Release Notes

Release 15.0, Monday April 2nd 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

  • 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**
GENE3D 3.3.0 2386 1441
HAMAP 201207.04 1749 1738
PANTHER 7.2 71246 2845
PIRSF 2.82 3147 3147
PRINTS 42.0 2106 2051
PROSITE patterns 20.83 1308 1291
PROSITE profiles 20.83 1035 1010
Pfam 26.0 13672 13064
PfamB 26.0 20000 0
ProDom 2006.1 1894 1108
SMART 6.2 1008 1001
SUPERFAMILY 1.73 1774 1207
TIGRFAMs 12.0 4203 4180
DATABASE VERSION ENTRIES PANTHER 6.1 30128 Pfam 21.0 8957 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 52.0 261513 UniProtKB/TrEMBL 35.0 3987044 InterPro 15.0 14764 GO Classification N/A 23937

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

Forthcoming changes

The next release of InterPro is scheduled for June 2007.