Nucleic Acids Research, 2001, Vol. 29, No. 1 37-40
© 2001 Oxford University Press
The InterPro database, an integrated documentation resource for protein families, domains and functional sites
1EMBL Outstation – European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, 2School of Biological Sciences, The University of Manchester, Manchester, UK, 3Swiss Institute for Bioinformatics, Geneva, Switzerland, 4The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, 5Swiss Institute for Experimental Cancer Research, Lausanne, Switzerland, 6CNRS/INRA, Toulouse, France and 7Department of Informatics, University of Bergen, HIB, Bergen, Norway
Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a functional description, annotation, literature references and links back to the relevant member database(s). Release 2.0 of InterPro (October 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification encoded by a total of 6804 different regular expressions, profiles, fingerprints and Hidden Markov Models. Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1 000 000 hits from 462 500 proteins in SWISS-PROT and TrEMBL). The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp{at}ebi.ac.uk.
* To whom correspondence should be addressed. Tel: +44 1223 494 435; Fax: +44 1223 494 468; Email: rolf.apweiler{at}ebi.ac.uk
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|
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|
|
|
|
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|
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|
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|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
K.-C. Chou and Y.-D. Cai Predicting enzyme family class in a hybridization space Protein Sci., November 1, 2004; 13(11): 2857 - 2863. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
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|
|
|
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