The European Bioinformatics Institute's data resources

Nucleic Acids Research

Volumn 31, Issue 1, 2003, Pages 43-50

  Brooksbank, Catherine ^a   Camon, Evelyn ^a   Harris, Midori A ^a   Magrane, Michele ^a   Martin, Maria Jesus ^a   Mulder, Nicola ^a   O'Donovan, Claire ^a   Parkinson, Helen ^a   Tuli, Mary Ann ^a   Apweiler, Rolf ^a   Birney, Ewan ^a   Brazma, Alvis ^a   Henrick, Kim ^a   Lopez, Rodrigo ^a   Stoesser, Guenter ^a   Stoehr, Peter ^a   Cameron, Graham ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA;

ACCESS TO INFORMATION; AMINO ACID SEQUENCE; COMPUTER PROGRAM; DNA SEQUENCE; DNA TRANSCRIPTION; DROSOPHILA; EMBL NUCLEOTIDE SEQUENCE DATABASE; EUROPEAN BIOINFORMATICS INSTITUTE; GENE EXPRESSION; HUMAN; INFORMATION PROCESSING; INTERNET; MEDICAL SPECIALIST; MOLECULAR BIOLOGY; MOUSE; NEMATODE; NONHUMAN; PLANT; PRIORITY JOURNAL; PROTEIN STRUCTURE; RAT; REVIEW; RNA TRANSLATION; SEQUENCE DATABASE; SWISS-PROT;

ANIMALS; COMPUTATIONAL BIOLOGY; COOPERATIVE BEHAVIOR; DATA COLLECTION; DATABASES, GENETIC; DATABASES, PROTEIN; EUROPE; GENOMICS; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION, GENETIC; VOCABULARY, CONTROLLED;

EID: 0037245986     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg066     Document Type: Review

References (35)

1. Stoesser,G. et al. (2002) The EMBL Nucleotide Sequence Database. Nucleic Acids Res., 30, 21-26.
2. Dennis,A. et al. (2002) GenBank. Nucleic Acids Res., 30, 17-20.
3. Tateno,Y. et al. (2002) DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Res., 30, 27-30.
4. Zdobnov,E.M. et al. (2002) The EBI SRS server - new features. Bioinformatics, 18, 1149-1150.
5. Beck,S. and Sterk,P. (1998) Genome-scale DNA sequencing: where are we? Curr. Opin. Biotechnol., 9, 116-120.
6. Apweiler,R. (2001) Functional annotation in SWISS-PROT: The basis for large-scale characterization of protein sequences. Brief Bioinform., 2, 9-18.
7. Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-48.
8. Apweiler,R., Attwood,T.K., Bairoch,A., Bateman,A., Birney,E., Biswas,M., Bucher,P., Cerutti,L., Corpet,F., Croning,M.D., Durbin,R., Falquet,L., Fleischmann,W., Gouzy,J., Hermjakob,H., Hulo,N., Jonassen,I., Kahn,D., Kanapin,A., Karavidopoulou,Y., Lopez,R., Marx,B., Mulder,N.J., Oinn,T.M., Pagni,M. and Servant,F. (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res., 29, 37-40.
9. Falquet,L. et al. (2002) The PROSITE database, its status in 2002. Nucleic Acids Res., 30, 235-238.
10. Attwood,T.K., Blythe,M.J., Flower,D.R., Gaulton,A., Mabey,J.E., Maudling,N., McGregor,L., Mitchell,A.L., Moulton,G., Paine,K. and Scordis,P. (2002) PRINTS and PRINTS-S shed light on protein ancestry. Nucleic Acids Res., 30, 239-241.
11. Corpet,F., Servant,F., Gouzy,J. and Kahn,D. (2000) ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res., 28, 267-269.
12. Bateman,A., Birney,E., Cerruti,L., Durbin,R., Etwiller,L., Eddy,S.R., Griffiths-Jones,S., Howe,K.L., Marshall,M. and Sonnhammer,E.L.L. (2002) The Pfam Protein Families Database, Nucleic Acids Res., 30, 276-280.
13. Letunic,I. et al. (2002) Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res., 30, 242-244.
14. Haft,D.H., Loftus,B.J., Richardson,D.L., Yang,F., Eisen,J.A., Paulsen,I.T. and White,O. (2001) TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res., 29, 41-43.
15. Zdobnov,E.M. and Apweiler,R. (2001) InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17, 847-848.
16. Boutselakis,H. et al. (2003) E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res., 31, 43-50.
17. Holm,L. and Sander,C. (1998) Touring protein fold space with Dali/FSSP. Nucleic Acids Res., 26, 316-319.
18. Lin,D. et al. (2000) Autodep: a web-based system for deposition and validation of macromolecular structural information. Acta Crystallogr., D56, 828-841.
19. Hubbard,T. et al. (2001) The Ensembl genome database project. Nucleic Acids Res., 30, 38-41.
20. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
21. Ning,Z. et al. (2001) SSAHA: a fast search method for large DNA databases. Genome Res., 11, 1725-1729.
22. Dowell,R.D. et al. (2001) The Distributed Annotation System. BMC Bioinformatics, 2, 7.
23. The Chipping Forecast (1999) Nature Genet., 21(Suppl.), 1-60.
24. Brazma,A. et al. (2001) Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nature Genet., 29, 365-371.
25. Spellman,P.T. et al. (2002) Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol., 3, research0046.1-0046.9.
26. Brazma,A. et al. (2003) ArrayExpress - a public repository for microarray gene expression data. Nucleic Acids Res., 31, 68-71.
27. Anon. (2002) Microarray standards at last. Nature, 419, 323.
28. Ashburner,M. et al. (2000) Gene Ontology: tool for the unification of biology. Nature Genet., 25, 25-29.
29. Ashburner,M. et al. (2001) Creating the Gene Ontology resource: design and implementation. Genome Res., 11, 1425-1433.
30. Rice,P., Longden,I. and Bleasby,A. (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.
31. Pearson,W.R. and Lipman,D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
32. Altschul,S.F. and Gish,W. (1996) Local alignment statistics. Methods Enzymol., 266, 460-480.
33. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
34. Holm,L. and Sander,C. (1991) Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors. J. Mol. Biol., 218, 183-194.
35. Camon,E., Barrell,D., Brocksbank,C., Magrane,M. and Aptveiler,R. The gene ontology annotation project-application of GO in SWISS-PROT, TrEMBL and InterPro. Comparative and Functional Genomics, in press.