Release Notes

Release 14.1, Monday February 19th 2007

http://www.ebi.ac.uk/interpro/
ftp://ftp.ebi.ac.uk/pub/databases/interpro/

Acknowledgements

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.

Current Release

Introduction

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

  • The protein matches have been updated according to the latest update of UniProtKB.
  • New matches to PROSITE release 20 and SUPERFAMILY release 1.69 are incorporated.
  • E-values have replaced bit scores in both match.xml amd match_complete.xml.
  • Match.xml, 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 will be discontinued with release 15.0.

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 14.1 contains 13826 entries, representing 3911 domains, 9610 families, 232 repeats, 34 active sites, 20 binding sites and 19 post-translational modification sites. Overall, there are 15880845 InterPro hits from 3100874 UniProtKB protein sequences. A complete list is available from the ftp site.

DATABASE VERSION ENTRIES
PANTHER 6.1 30128
Pfam 20.0 8296
PIRSF 2.68 1748
PRINTS 38.0 1900
ProDom 2005.1 1522
PROSITE 20.0 2006
SMART 5.0 706
TIGRFAMs 6.0 2946
GENE3D 3.0.0 2147
SUPERFAMILY 1.69 1538
UniProtKB/Swiss-Prot 51.5 257964
UniProtKB/TrEMBL 34.5 3745801
InterPro 14.1 13826
GO Classification N/A 22878

92.4% of UniProtKB/Swiss-Prot - 238310 of 257964 proteins

76.4% of UniProtKB/TrEMBL - 2862564 of 3745801 proteins

77.4% of UniProtKB - 3100874 of 4003765 proteins

Last entry: IPR014744

23548 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
  • Forthcoming changes

    The next release of InterPro is scheduled for April 2007.

    Feedback

    We need your help and would welcome any feedback. If you find errors or omissions please let us know. You can contact us at: EBI Support.

    Copyright

    InterPro - Integrated Resource Of Protein Domains And Functional Sites. Copyright (C) 2001 The InterPro Consortium. This manual and the accompanying database may be copied and redistributed freely, without advance permission, provided that this Copyright statement is reproduced with each copy.