InterPro

http://www.ebi.ac.uk/interpro/

Apweiler, R.¹, Attwood, T.K.², Bairoch, A.³, Bateman, A.⁴, Biswas, M¹, Bork, P⁶, Bucher, P.⁵, Copley, R.⁶, Croning, M.D.R.¹, Durbin, R.⁴, Falquet, L.⁵, Fleischmann, W.¹, Gouzy, J.⁷, Griffiths-Jones, S.⁴, Hermjakob, H.¹, Hulo, N.³, Jonassen, I.⁸, Kahn, D.⁷, Kanapin, A.¹, Karavidopoulou, Y.¹, Lopez, R.¹, Mulder, N.J.¹, Oinn, T.M.¹, Pagni, M.⁵, Ponting, C.P.⁹, Servant, F.¹, Sigrist, C.J.A.³, Zdobnov, E.M.¹

¹EMBL Outstation - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, 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
⁶Biocomputing Unit EMBL, Heidelberg, Germany
⁷CNRS/INRA, Toulouse, France
⁸Department of Informatics, University of Bergen, HIB, Bergen, Norway
⁹MRC Functional Genetics Unit, Department of Human Anatomy &Genetics, University of Oxford, UK

Contact mulder@ebi.ac.uk

Database Description

Databases with signatures diagnostic for protein families, domains or functional sites are important tools for the computational functional classification of newly determined sequences that lack biochemical characterisation. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam, ProDom and SMART database projects. Each InterPro entry includes a functional description, annotation, literature references, and links back to the relevant member database(s). A new feature includes mapping of InterPro entries to the relevant Gene Ontology (GO) terms, a useful tool for automatic mapping of proteins to GO terms. Release 3.2 of InterPro (July 2001) contains 3,939 entries, representing 2850 families, 1009 domains, 65 repeats and 15 sites of post-translational modification (PTMs). Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (nearly 2,000,000 hits from around 580,000 proteins in SWISS-PROT and TrEMBL). Integration of the next member database, TIGRFAMs, is currently in progress. The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to Interhelp@ebi.ac.uk.

Recent Developments

New diagnostic signatures from the member databases have been incorporated into InterPro. The SMART (a Simple Modular Architecture Research Tool) database, which allows the identification and annotation of genetically mobile domains and the analysis of domain architectures has been integrated into InterPro. This includes more than 500 domain families found in signalling, extracellular and chromatin-associated proteins. Currently in progress is the integration of the next member database, TIGRFAMs, which provides Hidden Markov Models to identify protein families with identical functions. Other new features includes an additional graphical user interface for viewing protein matches in a condensed graphical view, as well as mapping to Gene Ontology (GO) terms. Where possible, InterPro entries have been manually GO terms so that the terms apply to all proteins matching the entry.

REFERENCES

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., Servant F., Sigrist C.J., Zdobnov E.M. (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res., 29, 37-40.