Release Notes

Release 6.0, Tue Mar 11 11:42:18 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), 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).

(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.

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 and TIGRFAMs have subsequently joined InterPro. A detailed description of the project can be found in the user manual.

Changes since last major release

A new-look web site has been launched 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. The ordering of fields in the InterPro entries has changed to provide links to the protein matches at the top of the entry. An additional graphical match view is available in an overview format, which is also used in the entry to display the example lists. It is now possible to sort the protein matches by Swiss-Prot ID. The simple text search has been extended to include different search options and results outputs, and all pages may be viewed in the user's format of choice out of Normal, Printer friendly, Text, simple HTML and XML.

The protein matches have been updated according to the latest updates of Swiss-Prot and TrEMBL, and additional methods from new releases of the member databases have been added. Potential false positive hits from problem signatures are regularly being cleaned up with the implementation of family-specific thresholds in the InterProScan package. InterProScan has also been updated to include new member database signatures. The number of mappings to the Gene Ontology (GO) classification system has increased since the last release, and where applicable, InterPro entries now have links to the Transport Classification database.

We have also introduced FAQs pages to provide further help to InterPro users.

Contents of current release

InterPro release 6.0 contains 7751 entries, representing 1748 domains, 5841 families, 147 repeats, and 15 post-translational modification sites. Overall, there are 3408359 InterPro hits from 953089 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 41.0 122564
PRINTS 35.0 1750
TrEMBL 23.0 830525
Pfam 8.0 5193
PROSITE patterns 17.37 1605
PROSITE preprofiles N/A 150
ProDom 2002.1 1021
InterPro 6.0 7751
Smart 3.4 654
TIGRFAMs 2.1 1614

Forthcoming changes

The next release of InterPro will be a point release, 6.1, scheduled for April 2003. For release 6.1, we aim to integrate the first 50 signatures of a new member database, PIR Superfamilies. A project is underway to incorporate protein secondary and tertiary structure information and we hope to provide such links from InterPro entries where applicable in the near future.

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 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.