Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1994 Sep;22(17):3574–3577.

OWL--a non-redundant composite protein sequence database.

A J Bleasby 1, D Akrigg 1, T K Attwood 1
PMCID: PMC308323  PMID: 7937061

Abstract

A comprehensive, non-redundant composite protein sequence database is described. The database, OWL, is an amalgam of data from six publicly-available primary sources, and is generated using strict redundancy criteria. The database is updated monthly and its size has increased almost eight-fold in the last six years: the current version contains > 76,000 entries. For added flexibility, OWL is distributed with a tailor-made query language, together with a number of programs for database exploration, information retrieval and sequence analysis, which together form an integrated database and software resource for protein sequences.

Full text

PDF
3577

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Akrigg D., Attwood T. K., Bleasby A. J., Findlay J. B., North A. C., Maughan N. A., Parry-Smith D. J., Perkins D. N., Wootton J. C. SERPENT--an information storage and analysis resource for protein sequences. Comput Appl Biosci. 1992 Jun;8(3):295–296. doi: 10.1093/bioinformatics/8.3.295. [DOI] [PubMed] [Google Scholar]
  2. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  3. Attwood T. K., Beck M. E. PRINTS--a protein motif fingerprint database. Protein Eng. 1994 Jul;7(7):841–848. doi: 10.1093/protein/7.7.841. [DOI] [PubMed] [Google Scholar]
  4. Attwood T. K., Findlay J. B. Design of a discriminating fingerprint for G-protein-coupled receptors. Protein Eng. 1993 Feb;6(2):167–176. doi: 10.1093/protein/6.2.167. [DOI] [PubMed] [Google Scholar]
  5. Attwood T. K., Findlay J. B. Fingerprinting G-protein-coupled receptors. Protein Eng. 1994 Feb;7(2):195–203. doi: 10.1093/protein/7.2.195. [DOI] [PubMed] [Google Scholar]
  6. Bairoch A., Boeckmann B. The SWISS-PROT protein sequence data bank, recent developments. Nucleic Acids Res. 1993 Jul 1;21(13):3093–3096. doi: 10.1093/nar/21.13.3093. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Barker W. C., George D. G., Mewes H. W., Pfeiffer F., Tsugita A. The PIR-International databases. Nucleic Acids Res. 1993 Jul 1;21(13):3089–3092. doi: 10.1093/nar/21.13.3089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  9. Bleasby A. J., Wootton J. C. Construction of validated, non-redundant composite protein sequence databases. Protein Eng. 1990 Jan;3(3):153–159. doi: 10.1093/protein/3.3.153. [DOI] [PubMed] [Google Scholar]
  10. Burks C., Fickett J. W., Goad W. B., Kanehisa M., Lewitter F. I., Rindone W. P., Swindell C. D., Tung C. S., Bilofsky H. S. The GenBank nucleic acid sequence database. Comput Appl Biosci. 1985 Dec;1(4):225–233. [PubMed] [Google Scholar]
  11. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Doolittle R. F. Similar amino acid sequences: chance or common ancestry? Science. 1981 Oct 9;214(4517):149–159. doi: 10.1126/science.7280687. [DOI] [PubMed] [Google Scholar]
  13. George D. G., Barker W. C., Hunt L. T. The protein identification resource (PIR). Nucleic Acids Res. 1986 Jan 10;14(1):11–15. doi: 10.1093/nar/14.1.11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hamm G. H., Cameron G. N. The EMBL data library. Nucleic Acids Res. 1986 Jan 10;14(1):5–9. doi: 10.1093/nar/14.1.5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Pappin D. J., Hojrup P., Bleasby A. J. Rapid identification of proteins by peptide-mass fingerprinting. Curr Biol. 1993 Jun 1;3(6):327–332. doi: 10.1016/0960-9822(93)90195-t. [DOI] [PubMed] [Google Scholar]
  16. Parry-Smith D. J., Attwood T. K. ADSP--a new package for computational sequence analysis. Comput Appl Biosci. 1992 Oct;8(5):451–459. doi: 10.1093/bioinformatics/8.5.451. [DOI] [PubMed] [Google Scholar]
  17. Parry-Smith D. J., Attwood T. K. SOMAP: a novel interactive approach to multiple protein sequences alignment. Comput Appl Biosci. 1991 Apr;7(2):233–235. doi: 10.1093/bioinformatics/7.2.233. [DOI] [PubMed] [Google Scholar]
  18. Pattabiraman N., Namboodiri K., Lowrey A., Gaber B. P. NRL-3D: a sequence-structure database derived from the protein data bank (PDB) and searchable within the PIR environment. Protein Seq Data Anal. 1990 Oct;3(5):387–405. [PubMed] [Google Scholar]
  19. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES