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Volumn 12, Issue , 2011, Pages

Using context to improve protein domain identification

Author keywords

[No Author keywords available]

Indexed keywords

CONFIDENCE DOMAIN; FUNCTION PREDICTION; FUNCTIONAL ANNOTATION; MALARIA PARASITE; OPEN SOURCE LICENSE; PLASMODIUM FALCIPARUM; PROTEIN SEQUENCES; RECOGNITION METHODS;

EID: 79953168457     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-90     Document Type: Article
Times cited : (23)

References (45)
  • 1
    • 0035408587 scopus 로고    scopus 로고
    • Genome annotation: from sequence to biology
    • 10.1038/35080529, 11433356
    • Stein L. Genome annotation: from sequence to biology. Nat Rev Genet 2001, 2:493-503. 10.1038/35080529, 11433356.
    • (2001) Nat Rev Genet , vol.2 , pp. 493-503
    • Stein, L.1
  • 2
    • 0036228634 scopus 로고    scopus 로고
    • Predicting Gene Ontology Functions from ProDom and CDD Protein Domains
    • 10.1101/gr.222902, 187511, 11932249
    • Schug J, Diskin S, Mazzarelli J, Brunk BP, Stoeckert CJ. Predicting Gene Ontology Functions from ProDom and CDD Protein Domains. Genome Res 2002, 12:648-655. 10.1101/gr.222902, 187511, 11932249.
    • (2002) Genome Res , vol.12 , pp. 648-655
    • Schug, J.1    Diskin, S.2    Mazzarelli, J.3    Brunk, B.P.4    Stoeckert, C.J.5
  • 3
    • 48249113702 scopus 로고    scopus 로고
    • Predicting protein function from domain content
    • 10.1093/bioinformatics/btn312, 18591194
    • Forslund K, Sonnhammer ELL. Predicting protein function from domain content. Bioinformatics 2008, 24:1681-1687. 10.1093/bioinformatics/btn312, 18591194.
    • (2008) Bioinformatics , vol.24 , pp. 1681-1687
    • Forslund, K.1    Sonnhammer, E.L.L.2
  • 4
    • 58149203228 scopus 로고    scopus 로고
    • SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny
    • 10.1093/nar/gkn762, 2686452, 19036790
    • Wilson D, Pethica R, Zhou Y, Talbot C, Vogel C, Madera M, Chothia C, Gough J. SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. Nucl Acids Res 2009, 37:D380-386. 10.1093/nar/gkn762, 2686452, 19036790.
    • (2009) Nucl Acids Res , vol.37
    • Wilson, D.1    Pethica, R.2    Zhou, Y.3    Talbot, C.4    Vogel, C.5    Madera, M.6    Chothia, C.7    Gough, J.8
  • 6
    • 1542286754 scopus 로고    scopus 로고
    • Comparative Analysis of Protein Domain Organization
    • 10.1101/gr.1610504, 535408, 14993202
    • Ye Y, Godzik A. Comparative Analysis of Protein Domain Organization. Genome Res 2004, 14:343-353. 10.1101/gr.1610504, 535408, 14993202.
    • (2004) Genome Res , vol.14 , pp. 343-353
    • Ye, Y.1    Godzik, A.2
  • 7
    • 4444339460 scopus 로고    scopus 로고
    • Comparative Genomics of Transcriptional Control in the Human Malaria Parasite Plasmodium falciparum
    • 10.1101/gr.2218604, 509263, 15256513
    • Coulson RMR, Hall N, Ouzounis C. Comparative Genomics of Transcriptional Control in the Human Malaria Parasite Plasmodium falciparum. Genome Res 2004, 14:1548-1554. 10.1101/gr.2218604, 509263, 15256513.
    • (2004) Genome Res , vol.14 , pp. 1548-1554
    • Coulson, R.M.R.1    Hall, N.2    Ouzounis, C.3
  • 8
    • 37049002223 scopus 로고    scopus 로고
    • Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes
    • 10.1016/j.ijpara.2007.07.018, 17949725
    • Iyer LM, Anantharaman V, Wolf MY, Aravind L. Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes. Int J Parasitol 2008, 38:1-31. 10.1016/j.ijpara.2007.07.018, 17949725.
    • (2008) Int J Parasitol , vol.38 , pp. 1-31
    • Iyer, L.M.1    Anantharaman, V.2    Wolf, M.Y.3    Aravind, L.4
  • 9
    • 33646001426 scopus 로고    scopus 로고
    • Graph Theoretical Insights into Dollo Parsimony and Evolution of Multidomain Proteins
    • 10.1089/cmb.2006.13.351, 1815482, 16597245
    • Przytycka T, Davis G, Song N, Durand D. Graph Theoretical Insights into Dollo Parsimony and Evolution of Multidomain Proteins. J Comput Biol 2006, 13:351-363. 10.1089/cmb.2006.13.351, 1815482, 16597245.
    • (2006) J Comput Biol , vol.13 , pp. 351-363
    • Przytycka, T.1    Davis, G.2    Song, N.3    Durand, D.4
  • 10
    • 33846266906 scopus 로고    scopus 로고
    • Modeling the Evolution of Protein Domain Architectures Using Maximum Parsimony
    • 10.1016/j.jmb.2006.11.017, 1858635, 17166515
    • Fong JH, Geer LY, Panchenko AR, Bryant SH. Modeling the Evolution of Protein Domain Architectures Using Maximum Parsimony. J Mol Biol 2007, 366:307-315. 10.1016/j.jmb.2006.11.017, 1858635, 17166515.
    • (2007) J Mol Biol , vol.366 , pp. 307-315
    • Fong, J.H.1    Geer, L.Y.2    Panchenko, A.R.3    Bryant, S.H.4
  • 11
    • 57049169765 scopus 로고    scopus 로고
    • Just how versatile are domains?
    • 10.1186/1471-2148-8-285, 2588589, 18854028
    • Weiner J, Moore A, Bornberg-Bauer E. Just how versatile are domains?. BMC Evol Biol 2008, 8:285. 10.1186/1471-2148-8-285, 2588589, 18854028.
    • (2008) BMC Evol Biol , vol.8 , pp. 285
    • Weiner, J.1    Moore, A.2    Bornberg-Bauer, E.3
  • 12
    • 0035943340 scopus 로고    scopus 로고
    • Correlated sequence-signatures as markers of protein-protein interaction
    • 10.1006/jmbi.2001.4920, 11518523
    • Sprinzak E, Margalit H. Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol 2001, 311:681-692. 10.1006/jmbi.2001.4920, 11518523.
    • (2001) J Mol Biol , vol.311 , pp. 681-692
    • Sprinzak, E.1    Margalit, H.2
  • 13
    • 0036799752 scopus 로고    scopus 로고
    • Inferring Domain-Domain Interactions From Protein-Protein Interactions
    • 10.1101/gr.153002, 187530, 12368246
    • Deng M, Mehta S, Sun F, Chen T. Inferring Domain-Domain Interactions From Protein-Protein Interactions. Genome Res 2002, 12:1540-1548. 10.1101/gr.153002, 187530, 12368246.
    • (2002) Genome Res , vol.12 , pp. 1540-1548
    • Deng, M.1    Mehta, S.2    Sun, F.3    Chen, T.4
  • 14
    • 33847753484 scopus 로고    scopus 로고
    • Predicting domain-domain interactions using a parsimony approach
    • 1794579, 17094802
    • Guimarães K, Jothi R, Zotenko E, Przytycka T. Predicting domain-domain interactions using a parsimony approach. Genome Biol 2006, 7:R104. 1794579, 17094802.
    • (2006) Genome Biol , vol.7
    • Guimarães, K.1    Jothi, R.2    Zotenko, E.3    Przytycka, T.4
  • 15
    • 67149143183 scopus 로고    scopus 로고
    • Inferring Protein-Protein Interactions from Multiple Protein Domain Combinations
    • Kanaan SP, Huang C, Wuchty S, Chen DZ, Izaguirre JA. Inferring Protein-Protein Interactions from Multiple Protein Domain Combinations. Method Mol Biol 2009, 541:43-59.
    • (2009) Method Mol Biol , vol.541 , pp. 43-59
    • Kanaan, S.P.1    Huang, C.2    Wuchty, S.3    Chen, D.Z.4    Izaguirre, J.A.5
  • 16
    • 44949207428 scopus 로고    scopus 로고
    • Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins
    • 10.1371/journal.pcbi.1000063, 2377100, 18475320
    • Song N, Joseph JM, Davis GB, Durand D. Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins. PLoS Comput Biol 2008, 4:e1000063. 10.1371/journal.pcbi.1000063, 2377100, 18475320.
    • (2008) PLoS Comput Biol , vol.4
    • Song, N.1    Joseph, J.M.2    Davis, G.B.3    Durand, D.4
  • 17
    • 3242891265 scopus 로고    scopus 로고
    • CHOP: parsing proteins into structural domains
    • 10.1093/nar/gkh481, 441619, 15215452
    • Liu J, Rost B. CHOP: parsing proteins into structural domains. Nucl Acids Res 2004, 32:W569-W571. 10.1093/nar/gkh481, 441619, 15215452.
    • (2004) Nucl Acids Res , vol.32
    • Liu, J.1    Rost, B.2
  • 18
    • 0842268045 scopus 로고    scopus 로고
    • Supra-domains: Evolutionary Units Larger than Single Protein Domains
    • 10.1016/j.jmb.2003.12.026, 15095989
    • Vogel C, Berzuini C, Bashton M, Gough J, Teichmann SA. Supra-domains: Evolutionary Units Larger than Single Protein Domains. J Mol Biol 2004, 336:809-823. 10.1016/j.jmb.2003.12.026, 15095989.
    • (2004) J Mol Biol , vol.336 , pp. 809-823
    • Vogel, C.1    Berzuini, C.2    Bashton, M.3    Gough, J.4    Teichmann, S.A.5
  • 20
    • 0037446851 scopus 로고    scopus 로고
    • Enhanced protein domain discovery by using language modeling techniques from speech recognition
    • Coin L, Bateman A, Durbin R. Enhanced protein domain discovery by using language modeling techniques from speech recognition. P Natl Acad Sci USA 2003, 100:4516-4520.
    • (2003) P Natl Acad Sci USA , vol.100 , pp. 4516-4520
    • Coin, L.1    Bateman, A.2    Durbin, R.3
  • 22
    • 0028181441 scopus 로고
    • Hidden Markov Models in Computational Biology: Applications to Protein Modeling
    • 10.1006/jmbi.1994.1104, 8107089
    • Krogh A, Brown M, Mian IS, Sjölander K, Haussler D. Hidden Markov Models in Computational Biology: Applications to Protein Modeling. J Mol Biol 1994, 235:1501-1531. 10.1006/jmbi.1994.1104, 8107089.
    • (1994) J Mol Biol , vol.235 , pp. 1501-1531
    • Krogh, A.1    Brown, M.2    Mian, I.S.3    Sjölander, K.4    Haussler, D.5
  • 23
    • 58149194624 scopus 로고    scopus 로고
    • SMART 6: recent updates and new developments
    • 10.1093/nar/gkn808, 2686533, 18978020
    • Letunic I, Doerks T, Bork P. SMART 6: recent updates and new developments. Nucl Acids Res 2009, 37:D229-232. 10.1093/nar/gkn808, 2686533, 18978020.
    • (2009) Nucl Acids Res , vol.37
    • Letunic, I.1    Doerks, T.2    Bork, P.3
  • 24
    • 75949115003 scopus 로고    scopus 로고
    • Detection of new protein domains using co-occurrence: application to Plasmodium falciparum
    • 10.1093/bioinformatics/btp560, 19786484
    • Terrapon N, Gascuel O, Marechal E, Brehelin L. Detection of new protein domains using co-occurrence: application to Plasmodium falciparum. Bioinformatics 2009, 25:3077-3083. 10.1093/bioinformatics/btp560, 19786484.
    • (2009) Bioinformatics , vol.25 , pp. 3077-3083
    • Terrapon, N.1    Gascuel, O.2    Marechal, E.3    Brehelin, L.4
  • 25
    • 58149191270 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt) 2009
    • 10.1093/nar/gkn664, 2686606, 18836194, The UniProt Consortium
    • The UniProt Consortium The Universal Protein Resource (UniProt) 2009. Nucl Acids Res 2009, 37:D169-174. 10.1093/nar/gkn664, 2686606, 18836194, The UniProt Consortium.
    • (2009) Nucl Acids Res , vol.37
  • 30
    • 31344482543 scopus 로고    scopus 로고
    • Lp_solve: Open source (Mixed-Integer) Linear Programming system
    • lp_solve: Open source (Mixed-Integer) Linear Programming system. , http://lpsolve.sourceforge.net/
  • 31
    • 71849096141 scopus 로고    scopus 로고
    • How does multiple testing correction work?
    • Noble WS. How does multiple testing correction work?. Nat Biotech 2009, 27:1135-1137.
    • (2009) Nat Biotech , vol.27 , pp. 1135-1137
    • Noble, W.S.1
  • 32
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
    • 10.1101/gr.1224503, 403725, 12952885
    • Li L, Stoeckert CJ, Roos DS. OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Res 2003, 13:2178-2189. 10.1101/gr.1224503, 403725, 12952885.
    • (2003) Genome Res , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 33
    • 0034623005 scopus 로고    scopus 로고
    • T-coffee: a novel method for fast and accurate multiple sequence alignment
    • 10.1006/jmbi.2000.4042, 10964570
    • Notredame C, Higgins DG, Heringa J. T-coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302:205-217. 10.1006/jmbi.2000.4042, 10964570.
    • (2000) J Mol Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 34
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: Probabilistic consistency-based multiple sequence alignment
    • 10.1101/gr.2821705, 546535, 15687296
    • Do CB, Mahabhashyam MSP, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res 2005, 15:330-340. 10.1101/gr.2821705, 546535, 15687296.
    • (2005) Genome Res , vol.15 , pp. 330-340
    • Do, C.B.1    Mahabhashyam, M.S.P.2    Brudno, M.3    Batzoglou, S.4
  • 35
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • 10.1093/nar/gkh340, 390337, 15034147
    • Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 2004, 32:1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
    • (2004) Nucl Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 37
    • 74549193046 scopus 로고    scopus 로고
    • Genome wide identification of Plasmodium falciparum helicases: a comparison with human host
    • 10.4161/cc.9.1.10241, 20016272
    • Tuteja R. Genome wide identification of Plasmodium falciparum helicases: a comparison with human host. Cell Cycle 2010, 9:104-120. 10.4161/cc.9.1.10241, 20016272.
    • (2010) Cell Cycle , vol.9 , pp. 104-120
    • Tuteja, R.1
  • 38
    • 34547914091 scopus 로고    scopus 로고
    • Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN)
    • 10.1093/bioinformatics/btm240, 17483506
    • Beaussart F, Weiner J, Bornberg-Bauer E. Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN). Bioinformatics 2007, 23:1834-1836. 10.1093/bioinformatics/btm240, 17483506.
    • (2007) Bioinformatics , vol.23 , pp. 1834-1836
    • Beaussart, F.1    Weiner, J.2    Bornberg-Bauer, E.3
  • 39
    • 34548487255 scopus 로고    scopus 로고
    • Quantification of the Elevated Rate of Domain Rearrangements in Metazoa
    • 10.1016/j.jmb.2007.06.022, 17689563
    • Ekman D, Björklund T, Elofsson A. Quantification of the Elevated Rate of Domain Rearrangements in Metazoa. J Mol Biol 2007, 372:1337-1348. 10.1016/j.jmb.2007.06.022, 17689563.
    • (2007) J Mol Biol , vol.372 , pp. 1337-1348
    • Ekman, D.1    Björklund, T.2    Elofsson, A.3
  • 40
    • 67649850988 scopus 로고    scopus 로고
    • PROCAIN: protein profile comparison with assisting information
    • 10.1093/nar/gkp212, 2699500, 19357092
    • Wang Y, Sadreyev RI, Grishin NV. PROCAIN: protein profile comparison with assisting information. Nucl Acids Res 2009, 37:3522-3530. 10.1093/nar/gkp212, 2699500, 19357092.
    • (2009) Nucl Acids Res , vol.37 , pp. 3522-3530
    • Wang, Y.1    Sadreyev, R.I.2    Grishin, N.V.3
  • 42
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Söding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005, 21:951-960.
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Söding, J.1
  • 43
    • 54349085032 scopus 로고    scopus 로고
    • Hidden Markov Models Incorporating Fuzzy Measures and Integrals for Protein Sequence Identification and Alignment
    • Bidargaddi NP, Chetty M, Kamruzzaman J. Hidden Markov Models Incorporating Fuzzy Measures and Integrals for Protein Sequence Identification and Alignment. Genomics, Proteomics & Bioinformatics 2008, 6:98-110.
    • (2008) Genomics, Proteomics & Bioinformatics , vol.6 , pp. 98-110
    • Bidargaddi, N.P.1    Chetty, M.2    Kamruzzaman, J.3
  • 44
    • 0025259313 scopus 로고
    • Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
    • Karlin S, Altschul SF. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. P Natl Acad Sci USA 1990, 87:2264-2268.
    • (1990) P Natl Acad Sci USA , vol.87 , pp. 2264-2268
    • Karlin, S.1    Altschul, S.F.2


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