메뉴 건너뛰기




Volumn 25, Issue 14, 2009, Pages 1739-1745

ESG: Extended similarity group method for automated protein function prediction

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; AUTOMATION; BIOINFORMATICS; CLIENT SERVER APPLICATION; COMPUTER PREDICTION; CONTROLLED STUDY; INFORMATION RETRIEVAL; INTERMETHOD COMPARISON; PRIORITY JOURNAL; PROBABILITY; PROTEIN FUNCTION; SEQUENCE DATABASE;

EID: 67649868148     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp309     Document Type: Article
Times cited : (76)

References (31)
  • 1
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
    • (1990) J. Mol. Biol , vol.215 , pp. 403-410
    • Altschul, S.F.1
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 3
    • 13444273448 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt)
    • Bairoch,A. et al. (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res., 33, D154-D159.
    • (2005) Nucleic Acids Res , vol.33
    • Bairoch, A.1
  • 4
    • 0035424599 scopus 로고    scopus 로고
    • Intrinsic errors in genome annotation
    • Devos,D. and Valencia,A. (2001) Intrinsic errors in genome annotation. Trends Genet., 17, 429-431.
    • (2001) Trends Genet , vol.17 , pp. 429-431
    • Devos, D.1    Valencia, A.2
  • 5
    • 33947420442 scopus 로고    scopus 로고
    • The relationship between protein sequences and their gene ontology functions
    • Duan,Z.H. et al. (2006) The relationship between protein sequences and their gene ontology functions. BMC Bioinformatics, 7 (Suppl. 4), S11.
    • (2006) BMC Bioinformatics , vol.7 , Issue.SUPPL. 4
    • Duan, Z.H.1
  • 6
    • 0034178257 scopus 로고    scopus 로고
    • Homology a personal view on some of the problems
    • Fitch,W.M. (2000) Homology a personal view on some of the problems. Trends Genet., 16, 227-231.
    • (2000) Trends Genet , vol.16 , pp. 227-231
    • Fitch, W.M.1
  • 7
    • 33748776559 scopus 로고    scopus 로고
    • Automated protein function prediction - the genomic challenge
    • Friedberg,I. (2006) Automated protein function prediction - the genomic challenge. Brief Bioinform., 7, 225-242.
    • (2006) Brief Bioinform , vol.7 , pp. 225-242
    • Friedberg, I.1
  • 8
    • 33744471138 scopus 로고    scopus 로고
    • New avenues in protein function prediction
    • Friedberg,I. et al. (2006) New avenues in protein function prediction. Protein Sci., 15, 1527-1529.
    • (2006) Protein Sci , vol.15 , pp. 1527-1529
    • Friedberg, I.1
  • 9
    • 0032229196 scopus 로고    scopus 로고
    • Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement and operon disruption
    • Galperin,M.Y. and Koonin,E.V. (1998) Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement and operon disruption. In Silico Biol., 1, 55-67.
    • (1998) In Silico Biol , vol.1 , pp. 55-67
    • Galperin, M.Y.1    Koonin, E.V.2
  • 10
    • 0346801873 scopus 로고    scopus 로고
    • The gene ontology (GO) database and informatics resource
    • Harris,M.A. (2004) The gene ontology (GO) database and informatics resource. Nucleic Acid Res., 32, D258-D261.
    • (2004) Nucleic Acid Res , vol.32
    • Harris, M.A.1
  • 11
    • 34248155322 scopus 로고    scopus 로고
    • Function prediction of uncharacterized proteins
    • Hawkins,T. and Kihara,D. (2007) Function prediction of uncharacterized proteins. J. Bioinform. Comput. Biol., 5, 1-30.
    • (2007) J. Bioinform. Comput. Biol , vol.5 , pp. 1-30
    • Hawkins, T.1    Kihara, D.2
  • 12
    • 33744471931 scopus 로고    scopus 로고
    • Enhanced automated function prediction using distantly related sequences and contextual association by PFP
    • Hawkins,T. et al. (2006) Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Sci., 15, 1550-1556.
    • (2006) Protein Sci , vol.15 , pp. 1550-1556
    • Hawkins, T.1
  • 13
    • 39449130713 scopus 로고    scopus 로고
    • New paradigm in protein function prediction for large scale omics analysis
    • Hawkins,T. et al. (2008) New paradigm in protein function prediction for large scale omics analysis. Mol. Biosyst., 4, 223-231.
    • (2008) Mol. Biosyst , vol.4 , pp. 223-231
    • Hawkins, T.1
  • 14
    • 59849089151 scopus 로고    scopus 로고
    • PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data
    • Hawkins,T. et al. (2009) PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data. Proteins, 74, 556-582.
    • (2009) Proteins , vol.74 , pp. 556-582
    • Hawkins, T.1
  • 15
    • 0242490786 scopus 로고    scopus 로고
    • Functionality of system components: Conservation of protein function in protein feature space
    • Jensen,L.J. (2003) Functionality of system components: Conservation of protein function in protein feature space. Genome Res., 13, 2444-2449.
    • (2003) Genome Res , vol.13 , pp. 2444-2449
    • Jensen, L.J.1
  • 16
    • 0346734106 scopus 로고    scopus 로고
    • Detection of homologous proteins by an intermediate sequence search
    • John,B. and Sali,A. (2004) Detection of homologous proteins by an intermediate sequence search. Protein Sci., 13, 54-62.
    • (2004) Protein Sci , vol.13 , pp. 54-62
    • John, B.1    Sali, A.2
  • 17
    • 38549126643 scopus 로고    scopus 로고
    • KEGG for linking genomes to life and the environment
    • Kanehisa,M. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res., 36, D480-D484.
    • (2008) Nucleic Acids Res , vol.36
    • Kanehisa, M.1
  • 18
    • 13244285287 scopus 로고    scopus 로고
    • ProtoNet 4.0: A hierarchical classification of one million protein sequences
    • Kaplan,N. et al. (2005) ProtoNet 4.0: A hierarchical classification of one million protein sequences. Nucleic Acids Res. 33, D216-D218.
    • (2005) Nucleic Acids Res , vol.33
    • Kaplan, N.1
  • 19
    • 0348143187 scopus 로고    scopus 로고
    • GoFigure: Automated Gene Ontology annotation
    • Khan,S. et al. (2003) GoFigure: Automated Gene Ontology annotation. Bioinformatics, 19, 2484-2485.
    • (2003) Bioinformatics , vol.19 , pp. 2484-2485
    • Khan, S.1
  • 20
    • 49549101130 scopus 로고    scopus 로고
    • Connect the dots: Exposing hidden protein family connections from the entire sequence tree
    • Loewenstein,Y. and Linial,M. (2008) Connect the dots: Exposing hidden protein family connections from the entire sequence tree. Bioinformatics, 24, i193-i199.
    • (2008) Bioinformatics , vol.24
    • Loewenstein, Y.1    Linial, M.2
  • 21
    • 36748998785 scopus 로고    scopus 로고
    • Assessment of predictions submitted for the CASP7 function prediction category
    • Lopez,G. et al. (2007) Assessment of predictions submitted for the CASP7 function prediction category. Proteins, 69, 165-174.
    • (2007) Proteins , vol.69 , pp. 165-174
    • Lopez, G.1
  • 22
    • 13244268370 scopus 로고    scopus 로고
    • GOtcha: A new method for prediction of protein function assessed by the annotation of seven genomes
    • Martin,D.M. et al. (2004) GOtcha: A new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics, 5, 178.
    • (2004) BMC Bioinformatics , vol.5 , pp. 178
    • Martin, D.M.1
  • 23
    • 36549003965 scopus 로고    scopus 로고
    • InterPro and InterProScan: Tools for protein sequence classification and comparison
    • Mulder,N. and Apweiler,R. (2007) InterPro and InterProScan: Tools for protein sequence classification and comparison. Methods Mol. Biol. 396, 59-70.
    • (2007) Methods Mol. Biol , vol.396 , pp. 59-70
    • Mulder, N.1    Apweiler, R.2
  • 24
    • 0031576361 scopus 로고    scopus 로고
    • Intermediate sequences increase the detection of homology between sequences
    • Park,J. et al. (1997) Intermediate sequences increase the detection of homology between sequences. J. Mol. Biol., 273, 349-354.
    • (1997) J. Mol. Biol , vol.273 , pp. 349-354
    • Park, J.1
  • 25
    • 0043122907 scopus 로고    scopus 로고
    • PipeAlign: A new toolkit for protein family analysis
    • Plewniak,F. et al. (2003) PipeAlign: A new toolkit for protein family analysis. Nucleic Acids Res., 31, 3829-3832.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3829-3832
    • Plewniak, F.1
  • 26
    • 33748335463 scopus 로고    scopus 로고
    • A new measure for functional similarity of gene products based on Gene Ontology
    • Schlicker,A. et al. (2006) A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics, 7 302.
    • (2006) BMC Bioinformatics , vol.7 , pp. 302
    • Schlicker, A.1
  • 27
    • 44949207428 scopus 로고    scopus 로고
    • Song,N. et al. (2008) Sequence similarity network reveals common ancestry of multidomain proteins. PLoS Comput. Biol., 4, e1000063.
    • Song,N. et al. (2008) Sequence similarity network reveals common ancestry of multidomain proteins. PLoS Comput. Biol., 4, e1000063.
  • 28
    • 0142106373 scopus 로고    scopus 로고
    • How well is enzyme function conserved as a function of pairwise sequence identity?
    • Tian,W. and Skolnick,J. (2003) How well is enzyme function conserved as a function of pairwise sequence identity? J. Mol. Biol., 333 863-882.
    • (2003) J. Mol. Biol , vol.333 , pp. 863-882
    • Tian, W.1    Skolnick, J.2
  • 29
    • 33645790811 scopus 로고    scopus 로고
    • GOPET: A tool for automated predictions of Gene Ontology terms
    • Vinayagam,A. et al. (2006) GOPET: A tool for automated predictions of Gene Ontology terms. BMC Bioinformatics, 7, 161.
    • (2006) BMC Bioinformatics , vol.7 , pp. 161
    • Vinayagam, A.1
  • 30
    • 38549107541 scopus 로고    scopus 로고
    • Gene3D: Comprehensive structural and functional annotation of genomes
    • Yeats,C. et al. (2008) Gene3D: Comprehensive structural and functional annotation of genomes. Nucleic Acids Res., 36, D414-D418.
    • (2008) Nucleic Acids Res , vol.36
    • Yeats, C.1
  • 31
    • 0043122923 scopus 로고    scopus 로고
    • OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms
    • Zehetner,G. (2003) OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms. Nucleic Acids Res., 31, 3799-3803.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3799-3803
    • Zehetner, G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.