Abstract
The family and motif databases, PROSITE, PRINTS, Pfam and ProDom, have been integrated into a powerful resource for protein secondary annotation. As of June 2000, InterPro had processed 384 572 proteins in SWISS-PROT and TrEMBL. Because the contributing databases have different clustering principles and scoring sensitivities, the combined assignments compliment each other for grouping protein families and delineating domains. The graphic displays of all matches above the scoring thresholds enables judgements to be made on the concordances or differences between the assignments. The website links can be used to analyse novel sequences and for queries across the proteomes of 32 organisms, including the partial human set, by domain and/or protein family. An analysis of selected HtrA/DegQ proteases demonstrates the utility of this website for detailed comparative genomics. Further information on the project can be found at the European Bioinformatics Institute at http://www.ebi.ac.uk/interpro/.
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Selected References
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- Attwood T. K., Croning M. D., Flower D. R., Lewis A. P., Mabey J. E., Scordis P., Selley J. N., Wright W. PRINTS-S: the database formerly known as PRINTS. Nucleic Acids Res. 2000 Jan 1;28(1):225–227. doi: 10.1093/nar/28.1.225. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bateman A., Birney E., Durbin R., Eddy S. R., Howe K. L., Sonnhammer E. L. The Pfam protein families database. Nucleic Acids Res. 2000 Jan 1;28(1):263–266. doi: 10.1093/nar/28.1.263. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Corpet F., Servant F., Gouzy J., Kahn D. ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res. 2000 Jan 1;28(1):267–269. doi: 10.1093/nar/28.1.267. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Henikoff J. G., Greene E. A., Pietrokovski S., Henikoff S. Increased coverage of protein families with the blocks database servers. Nucleic Acids Res. 2000 Jan 1;28(1):228–230. doi: 10.1093/nar/28.1.228. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hofmann K., Bucher P., Falquet L., Bairoch A. The PROSITE database, its status in 1999. Nucleic Acids Res. 1999 Jan 1;27(1):215–219. doi: 10.1093/nar/27.1.215. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pallen M. J., Wren B. W. The HtrA family of serine proteases. Mol Microbiol. 1997 Oct;26(2):209–221. doi: 10.1046/j.1365-2958.1997.5601928.x. [DOI] [PubMed] [Google Scholar]
- Schultz J., Copley R. R., Doerks T., Ponting C. P., Bork P. SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res. 2000 Jan 1;28(1):231–234. doi: 10.1093/nar/28.1.231. [DOI] [PMC free article] [PubMed] [Google Scholar]