InterPro-一个关于蛋白家族、区域和功能位点知识的集成文献资源

InterPro – An integrated documentation resource for protein families, domains and functional sites

R.Apweiler (1), T.K.Attwood (4), A.Bairoch (2), A.Bateman (5), E.Birney (5), P.Bucher (3), J-J.Codani (8), F.Corpet (6), M.D.R.Croning (1,4), R.Durbin (5), T.Etzold (9), W.Fleischmann (1), J.Gouzy (6), H.Hermjakob (1), I.Jonassen (7), D.Kahn (6), A.Kanapin (1), R.Schneider (9), F.Servant (6), E.Zdobnov (1)

 

1 EMBL Outstation – European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
2 Swiss Institute for Bioinformatics, Geneva, Switzerland.
3 Swiss Institute for Experimental Cancer Research, Lausanne, Switzerland.
4 School of Biological Sciences, The University of Manchester, Manchester, UK.
5 The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
6 CNRS/INRA, Toulouse, France.
7 University of Bergen, Norway.
8 INRIA, 78153 Le-Chesnay Cedex, France.
9 LION bioscience AG

Abstract

InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed as a means of rationalising the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Merged annotations from PRINTS, PROSITE and Pfam form the InterPro core. Each combined InterPro entry includes functional descriptions and literature references, and links are made back to the relevant parent database(s), allowing users to see at a glance whether a particular family or domain has associated patterns, profiles, fingerprints, etc.. Merged and individual entries (i.e., those that have no counterpart in the companion resources) are assigned unique accession numbers. The first release of InterPro contains around 2,400 entries, representing families, domains, repeats and sites of post-translational modification (PTMs) encoded by 4,300 regular expressions, profiles, fingerprints and Hidden Markov Models (HMMs). Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 370,000 hits in total). The database is accessible for text-based searches at http://www.ebi.ac.uk/ interpro/.

Introduction

Pattern databases have become vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. During the last decade, several pattern-recognition methods have evolved to address different sequence analysis problems, resulting in rather different and, for the most part, independent databases. To perform a comprehensive analysis, a user therefore has to know several important things. For example, what are the resources and where can they be found? What