Release NotesRelease 15.0, Monday April 2nd 2007
R.Apweiler (1), T.K.Attwood (4), A.Bairoch (2), A.Bateman (5), D.Binns (1), P.Bork (8), P.Bucher (3), L.Cerutti (3), R.Copley (13), E.Courcelle (6), U.Das (1), L.Daugherty (1), M.Dibley (7), R.Finn (5), J.Gough (11), D.Haft (9), N.Hulo (2), S.Hunter (1), D.Kahn (6), A.Kanapin (1), A. Kejariwal (14), D.Lonsdale (1), R.Lopez (1), I.Letunic (8), M.Madera (12), J.Maslen (1), C.McAnulla (1), J.McDowall (1), J.Mistry (5), A.Mitchell (1,4), N.Mulder (1), A.N.Nikolskaya (10), S.Orchard (1), C.Orengo (7), M.Pagni (3), R. Petryszak (1), C.Sigrist (2), P.D.Thomas (14), D.Wilson (12), C.H.Wu (10), C.Yates (7).
(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) Biochemistry and Molecular Biology Department, University College London, University of London, UK;
(8) Biocomputing Unit, EMBL-Heidelberg, Germany;
(9) The Institute for Genomic Research, Maryland, USA;
(10) Protein Information Resource, Georgetown University Medical Center, Washington, D.C., USA;
(11) Unite de Bioinformatique Structurale, Institut Pasteur, Paris, France;
(12) MRC Laboratory of Molecular Biology, Cambridge, UK;
(13) Wellcome Trust Centre for Human Genetics, Oxford, UK;
(14) Computational Biology, SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
The databases Swiss-Prot and TrEMBL (now part of UniProtKB), PROSITE, PRINTS, Pfam and ProDom joined forces to launch an Integrated Documentation Resource of Protein Families, Domains and Functional Sites, abbreviated InterPro. Since then SMART, TIGRFAMs, PIRSF, SUPERFAMILY and more recently PANTHER and Gene3D, have joined InterPro. A detailed description of the project can be found in the user manual.
Changes since last release
- InterPro Advanced Search has been extended to allow separate fields of the entry, and different entry types, to be searched. These include names/short names, abstracts, publications and cross references.
- Match displays have been extended to include a selection for proteins from the non-redundant proteome set of a specific taxonomic ID where the complete genome has been sequenced.
- The taxonomy wheel has been expanded; clicking on a lineage or match count provides a pop-up display showing the match counts associated with the taxonomic sub-group(s).
- Match_complete.xml and UniParc matches to InterPro methods (uniparc_match.tar.gz) have been updated and are available from the ftp site in XML format. Due to the large size of UniParc the data has been divided into chunks and the latest updates are provided in these files at each InterPro release.
- Match.xml has been discontinued.
Contents and coverage of the current release
InterPro protein matches are now calculated for all UniProtKB and UniParc proteins. The following statistics are for all UniProtkB proteins:
InterPro release 15.0 contains 14764 entries, representing 4454 domains, 10006 families, 231 repeats, 34 active sites, 20 binding sites and 19 post-translational modification sites. Overall, there are 17059363 InterPro hits from 3296212 UniProtKB protein sequences. A complete list is available from the ftp site.
|Signature database||Version||Signatures*||Integrated signatures**|
92.6% of UniProtKB/Swiss-Prot - 242049 of 261513 proteins
76.6% of UniProtKB/TrEMBL - 3054163 of 3987044 proteins
77.6% of UniProtKB - 3296212 of 4248557 proteins
Last entry: IPR015812
24213 publications in PUBMED are referenced from InterPro.
Lists of InterPro entries by type and to GO
- Family - Domain - Repeat - PTM - Binding Site - Active Site
- List of InterPro to GO mappings. These are also available through the EBI GO browser QuickGO
The next release of InterPro is scheduled for June 2007.