Release Notes

Release 6.2, Thur Apr 24 14:00 2003

Acknowledgements

R.Apweiler (1), T.K.Attwood (4), A.Bairoch (2), A.Bateman (5), D.Binns (1), P.Bradley (1,4), P.Bork (8), P.Bucher (3), L. Cerutti (3), R.Copley (8), E.Courcelle (6), U.Das (1) R.Durbin (5), W.Fleischmann (1), J.Gouzy (6), S.Griffiths-Jones (5) D.Haft (9), N.Hulo (2), D.Kahn (6), A.Kanapin (1), M.Krestyaninova (1), D.Lonsdale (1), R.Lopez (1), I.Letunic (8), A.N. Nikolskaya (10), J.McDowall (1), N.Mulder (1), S. Orchard (1), M.Pagni (3), D.Peyruc (6), C.Ponting (7), E.Quevillon (1), F.Servant (1), C.Sigrist (2), D.J.Studholme (5), C.H. Wu (10).

(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) MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, 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.

Introduction

The databases SWISS-PROT, TrEMBL, PROSITE, PRINTS, Pfam, and ProDom joined forces to launch an Integrated Documentation Resource of Protein Families, Domains and Functional Sites, abbreviated InterPro. SMART, TIGRFAMs and most recently PIR SuperFamilies have subsequently joined InterPro. A detailed description of the project can be found in the user manual.

Changes since last release

The second batch of PIR SuperFamily HMMs has been integrated, as well as methods from new releases of Pfam and PRINTS.

A new-look web site was launched in the last release for the InterPro and QuickGO browsers. The pages have changed to reflect the new style of the EBI pages in general, but in addition, have increased capabilities and new features. New to this release are links to the PDB protein of the month, with information on the corresponding protein family in InterPro. InterPro entries now contain a new field with links to curated structural information where available for a protein(s) in the match list.

The protein matches have been updated according to the latest updates of SWISS-PROT and TrEMBL. InterProScan has also been updated to include new member database signatures. Where applicable, InterPro entries now have links to the IUPHAR Receptor database. In addition, two new entry types have been introduced to signify "Active sites" and "Binding sites". A new taxonomy servlet has been introduced to display the taxonomic range of proteins matching an entry. It is displayed in a tree listing the number of proteins from each taxonmic group. We hope to extend this servlet to include protein retrieval capabilities in the future.

In the last release we also introduced FAQs pages to provide further help to InterPro users, and an online tutorial. The XML schema has been updated to include new features in InterPro entries.

Contents of current release

InterPro release 6.2 contains 8423 entries, representing 1815 domains, 6383 families, 160 repeats, 25 active sites, 20 binding sites and 20 post translational modifications. Overall, InterPro hits 780029 of 1071690 SWISS-PROT + TrEMBL protein sequences. A complete list is available from the ftp site.

The current version of InterPro consists of:

DATABASE VERSION ENTRIES
SWISS-PROT 41.11 127863
PRINTS 36.0 1800
TrEMBL 23.16 857951
Pfam 9.0 5724
PROSITE patterns 17.37 1605
PROSITE preprofiles N/A 150
ProDom 2002.1 1021
Smart 3.4 654
TIGRFAMs 2.1 1614
PIR SuperFamily 2.0 100

Forthcoming changes

The next release of InterPro will be release 7.0 scheduled for August 2003. This will include a new member database, SUPERFAMILY, the first methods based on structure rather than sequence.

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: Interhelp@ebi.ac.uk.

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.