Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes

Nucleic Acids Research

Volumn 34, Issue 2, 2006, Pages 647-658

  Uchiyama, Ikuo ^a  

^a NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; CLASSIFICATION; CLUSTER ANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; GENE CLUSTER; GENETIC ALGORITHM; GENETIC DATABASE; GENOME ANALYSIS; INTERMETHOD COMPARISON; ORTHOLOGY; PARALOGY; PRIORITY JOURNAL;

ALGORITHMS; CLUSTER ANALYSIS; GENOMICS; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 32644443138     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkj448     Document Type: Article

References (45)

1. Liu,J. and Rost,B. (2003) Domains, motifs and clusters in the protein universe. Curr. Opin. Chem. Biol., 7, 5-11.
2. Ouzounis,C.A., Coulson,R.M., Enright,A.J., Kunin,V. and Pereira-Leal,J.B. (2003) Classification schemes for protein structure and function. Nature Rev. Genet., 4, 508-519.
3. Sonnhammer,E.L., Eddy,S.R. and Durbin,R. (1997) Pfam: A comprehensive database of protein domain families based on seed alignments. Proteins, 28, 405-420.
4. Schultz,J., Milpetz,F., Bork,P. and Ponting,C.P. (1998)SMART,a simple modular architecture research tool: Identification of signaling domains. Proc. Natl Acad. Sci. USA, 95, 5857-5864.
5. Sasson,O., Vaaknin,A., Fleischer,H., Portugaly,E., Bilu,Y., Linial,N. and Linial,M. (2003) ProtoNet: Hierarchical classification of the protein space. Nucleic Acids Res., 31, 348-352.
6. Sonnhammer,E.L. and Kahn,D. (1994) Modular arrangement of proteins as inferred from analysis of homology. Protein Sci., 3, 482-492.
7. Gracy,J. and Argos,P. (1998) Automated protein sequence database classification. II. Delineation of domain boundaries from sequence similarities. Bioinformatics, 14, 174-187.
8. Yona,G., Linial,N. and Linial,M. (1999) ProtoMap: Automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space. Proteins, 37, 360-378.
9. Enright,A.J., Van Dongen,S. and Ouzounis,C.A. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
10. Heger,A. and Holm,L. (2003) Exhaustive enumeration of protein domain families. J. Mol. Biol., 328, 749-767.
11. Enright,A.J. and Ouzounis,C.A. (2000) GeneRAGE: A robust algorithm for sequence clustering and domain detection. Bioinformatics, 16, 451-457.
12. Fitch,W.M. (1970) Distinguishing homologous from analogous proteins. Syst. Zool., 19, 99-113.
13. Goodman,M., Czelusniak,J., Moore,W.M., Romero-Herrera,A.E. and Matsuda,G. (1979) Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool., 28, 132-163.
14. Page,R.D.M. (1994) Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst. Biol., 43, 58-77.
15. Pellegrini,M., Marcotte,E.M., Thompson,M.J., Eisenberg,D. and Yeates,T.O. (1999) Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc. Natl Acad. Sci. USA, 96, 4285-4288.
16. Marcotte,E.M., Pellegrini,M., Ng,H.L., Rice,D.W., Yeates,T.O. and Eisenberg,D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science, 285, 751-753.
17. Enright,A.J., Iliopoulos,I., Kyrpides,N.C. and Ouzounis,C.A. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature, 402, 86-90.
18. Overbeek,R., Fonstein,M., D'Souza,M., Pusch,G.D. and Maltsev,N. (1999) The use of gene clusters to infer functional coupling. Proc. Natl Acad. Sci. USA, 96, 2896-2901.
19. Eisenberg,D., Marcotte,E.M., Xenarios,I. and Yeates,T.O. (2000) Protein function in the post-genomic era. Nature, 405, 823-826.
20. Galperin,M.Y. and Koonin,E.V. (2000) Who's your neighbor? New computational approaches for functional genomics. Nat. Biotechnol., 18, 609-613.
21. Jim,K., Parmar,K., Singh,M. and Tavazoie,S. (2004) A cross-genomic approach for systematic mapping of phenotypic traits to genes. Genome Res., 14, 109-115.
22. Tatusov,R.L., Koonin,E.V. and Lipman,D.J. (1997) A genomic perspective on protein families. Science, 278, 631-637.
23. Tatusov,R.L., Natale,D.A., Garkavtsev,I.V., Tatusova,T.A., Shankavaram,U.T., Rao,B.S., Kiryutin,B., Galperin,M.Y., Fedorova,N.D. and Koonin,E.V. (2001) The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res., 29, 22-28.
24. Remm,M., Storm,C.E. and Sonnhammer,E.L. (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol., 314, 1041-1052.
25. Abascal,F. and Valencia,A. (2002) Clustering of proximal sequence space for the identification of protein families. Bioinformatics, 18, 908-921.
26. Zmasek,C.M. and Eddy,S.R. (2002) RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics, 3, 14.
27. Storm,C.E. and Sonnhammer,E.L. (2002) Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics, 18, 92-99.
28. Cotter,P.J., Caffrey,D.R. and Shields,D.C. (2002) Improved database searches for orthologous sequences by conditioning on outgroup sequences. Bioinformatics, 18, 83-91.
29. Cannon,S.B. and Young,N.D. (2003) OrthoParaMap: Distinguishing orthologs from paralogs by integrating comparativegenomedata and gene phylogenies. BMC Bioinformatics, 4, 35.
30. Li,L., Stoeckert,C.J.,Jr and Roos,D.S. (2003) OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res., 13, 2178-2189.
31. Storm,C.E. and Sonnhammer,E.L. (2003) Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res., 13, 2353-2362.
32. Uchiyama,I. (2003) MBGD: Microbial genome database for comparative analysis. Nucleic Acids Res., 31, 58-62.
33. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
34. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
35. Jones,D.T., Taylor,W.R. and Thornton,J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci., 8, 275-282.
36. Sneath,P.H.A. and Sokal,R.R. (1973) Numerical taxonomy. Freeman, San Francisco, CA.
37. Snel,B., Bork,P. and Huynen,M. (2000) Genome evolution. Gene fusion versus gene fission. Trends Genet., 16, 9-11.
38. Tatusov,R.L., Fedorova,N.D., Jackson,J.D., Jacobs,A.R., Kiryutin,B., Koonin,E.V., Krylov,D.M., Mazumder,R., Mekhedov,S.L., Nikolskaya,A.N. et al. (2003) The COG database: An updated version includes eukaryotes. BMC Bioinformatics, 4, 41.
39. McNicholas,P.M., Mazzotta,M.M., Rech,S.A. and Gunsalus,R.P. (1998) Functional dissection of the molybdate-responsive transcription regulator, ModE, from Escherichia coli. J. Bacteriol., 180, 4638-4643.
40. Hall,D.R., Gourley,D.G., Leonard,G.A., Duke,E.M., Anderson,L.A., Boxer,D.H. and Hunter,W.N. (1999) The high-resolution crystal structure of the molybdate-dependent transcriptional regulator (ModE) from Escherichia coli: A novel combination of domain folds. EMBO J., 18, 1435-1446.
41. Sonnhammer,E.L. and Koonin,E.V. (2002) Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet., 18, 619-620.
42. Fitch,W.M. (2000) Homology a personal view on some of the problems. Trends Genet., 16, 227-231.
43. Heger,A. and Holm,L. (2000) Towards a covering set of protein family profiles. Prog. Biophys. Mol. Biol., 73, 321-337.
44. Kriventseva,E.V., Fleischmann,W., Zdobnov,E.M. and Apweiler,R. (2001) CluSTr: A database of clusters of SWISS-PROT+TrEMBL proteins. Nucleic Acids Res., 29, 33-36.
45. Sasson,O., Linial,N. and Linial,M. (2002) The metric space of proteins-comparative study of clustering algorithms. Bioinformatics, 18, S14-S21.