Efficient functional clustering of protein sequences using the Dirichlet process

Bioinformatics

Volumn 24, Issue 16, 2008, Pages 1765-1771

  Brown, Duncan P ^a,b  

^a University of California at Berkeley   (United States)

^b MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; CLASSIFICATION; CLUSTER ANALYSIS; CONFERENCE PAPER; CONTROLLED STUDY; NORMAL DISTRIBUTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN FUNCTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

EID: 49549118253     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn244     Document Type: Conference Paper

References (25)

1. Abascal,F. and Valencia,A. (2002) Clustering of proximal sequence space for the identification of protein families. Bioinformatics, 18 908-921.
2. Blackwell,D. and MacQueen,J.B. (1973) Ferguson distributions via Polya Urn schemes. Ann. Stat., 1, 353-355.
3. Brown,D.P. et al. (2007) Automated protein subfamily identification and classification. PLoS Comput. Biol., 3, e160.
4. Chandonia,J.M. et al. (2004) Structural genomics and structural biology: Compare and contrast. Genome Biol, 5, 343.
5. Dald,D.B. (2003) An improved merge-split sampler for conjugate dirichlet process mixture models. Technical Report 1086. University of Wisconsin, Madison.
6. Dubey,A. et al. (2004) Clustering protein sequence and structure space with infinite Gaussian mixture models. Pac. Symp. Biocomput. 399-410.
7. Edgar,R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
8. Enright,A.J. and Ouzounis,C.A. (2000) GeneRAGE: A robust algorithm for sequence clustering and domain detection. Bioinformatics, 16 451-457.
9. Horn,F. et al. (2001) Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems. Nucleic Acids Res., 29, 346-349.
10. Horn,F. et al. (2003) GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res., 31, 294-297.
11. Jain,S. and Ncal,R.M. (2000) A split-merge markov chain Monte Carlo procedure for the dirichlet mixmre model. Technical Report 2003. University of Toronto, Toronto, Canada.
12. Karplus,IC et al. (1997) Predicting protein structure using hidden Markov models. Proteins, (Suppl. 1), 134-139.
13. Krause,A. and Vingron,M. (1998) A set-theoretic approach to database searching and clustering. Bioinformatics, 14, 430-438.
14. Li,W. and Godzik,A, (2006) cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
15. Lunter,G. et al. (2005) Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics, 6, 83.
16. Meila,M. (2003) Comparing clusterings by the variation of information. In Carbonell,J.G and Siekmann,J. (eds.) Learning Theory And Kernel Machines. Vol. 2777 of Lecture Notes In Artificial Intelligence. Springer-Verlag, Heidelberg, Germany, pp. 1713-187.
17. Metzler,D. et al. (2001) Assessing variability by joint sampling of alignments and mutation rates. J. Mol. Evol., 53, 660-669.
18. Neal,R.M. (2000) Markov chain sampling methods for Dirichlet process mixture. J. Comput. Graph. Stat., 9, 249-265.
19. Webb,E.C. and Committee of the International Union of Biochemistry and Molecular Biology (1992) Enzyme nomenclature 1992: Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes Academic Press, San Diego.
20. Pegg,S.C. et al. (2006) Leveraging enzyme structurc-function relationships for functional inference and experimental design: The structure-function linkage database. Biochemistry, 45, 2545-2555.
21. Sethuraman,J. (1994) A constructive definition of dirichlet priors. Stat. Sin., 4, 639-650.
22. Sjölander,K (1998) Phylogenetic inference in protein superfamilies: analysis of SH2 domains. Prac. Int. Conf. Intell. Syst. Mol. Biol. 6, 165-174.
23. Sjölandcr,K. et al. (1996) Dirichlet mixtures: A method for improved detection of weak but significant protein sequence homology. Comput. Appl. Biosci., 12, 327-345.
24. Wicker,N. et al. (2001) Secator: A program for inferring protein subfamilies from phylogenetic trees. Mol. Biol. Evol., 18, 1435-1441.
25. Yona,G. et al. (1998) A map of the protein space-an automatic hierarchical classification of all protein sequences. Proc. Int. Conf. Intel. Syst. Mol. Biol., 6, 212-221.