QuasiMotiFinder: Protein annotation by searching for evolutionarily conserved motif-like patterns

Nucleic Acids Research

Volumn 33, Issue SUPPL. 2, 2005, Pages

  Gutman, Roee ^a   Berezin, Carine ^a   Wollman, Roy ^a   Rosenberg, Yossi ^a   Ben Tal, Nir ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE LIBRARY; FURIN; AMINO ACID DERIVATIVE;

AMINO ACID SEQUENCE; ANALYTICAL ERROR; ARTICLE; CALCULATION; CLIENT SERVER APPLICATION; INTERMETHOD COMPARISON; MOLECULAR EVOLUTION; PHYSICAL CHEMISTRY; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; ANIMAL; CATTLE; CHEMISTRY; COMPUTER PROGRAM; INTERNET; METHODOLOGY; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS; STATISTICAL MODEL; COMPUTER PREDICTION; CONTROLLED STUDY; GENE ASSIGNMENT; GENETIC CONSERVATION; HUMAN; NONHUMAN; SEQUENCE DATABASE; STATISTICAL ANALYSIS;

AMINO ACID MOTIFS; ANIMALS; CATTLE; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; FURIN; INTERNET; LOGISTIC MODELS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 23144445962     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki496     Document Type: Article

References (16)

1. Hulo,N., Sigrist,C.J., LeSaux,V., Langendijk-Genevaux,P.S., Bordoli,L., Gattiker,A., De Castro,E., Bucher,P. and Bairoch,A. (2004) Recent improvements to the PROSITE database. Nucleic Acids Res., 32, D134-D137.
2. Puntervoll,P., Linding,R., Gemünd,C., Chabanis-Davidson,S., Mattingsdal,M., Cameron,S., Martin,D.M.A., Ausiello,G., Brannetti,B., Costantini,A. et al. (2003) ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res., 31, 3625-3630.
3. Jonassen,I. (2000) Methods for discovering conserved patterns in protein sequences and structures. In Higgins,D. and Taylor,W. (eds), Bioinformatics: Sequence, Structure and Databanks. Oxford University Press, NY.
4. Huang,J.Y. and Brutlag,D.L. (2001) The EMOTIF database. Nucleic Acids Res., 29, 202-204.
5. Su,Q.J., Lu,L., Saxonov,S. and Brutlag,D.L. (2005) eBLOCKs: Enumerating conserved protein blocks to achieve maximal sensitivity and specificity. Nucleic Acids Res., 33, D178-D182.
6. 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.
7. Boeckmann,B., Bairoch,A., Apweiler,R., Blatter,M.C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan,I., Pilbout,S. and Schneider,M. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
8. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
9. Pupko,T., Bell,R.E., Mayrose,I., Glaser,F. and Ben-Tal,N. (2002) Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics, 18 (Suppl. 1), 71-77.
10. Saitou,N. and Nei,M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
11. Miyata,T., Miyazawa,S. and Yasunaga,T. (1979) Two types of amino acid substitutions in protein evolution. J. Mol. Evol., 12, 219-236.
12. Bateman,A., Coin,L., Durbin,R., Finn,R.D., Hollich,V., Griffiths-Jones,S., Khanna,A., Marshall,M., Mozon,S., Sonnhammer,E.L. et al. (2004) The Pfam protein families database. Nucleic Acids Res., 32, D138-D141.
13. Conover,W.J. (1980) Practical Nonparametric Statistics. Wiley, NY.
14. Siezen,R. and Leunissen,J. (1997) Subtilases: The superfamily of subtilisin-like serine proteases. Protein Sci., 6, 501-523.
15. Breiman,L., Friedman,J.H., Olshen,R.A. and Stone,C.J. (1984) Classification and Regression Trees. Chapman & Hall, NY.
16. Bork,P., Gellerich,J., Groth,H., Hooft,R. and Martin,F. (1995) Divergent evolution of a beta/alpha-barrel subclass: Detection of numerous phosphate-binding sites by motif search. Protein Sci., 4, 268-274.