Release NotesRelease 15.1, Wednesday May 30th 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, PRABI, 69622 Villeurbanne Cedex, 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
- PubMed Identifiers in the Publications and Additional Reading fields now link to Europe PubMed Central. Europe PubMed Central combines literature searching with text mining tools for biology. Search results are cross referenced to EBI applications based on publication identifiers. Links to full text versions are provided where available.
- Matches to PANTHER HMMs are now represented by a single unbroken bar
- 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.
- UniMES Release 1.0 matches to InterPro methods (unimes_match.tar.gz) are now available from the ftp site in XML format.
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 15.1 contains 14978 entries, representing 4605 domains, 10066 families, 234 repeats, 34 active sites, 21 binding sites and 18 post-translational modification sites. Overall, there are 18458109 InterPro hits from 3559140 UniProtKB protein sequences. A complete list is available from the ftp site.
|Signature database||Version||Signatures*||Integrated signatures**|
92.5% of UniProtKB/Swiss-Prot - 247187 of 267354 proteins
75.9% of UniProtKB/TrEMBL - 3311953 of 4361897 proteins
76.9% of UniProtKB - 3559140 of 4629251 proteins
Last entry: IPR015873
24669 publications in PUBMED are referenced from InterPro.
Lists of InterPro entries by type and mappings to GO terms
- 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 July 2007.