:id . 150))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 500) (:start . 499)\n (:id . 151))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 503) (:start . 501)\n (:id . 152))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 510)\n (:start . 504) (:id . 153))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 511) (:start . 510)\n (:id . 154)))@@@1@113@((:ncues ((:id . :x6.320.1) (:span 428 435)))\n (:nscopes ((:id . :x6.320.1) (:span 428 440)))\n (:identifiers (:sid . :s6.320) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102069@unknown@formal@none@1@S@One of the 5-bp TSDs flanking the 3? terminus of a Transib was excluded in each case.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 6) (:start . 4)\n (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n (:id . 44))\n ((:tag . "JJ") (:stem . "5-bp") (:form . "5-bp") (:end . 15) (:start . 11)\n (:id . 45))\n ((:tag . "NNS") (:stem . "tsd") (:form . "TSDs") (:end . 20) (:start . 16)\n (:id . 46))\n ((:tag . "VBG") (:stem . "flank") (:form . "flanking") (:end . 29)\n (:start . 21) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n (:id . 48))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 35) (:start . 34)\n (:id . 49))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 36) (:start . 35)\n (:id . 50))\n ((:tag . "NN") (:stem . "terminus") (:form . "terminus") (:end . 45)\n (:start . 37) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 50) (:start . 49)\n (:id . 53))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 58)\n (:start . 51) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 62) (:start . 59)\n (:id . 55))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 71)\n (:start . 63) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n (:id . 57))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 79) (:start . 75)\n (:id . 58))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 84) (:start . 80)\n (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.330) (:did . :pmc1131882) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102079@unknown@formal@none@1@S@Multiple Alignment of the RAG1 Core and Transib TPase Proteins@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "alignment") (:form . "Alignment") (:end . 18)\n (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . 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(:end . 98) (:start . 97)\n (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.41) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102179@unknown@formal@none@1@S@This result confirms that the mutant phenotype is caused by the mutation in the ADGF-A gene.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 11) (:start . 5)\n (:id . 43))\n ((:tag . "VBZ") (:stem . "confirm") (:form . "confirms") (:end . 20)\n (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n (:id . 46))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 36)\n (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 46)\n (:start . 37) (:id . 48))\n ((:tag . 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(:end . 92) (:start . 91)\n (:id . 58)))@@@1@17@((:identifiers (:sid . :s7.51) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102189@unknown@formal@none@1@S@Each experiment was repeated at least four times (with 20–30 animals in each vial) and the standard error is shown.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 15)\n (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 19) (:start . 16)\n (:id . 44))\n ((:tag . "VBN") (:stem . "repeat") (:form . "repeated") (:end . 28)\n (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 31) (:start . 29)\n (:id . 46))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 37) (:start . 32)\n (:id . 47))\n ((:tag . "CD") (:stem . "four") (:form . 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(:end . 163) (:start . 162)\n (:id . 68)))@@@1@27@((:identifiers (:sid . :s7.291) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102429@unknown@formal@none@1@S@Fat body observation@(((:tag . "NNP") (:stem . "Fat") (:form . "Fat") (:end . 3) (:start . 0)\n (:id . 42))\n ((:tag . "NN") (:stem . "body") (:form . "body") (:end . 8) (:start . 4)\n (:id . 43))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 20)\n (:start . 9) (:id . 44)))@@@1@3@((:identifiers (:sid . :s7.301) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011 5102439@unknown@formal@none@1@S@To observe hemocyte morphology, samples were analyzed at least 10 min after the deposition of solution with hemocytes, in order to allow the cells to adhere to the surface of the slide.@(((:tag . "TO") (:stem . "to") (:form . 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"CD") (:stem . "3") (:form . "3") (:end . 188) (:start . 187)\n (:id . 77))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 189) (:start . 188)\n (:id . 78))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 193) (:start . 190)\n (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 194) (:start . 193)\n (:id . 80))\n ((:tag . "VBN") (:stem . "cut") (:form . "cut") (:end . 198) (:start . 195)\n (:id . 81))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 201) (:start . 199)\n (:id . 82))\n ((:tag . "NNP") (:stem . "XhoI/XbaI") (:form . "XhoI/XbaI") (:end . 211)\n (:start . 202) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n (:id . 84)))@@@1@43@((:identifiers (:sid . :s7.321) (:did . :pmc1135298) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011 5102459@unknown@formal@none@1@S@A comparison of programmed cell death between species@(((:tag . "DT") (:stem . "a") (:form . 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"species") (:end . 53)\n (:start . 46) (:id . 49)))@@@1@8@((:identifiers (:sid . :s8.1) (:did . :pmc138857) (:did-type . :pmcid)\n (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011 5102469@unknown@formal@none@1@S@Programmed cell death has long been known to be a part of normal development, but it was not until the discovery of the first genes essential for the phenomenon that our understanding of the events leading up to the deliberate elimination of a cell began to take shape.@(((:tag . "VBN") (:stem . "program") (:form . "Programmed") (:end . 10)\n (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 15) (:start . 11)\n (:id . 43))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 21) (:start . 16)\n (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 25) (:start . 22)\n (:id . 45))\n ((:tag . "RB") (:stem . "long") (:form . "long") (:end . 30) (:start . 26)\n (:id . 46))\n ((:tag . "VBN") (:stem . 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