EDITtoTrEMBL: A distributed approach to high-quality automated protein sequence annotation

Bioinformatics

Volumn 15, Issue 3, 1999, Pages 219-227

  Möller, Steffen ^b   Leser, Ulf ^a,b   Fleischmann, Wolfgang ^b   Apweiler, Rolf ^b  

^a TECHNISCHE UNIVERSITÄT BERLIN   (Germany)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; COMPUTER PROGRAM; CONFERENCE PAPER; DATA BASE; INFORMATION PROCESSING; MOLECULAR BIOLOGY; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

EID: 0345299211     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/15.3.219     Document Type: Conference Paper

References (19)

1. Apweiler, R., O'Donovan, C., Martin, M.J., Fleischmann, W., Hermjakob, H., Möller, S., Contrino, S. and Junker, V. (1998) SWISS-PROT and its computer-annotated supplement TrEMBL: how to produce high-quality automatic annotation. In Proceedings of Systems, Cybernetics and Informatics. IIIS, Orlando, FL, Vol. 4, pp. 184-191.
2. Attwood, T.K., Beck, M.E., Flower, D.R., Scordis, P. and Selley, J. (1998) The PRINTS protein fingerprint database in its fifth year. Nucleic Acids Res., 26, 304-308.
3. Bailey, C., Fischer, S., Schug, J., Crabtree, J., Gibson, M. and Overton, G.C. (1998) Gaia: Framework annotation of genomic sequences. Genome Res., 8, 234-250.
4. Bairoch, A. (1996) The ENZYME data bank in 1995. Nucleic Acids Res., 24, 221-222.
5. Bairoch, A. (1997) SWISS-PROT user manual. http://www.expasy.ch/ txt/userman.txt.
6. Bairoch, A. and Apweiler, R. (1999) The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucleic Acids Res., 27, 49-54.
7. Bairoch, A., Bucher, P. and Hofmann, K. (1997) The PROSITE database, its status in 1997. Nucleic Acids Res., 25, 217-221.
8. Casari, G., Ouzounis, C., Valencia, A. and Sander, C. (1996) Genequiz II: automatic function assignment for genome sequence analysis. In Proceedings of the First Annual Pacific Symposium on Biocomputing. World Scientific, Singapore, pp. 707-709.
9. Fleischmann, W., Möller, S., Gateau, A. and Apweiler, R. (1998) A novel method for automatic and reliable functional annotation of proteins. Bioinformatics, 15, 228-233.
10. Frishman, D. and Mewes, H.-W. (1997) Protein structural classes in five complete genomes. Nature Struct. Biol., 4, 626-628.
11. Gaasterland, T. and Sensen, C. (1996) MAGPIE - automated genome interpretation. Trends Genet., 12, 76-78.
12. Gaasterland, T., Karp, P., Karplus, K., Ouzounis, C., Sander, C. and Valencia, A. (eds) (1997) Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA.
13. Georgskopoulos, D., Hornick, M. and Sheth, A. (1995) An overview of workflow management: From process modeling to workflow automation infrastructure. J. Distrib. Parallel Databases, 3, 119-154.
14. Harris, N.L. (1997) Genotator: A workbench for sequence annotation. Genome Res., 7, 754-762.
15. Reinhardt, A. and Hubbard, T. (1998) Using neural networks for prediction of the subcellular location of proteins. Nucleic Acids Res., 26, 2230-2236.
16. Sonnhammer, E.L.L., Eddy, S.R., Birney, E., Bateman, A. and Durbin, R. (1998a) Pfam: Multiple sequence alignments and HMM-profiles of protein. Nucleic Acids Res., 26, 320-322.
17. Sonnhammer, E.L.L., von Heijne, G. and Krogh, A. (1998b) A hidden Markov model for predicting transmembrane helices in protein sequences. In Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 122-130.
18. Stoesser, G., Moseley, M.A., Sleep, J., McGowran, M., Garcia-Pastor, M. and Sterk, P. (1998) The EMBL nucleotide sequence database. Nucleic Acids Res., 26, 8-15.
19. Ullman, J.D. (1988) Principles of Database and Knowledgebase Systems. Principles of Computer Science Series, Vol. 1. Computer Science Press, Rockville, MD.