MACHOS: Markov clusters of homologous subsequences

Bioinformatics

Volumn 24, Issue 13, 2008, Pages

  Wong, Simon ^a   Ragan, Mark A ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

GLUTAMINE TRANSFER RNA LIGASE;

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; AUTOMATION; CLUSTER ANALYSIS; HUMAN; INTERMETHOD COMPARISON; MACHINE LEARNING; MARKOV CLUSTERS OF HOMOLOGOUS SUBSEQUENCE; MOLECULAR SYSTEMATICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; PROTEOMICS; QUALITY CONTROL; SEQUENCE HOMOLOGY; VALIDATION PROCESS; WEB BROWSER;

EUKARYOTA;

INFERENCE ENGINES; INTELLIGENT SYSTEMS; MOLECULAR BIOLOGY; PROTEINS;

CLASSIFICATION METHODS; EUKARYOTIC GENOME; EUKARYOTIC PROTEINS; EVOLUTIONARY HISTORY; FULLY AUTOMATED; LOCAL REGION; PROTEIN SEQUENCES; QUALITY MEASURES;

CLUSTERING ALGORITHMS;

EID: 46249129962     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn144     Document Type: Article

References (40)

1. Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Apic,G. et al. (2001) Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol., 310, 311-325.
3. Bateman,A. et al. (2004) The Pfam protein families database. Nucleic Acids Res., 32, D138-D141.
4. Benson,D.A. et al. (2007) GenBank. Nucleic Acids Res., 35 D21-D25.
5. Berman,H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
6. Birney,E. et al. (2006) Ensembl 2006. Nucleic Acids Res., 34, D556-D561.
7. Bork,P. (1991) Shuffled domains in extracellular proteins. FEBS Lett. 286, 47-54.
8. Bru,C. et al. (2005) The ProDom database of protein domain families: More emphasis on 3D. Nucleic Acids Res., 33, D212-D215.
9. Caminci,P. et al. (2005) The transcriptional landscape of the mammalian genome. Science, 309, 1559-1563.
10. Dorit,R.L. et al. (1990) How big is the universe of exons? Science, 250, 1377-1382.
11. Enright,A.J. et al. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
12. Finn,R.D. et al. (2006) Pfam: Clans, web tools and services. Nucleic Acids Res., 34, D247-D251.
13. Fitch,W.M. (1970) Distinguishing homologous from analogous proteins. Syst. Zool., 19, 99-113.
14. Gracy,J. and Argos,P. (1998) Automated protein sequence database classification. II. Delineation of domain boundaries from sequence similarities. Bioinformatics, 14, 174-187.
15. Hall, B.K. (1994) Homology. The hierarchical basis of comparative biology. Academic Press, San Diego.
16. Harlow,T.J. et al. (2004) A hybrid clustering approach to recognition of protein families in 114 microbial genomes. BMC Bioinformatics, 5, 45.
17. Heger,A. and Holm,L. (2003) Exhaustive enumeration of protein domain families. J. Mol. Biol., 328, 749-767.
18. Holm,L. and Sander,C. (1996) Mapping the protein universe. Science 273, 595-603.
19. Huang,X.Q. et al. (1990) A space-efficient algorithm for local similarities. Comput. Appl. Biosci., 6, 373-381.
20. John,B. et al. (2004) Human microRNA targets. PLoS Biol., 2, e363.
21. Jones,S. et al. (1998) Domain assignment for protein structures using a consensus approach: Characterization and analysis. Protein Sci., 7, 233-242.
22. Koonin,E.V. (2005) Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet., 39, 309-338.
23. Krause,A. et al. (2005) Large scale hierarchical clustering of protein sequences. BMC Bioinformatics, 6, 15.
24. Kriventseva,E.V. et al. (2001) Clustering and analysis of protein families. Curr. Opin. Struct. Biol., 11, 334-339.
25. Kunin,V. et al. (2005) The properties of protein family space depend on experimental design. Bioinformatics, 21, 2618-2622.
26. Lankester,E.R. (1870) On the use of the term homology in modern zoology. Ann. Mag. Nat. Hist., 6, 34-43.
27. Lund,C. and Yannakakis,M. (1994) On the hardness of approximating minimization problems. J. ACM, 41, 960-981.
28. Margoliash,E. (1969) Homology: A definition. Science, 163, 127.
29. Owen,R. (1843) Lectures on the comparative anatomy and physiology of the invertebrate animals, delivered at the Royal College of Surgeons, I 1843. Longmans Brown Green & Longmans, London. pp. 379.
30. Pearson,W.R. (1991) Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics, 11, 635-650.
31. Price,G.A. et al. (2005) Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap. Bioinformatics, 21, 3824-3831.
32. Richardson,J.S. (1981) The anatomy and taxonomy of protein structure. Adv. Protein Chem., 34, 167-339.
33. Servant,F. et al. (2002) ProDom: Automated clustering of homologous domains. Brief. Bioinform., 3, 246-251.
34. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
35. The Uniprot Consortium (2007) The Universal Protein Resource (UniProt). Nucleic Acids Res., 35, D193-D197.
36. van Dongen,S. (2000) Graph Clustering by Flow Simulation. PhD thesis University of Utrecht, Utrecht.
37. Yona,G. et al. (1999) ProtoMap: Automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space. Proteins, 37, 360-378.
38. Yona,G. et al. (2000) ProtoMap: Automatic classification of protein sequences and hierarchy of protein families. Nucleic Acids Res., 28, 49-55.
39. Zuckerkandl,E. and Pauling,L. (1965a) Evolutionary divergence arid convergence in proteins. In Bryson,V. and Vogel,H.J. (eds.), Evolving Genes and Proteins. Academic Press, New York, pp. 97-166.
40. Zuckerkandl,E. and Pauling,L. (1965b) Molecules as documents of evolutionary history. J. Theor. Biol., 8, 357-366.