Cluster-C, an algorithm for the large-scale clustering of protein sequences based on the extraction of maximal cliques

Computational Biology and Chemistry

Volumn 28, Issue 3, 2004, Pages 211-218

  Mohseni Zadeh, S ^a   Brezellec P ^a   Risler, J L ^a  

^a CNRS   (France)

Author keywords

Cluster C; Maximal clique; Multidomain proteins; Protein clustering; Sequence similarity

Indexed keywords

ALGORITHMS; BIOCHEMICAL ENGINEERING; DATABASE SYSTEMS; FUNCTIONS; GENES; PARAMETER ESTIMATION;

CLUSTER-C; MAXIMAL CLIQUE; MULTIDOMAIN PROTEINS; PROTEIN CLUSTERING; SEQUENCE SIMILARITY;

PROTEINS;

ARABIDOPSIS PROTEIN; BACTERIAL PROTEIN; FUNGAL PROTEIN; PROTEOME;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BIOLOGY; CHEMISTRY; CLUSTER ANALYSIS; GENETICS; METHODOLOGY; PROTEIN DATABASE; SEQUENCE ALIGNMENT;

ALGORITHMS; AMINO ACID SEQUENCE; ARABIDOPSIS PROTEINS; BACTERIAL PROTEINS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; FUNGAL PROTEINS; PROTEOME; SEQUENCE ALIGNMENT;

EID: 4444270864     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2004.03.002     Document Type: Article

References (18)

1. Abascal F., Valencia A. Clustering of proximal sequence space for the identification of protein families. Bioinformatics. 18:2002;908-921.
2. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
3. Andrade M.A., Brown N.P., Leroy C., Hoersch S., de Daruvar A., Reich C., Franchini A., Tamames J., Valencia A., Ouzounis C., Sander C. Automated genome sequence analysis and annotation. Bioinformatics. 15:1999;391-412.
4. Bolten E., Schliep A., Schneckener S., Schomburg D., Schrader R. Clustering protein sequences-structure prediction by transitive homology. Bioinformatics. 17:2001;935-941.
5. Comet J.-P., Aude J.-C., Glémet E., Risler J.-L., Hénaut A., Slonimski P.P., Codani J.J. Significance of Z-value statistics of Smith-Waterman scores for protein alignments. Comput. Chem. 23:1999;317-331.
6. Enright A.J., Ouzounis C.A. GeneRAGE: a robust algorithm for sequence clustering and domain detection. Bioinformatics. 16:2000;451-457.
7. Glémet E., Codani J.J. LASSAP, a large scale sequence comparison package. Comput. Appl. Biosci. 13:1997;137-143.
8. Hartuv E., Shamir R. A clustering algorithm based on graph connectivity. Inf. Process. Lett. 76:2000;175-181.
9. Hulo N., Sigrist C., Le Saux V., Langendijk-Genevaux P.S., Bordoli L., Gattiker A., De Castro E., Bucher P., Bairoch A. Recent improvements to the PROSITE database. Nucleic Acids Res. 32:2004;D134-D137.
10. Kawaji H., Yamaguchi Y., Matsuda H., Hashimoto A. A graph-based clustering method for a large set of sequences using a graph partitioning algorithm. Genome Inform. 12:2001;93-102.
11. Krause A., Vingron M. A set-theoretic approach to database searching and clustering. Bioinformatics. 14:1998;430-438.
12. Kriventseva E.V., Fleischmann W., Zdobnov E.M., Apweiler R. CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins. Nucleic Acids Res. 29:2001;33-36.
13. Louis A., Ollivier E., Aude J.-C., Risler J.-L. Massive sequence comparisons as a help in annotating genomic sequences. Genome Res. 11:2001;1296-1303.
14. Mohseni-Zadeh S., Louis A., Brézellec P., Risler J.-L. PHYTOPROT: a database of clusters of plant proteins. Nucleic Acids Res. 32:2004;D351-D353.
15. Pearson W.R., Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U.S.A. 85:1988;2444-2448.
16. Smith T.F., Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 147:1981;195-197.
17. Tatusov R.L., Galperin M.Y., Natale D.A., Koonin E.V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28:2000;33-36.
18. Yona G., Linial N., Linial M. ProtoMap: automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space and hierarchy of protein families. Proteins. 37:1999;360-378.