메뉴 건너뛰기




Volumn 28, Issue 8, 2012, Pages 1078-1085

High-quality sequence clustering guided by network topology and multiple alignment likelihood

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 84859778326     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts098     Document Type: Article
Times cited : (28)

References (34)
  • 1
    • 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
  • 2
    • 79958082066 scopus 로고    scopus 로고
    • Detecting network communities: an application to phylogenetic analysis
    • Andrade, R.F. et al. (2011) Detecting network communities: an application to phylogenetic analysis. PLoS Comput. Biol., 7, e1001131.
    • (2011) PLoS Comput. Biol. , vol.7
    • Andrade, R.F.1
  • 3
    • 79551607374 scopus 로고    scopus 로고
    • Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution
    • Apeltsin, L. et al. (2011) Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinformatics, 27, 326-333.
    • (2011) Bioinformatics , vol.27 , pp. 326-333
    • Apeltsin, L.1
  • 4
    • 84864278347 scopus 로고    scopus 로고
    • Using sequence similarity networks for visualization of relationships across diverse protein superfamilies
    • Atkinson, H.J. et al. (2009) Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS ONE, 4, e4345.
    • (2009) PLoS ONE , vol.4
    • Atkinson, H.J.1
  • 5
    • 0034228914 scopus 로고    scopus 로고
    • Assessing a mixture model for clustering with the integrated completed likelihood
    • Biernacki, C. et al. (2000)Assessing a mixture model for clustering with the integrated completed likelihood. IEEE Trans. Pattern Anal. Mach. Intell., 22, 719-725.
    • (2000) IEEE Trans. Pattern Anal. Mach. Intell. , vol.22 , pp. 719-725
    • Biernacki, C.1
  • 6
    • 56349094785 scopus 로고    scopus 로고
    • Fast unfolding of communities in large networks
    • Blondel, V.D. et al. (2008) Fast unfolding of communities in large networks. J. Stat. Mech.-Theory E., 2008, P10008+.
    • (2008) J. Stat. Mech. -Theory E. , vol.2008
    • Blondel, V.D.1
  • 7
    • 33745027619 scopus 로고    scopus 로고
    • A gold standard set of mechanistically diverse enzyme superfamilies
    • Brown, S.D. et al. (2006) A gold standard set of mechanistically diverse enzyme superfamilies. Genome Biol., 7, R8.
    • (2006) Genome Biol. , vol.7
    • Brown, S.D.1
  • 8
    • 13444305296 scopus 로고    scopus 로고
    • The ProDom database of protein domain families: more emphasis on 3D
    • Bru, C. et al. (2005)The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res., 33, D212-D215.
    • (2005) Nucleic Acids Res. , vol.33
    • Bru, C.1
  • 10
    • 77952988108 scopus 로고    scopus 로고
    • A new generation of homology search tools based on probabilistic inference
    • Eddy, S. (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform., 23, 205-211.
    • (2009) Genome Inform. , vol.23 , pp. 205-211
    • Eddy, S.1
  • 11
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright, A.J. et al. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1575-1584
    • Enright, A.J.1
  • 12
    • 75549090603 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Finn, R.D. et al. (2010) The Pfam protein families database. Nucleic Acids Res., 38, D211-D222.
    • (2010) Nucleic Acids Res. , vol.38
    • Finn, R.D.1
  • 13
    • 67749108209 scopus 로고    scopus 로고
    • INDELible: a flexible simulator of biological sequence evolution
    • Fletcher, W. and Yang, Z. (2009)INDELible: a flexible simulator of biological sequence evolution.Mol. Biol. Evol., 26, 1879-1888.
    • (2009) Mol. Biol. Evol. , vol.26 , pp. 1879-1888
    • Fletcher, W.1    Yang, Z.2
  • 14
    • 77949455880 scopus 로고    scopus 로고
    • Enrichment of homologs in insignificant BLAST hits by cocomplex network alignment
    • Fokkens, L. et al. (2010) Enrichment of homologs in insignificant BLAST hits by cocomplex network alignment. BMC Bioinformatics, 11, 86.
    • (2010) BMC Bioinformatics , vol.11 , pp. 86
    • Fokkens, L.1
  • 15
    • 74049087026 scopus 로고    scopus 로고
    • Community detection in graphs
    • Fortunato, S. (2010)Community detection in graphs. Phys. Rep., 486, 75-174.
    • (2010) Phys. Rep. , vol.486 , pp. 75-174
    • Fortunato, S.1
  • 16
    • 77949911836 scopus 로고    scopus 로고
    • Diversity of structure and function of response regulator output domains
    • Galperin, M.Y. (2010) Diversity of structure and function of response regulator output domains.Curr. Opin. Microbiol., 13, 150-159.
    • (2010) Curr. Opin. Microbiol. , vol.13 , pp. 150-159
    • Galperin, M.Y.1
  • 17
    • 0037062448 scopus 로고    scopus 로고
    • Community structure in social and biological networks
    • Girvan, M. and Newman, M.E. (2002) Community structure in social and biological networks.Proc. Natl Acad. Sci. USA, 99, 7821-7826.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 7821-7826
    • Girvan, M.1    Newman, M.E.2
  • 18
    • 77952296596 scopus 로고    scopus 로고
    • Homologous over-extension: a challenge for iterative similarity searches
    • Gonzalez, M.W. and Pearson, W.R. (2010)Homologous over-extension: a challenge for iterative similarity searches. Nucleic Acids Res., 38, 2177-2189.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 2177-2189
    • Gonzalez, M.W.1    Pearson, W.R.2
  • 19
    • 70350572462 scopus 로고    scopus 로고
    • Strategies to improve the robustness of agglomerative hierarchical clustering under data source variation for speaker diarization
    • Han, K.J. et al. (2008)Strategies to improve the robustness of agglomerative hierarchical clustering under data source variation for speaker diarization. IEEE T Audio Speech, 16, 1590-1601.
    • (2008) IEEE T Audio Speech , vol.16 , pp. 1590-1601
    • Han, K.J.1
  • 20
    • 68049142320 scopus 로고    scopus 로고
    • Multiple alignment of DNA sequences with MAFFT
    • Katoh, K. et al. (2009) Multiple alignment of DNA sequences with MAFFT. Methods Mol. Biol., 537, 39-64.
    • (2009) Methods Mol. Biol. , vol.537 , pp. 39-64
    • Katoh, K.1
  • 21
    • 33846025119 scopus 로고    scopus 로고
    • Protein homology network families reveal step-wise diversification of Type III and Type IV secretion systems
    • Medini, D. et al. (2006) Protein homology network families reveal step-wise diversification of Type III and Type IV secretion systems. PLoS Comput. Biol., 2, e173.
    • (2006) PLoS Comput. Biol. , vol.2
    • Medini, D.1
  • 22
    • 79955013072 scopus 로고    scopus 로고
    • Ultra-fast sequence clustering from similarity networks with SiLiX
    • Miele, V. et al. (2011) Ultra-fast sequence clustering from similarity networks with SiLiX. BMC Bioinformatics, 12, 116.
    • (2011) BMC Bioinformatics , vol.12 , pp. 116
    • Miele, V.1
  • 23
    • 0442296603 scopus 로고    scopus 로고
    • Estimation and prediction for stochastic blockstructures
    • Nowicki, K. and Snijders, T.A.B. (2001) Estimation and prediction for stochastic blockstructures.J. Am. Stat. Assoc., 96, 1077-1087.
    • (2001) J. Am. Stat. Assoc. , vol.96 , pp. 1077-1087
    • Nowicki, K.1    Snijders, T.A.B.2
  • 24
    • 33645523636 scopus 로고    scopus 로고
    • Spectral clustering of protein sequences
    • Paccanaro, A. et al. (2006)Spectral clustering of protein sequences. Nucleic Acids Res., 34, 1571-1580.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 1571-1580
    • Paccanaro, A.1
  • 25
    • 67649115335 scopus 로고    scopus 로고
    • Databases of homologous gene families for comparative genomics
    • Penel, S. et al. (2009)Databases of homologous gene families for comparative genomics. BMC Bioinformatics, 10 (Suppl. 6), S3.
    • (2009) BMC Bioinformatics , vol.10 , Issue.SUPPL. 6
    • Penel, S.1
  • 26
    • 67649123146 scopus 로고    scopus 로고
    • Deciphering the connectivity structure of biological networks using MixNet
    • Picard, F. et al. (2009) Deciphering the connectivity structure of biological networks using MixNet. BMC Bioinformatics, 10 (Suppl. 6), S17.
    • (2009) BMC Bioinformatics , vol.10 , Issue.SUPPL. 6
    • Picard, F.1
  • 27
    • 37549027613 scopus 로고    scopus 로고
    • SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    • Pruesse, E. et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res., 35, 7188-7196.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 7188-7196
    • Pruesse, E.1
  • 28
    • 38549163152 scopus 로고    scopus 로고
    • TreeFam: 2008 update
    • Ruan, J. et al. (2008)TreeFam: 2008 update. Nucleic Acids Res., 36, D735-D740.
    • (2008) Nucleic Acids Res. , vol.36
    • Ruan, J.1
  • 29
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: a software environment for integrated models of biomolecular interaction networks
    • Shannon, P. et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
    • (2003) Genome Res. , vol.13 , pp. 2498-2504
    • Shannon, P.1
  • 30
    • 44949207428 scopus 로고    scopus 로고
    • Sequence similarity network reveals common ancestry of multidomain proteins
    • Song, N. et al. (2008) Sequence similarity network reveals common ancestry of multidomain proteins. PLoS Comput. Biol., 4, e1000063.
    • (2008) PLoS Comput. Biol. , vol.4
    • Song, N.1
  • 31
    • 0035162592 scopus 로고    scopus 로고
    • The COG database: new developments in phylogenetic classification of proteins from complete genomes
    • Tatusov, R.L. et al. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res., 29, 22-28.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 22-28
    • Tatusov, R.L.1
  • 32
    • 59949096873 scopus 로고    scopus 로고
    • EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates
    • Vilella, A.J. et al. (2009) EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res., 19, 327-335.
    • (2009) Genome Res. , vol.19 , pp. 327-335
    • Vilella, A.J.1
  • 33
    • 77952983494 scopus 로고    scopus 로고
    • Partitioning biological data with transitivity clustering
    • Wittkop, T. et al. (2010) Partitioning biological data with transitivity clustering. Nat. Methods, 7, 419-420.
    • (2010) Nat. Methods , vol.7 , pp. 419-420
    • Wittkop, T.1
  • 34
    • 79957514991 scopus 로고    scopus 로고
    • Phylogeny inference based on spectral graph clustering
    • Zhang, S.B. et al. (2011) Phylogeny inference based on spectral graph clustering. J. Comput. Biol., 18, 627-637.
    • (2011) J. Comput. Biol. , vol.18 , pp. 627-637
    • Zhang, S.B.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.