Release Notes

Release 12.1, Wednesday March 8th 2006

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), W.Fleischmann (1), 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), S.Schulze-Kremer (15) 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) Genomic Sciences Centre, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Japan;
(12) MRC Laboratory of Molecular Biology, Cambridge, UK;
(13) Wellcome Trust Centre for Human Genetics, Oxford, UK;
(14) Computational Biology, Applied Biosystems, 850 Lincoln Center Drive, Foster City, CA 94404, USA.
(15) Norddeutscher Verbund fur Hoch- und Hochstleistungsrechnen (HLRN)

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 and new methods from Gene3D, Pfam and TIGRFAMs have been integrated.

  • Match_complete.xml is released in addition to match.xml. It contains all matches to UniProtKB protein sequences and all matches to unintegrated methods and has a new format
  • The Additional Reading field has been updated with new references from the member databases

Contents and coverage of the current release

InterPro protein matches are now calculated for all UniProtKB proteins. For more information see UniProtKB.

InterPro release 12.1 contains 12953 entries, representing 3585 domains, 9055 families, 238 repeats, 32 active sites, 22 binding sites and 21 post-translational modification sites. Overall, there are 11318934 InterPro hits from 2207141 UniProtKB protein sequences. A complete list is available from the ftp site.

ProDom 2004.1 1522
PRINTS 38.0 1900
Pfam 19.0 8183
InterPro 12.1 12953
PROSITE patterns 19.10 1882
PROSITE preprofiles N/A 109
SMART 5.0 668
UniProtKB/Swiss-Prot 49.0 208005
UniProtKB/TrEMBL 32.0 2618388
PIRSF 2.68 1347
PANTHER 6.0 46462
Gene3D 3.0 150
SUPERFAMILY 1.65 1160
TIGRFAMs 4.2 2626
GO Classification N/A 20531

92.2% of UniProtKB/Swiss-Prot - 191686 of 208005 proteins

77.0% of UniProtKB/TrEMBL - 2015455 of 2618388 proteins

78.1% of UniProtKB - 2207141 of 2826393 proteins

Last entry: IPR013767

16992 publications in PUBMED are referenced from InterPro.

Forthcoming changes

The next release of InterPro will be release 13.0 scheduled for July 2006. It will incorporate:

  • Links to IntAct, the protein interaction database.