MyHits: A new interactive resource for protein annotation and domain identification

Nucleic Acids Research

Volumn 32, Issue WEB SERVER ISS., 2004, Pages

  Pagni, Marco ^a   Ioannidis, Vassilios ^a   Cerutti, Lorenzo ^a   Zahn Zabal, Monique ^a,b   Jongeneel, C Victor ^a,b   Falquet, Laurent ^a  

^a SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^b LUDWIG INSTITUTE FOR CANCER RESEARCH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SYSTEM; EMBL NUCLEOTIDE SEQUENCE DATABASE; GENETIC VARIABILITY; HUMAN COMPUTER INTERACTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN MOTIF; RNA SPLICING; SEQUENCE DATABASE; SWISS-PROT;

COMPUTER GRAPHICS; DATABASES, PROTEIN; INTERNET; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; SYSTEMS INTEGRATION; USER-COMPUTER INTERFACE;

EID: 3242882168     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh479     Document Type: Article

References (16)

1. Hofmann,K. (2000) Sensitive protein comparisons with profiles and hidden Markov models. Brief. Bioinformatics, 1, 167-178.
2. Schaffer,A.A., Aravind,L., Madden,T.L., Shavirin,S., Spouge,J.L., Wolf,Y.I., Koonin,E.V. and Altschul,S.F. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res., 29, 2994-3005.
3. Bateman,A., Coin,L., Durbin,R., Finn,R.D., Hollich,V., Griffiths-Jones,S., Khanna,A., Marshall,M., Moxon,S., Sonnhammer,E.L. et al. (2004) The Pfam protein families database. Nucleic Acids Res., 32, D138-D141.
4. Schultz,J., Copley,R.R., Doerks,T., Ponting,C.P. and Bork,P. (2000) SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res., 28, 231-234.
5. Mulder,N.J., Apweiler,R., Attwood,T.K., Bairoch,A., Barrell,D., Bateman,A, Binns,D., Biswas,M., Bradley,P., Bork,P. et al. (2003) The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res., 31, 315-318.
6. Boeckmann,B., Bairoch,A., Apweiler,R., Blatter,M.C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan,I. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
7. Jongeneel,C.V. (2000) Searching the expressed sequence tag (EST) databases: panning for genes. Brief. Bioinformatics, 1, 76-92.
8. Pagni,M., Iseli,C., Junier,T., Falquet,L., Jongeneel,V. and Bucher,P. (2001) trEST, trGEN and Hits: access to databases of predicted protein sequences. Nucleic Acids Res., 29, 148-151.
9. Sperisen,P., Iseli,C., Pagni,M., Stevenson,B.J., Bucher,P. and Jongeneel,C.V. (2004) trome, trEST and trGEN: databases of predicted protein sequences. Nucleic Acids Res., 32, D509-D511.
10. Junier,T. and Bucher,P. (1998) SEView: a Java applet for browsing molecular sequence data. In Silico Biol., 1, 13-20.
11. Junier,T. and Pagni,M. (2000) Dotlet: diagonal plots in a web browser. Bioinformatics, 16, 178-179.
12. Clamp,M., Cuff,J., Searle,S.M. and Barton,G.J. (2004) The Jalview Java alignment editor. Bioinformatics, 20, 426-427.
13. Sigrist,C.J., Cerutti,L., Hulo,N., Gattiker,A., Falquet,L., Pagni,M., Bairoch,A. and Bucher,P. (2002) PROSITE: a documented database using patterns and profiles as motif descriptors. Brief. Bioinformatics, 3, 265-274.
14. 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.
15. Notredame,C., Higgins,D.G. and Heringa,J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
16. Falquet,L., Bordoli,L., Ioannidis,V., Pagni,M. and Jongeneel,C.V. (2003) Swiss EMBnet node web server. Nucleic Acids Res., 31, 3782-3783.