Release Notes

Release 7.1, Monday December 8 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 (13), E.Courcelle (6), U.Das (1) R.Durbin (5), W.Fleischmann (1), J.Gough (11), J.Gouzy (6), S.Griffiths-Jones (5) D.Haft (9), N.Harte (1), N.Hulo (2), D.Kahn (6), A.Kanapin (1), M.Krestyaninova (1), D.Lonsdale (1), R.Lopez (1), I.Letunic (8), M.Madera (12), J.Maslen (1), J.McDowall (1), N.Mulder (1), A.N. Nikolskaya (10), 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;
(11) Department of Structural Biology School of Medicine, Stanford University, California, U.S.A;
(12) MRC Laboratory of Molecular Biology, Cambridge, UK.
(13) Wellcome Trust Centre for Human Genetics, Oxford, UK

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, PIR SuperFamilies and more recently SUPERFAMILY 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 updates of Swiss-Prot and TrEMBL. New methods from SUPERFAMILY, TIGRFAMs, Pfam and PROSITE have been integrated. In the match.xml file element, 'match', now contains new attribute 'score', which corresponds to the score given by InterProScan. Also, every match element now contains start and end positions. In the cases where there is no position information (manual assignment by curators) both values equal to zero.

Links to COMe, the bioinorganic motif database and MEROPS, a database of peptidases and protein inhibitors have been included.

COMe is an attempt to classify metalloproteins and some other complex proteins using the concept of bioinorganic motif. A bioinorganic motif (BIM) may be defined as a common structural feature of a class of functionally related, but not necessarily homologous, proteins, that includes the metal atom(s) and first coordination shell ligands.

MEROPS classifies peptidase inhibitors and peptidases. Only links to the peptidases are available in this release.

InterProScan has been updated to include new member database signatures and SUPERFAMILY HMMs and a new version implemented, which has increases functionality and new capabilities. In this release upto a maximum of 10 protein sequences or 1 nucleic acid coding sequence sequence can be submitted. For the analysis of nucleic acid sequences the minimum open reading frame size can be selected (range 20 to 150).

Contents of current release

InterPro release 7.1 contains 10403 entries, representing 2239 domains, 7901 families, 197 repeats, 26 active sites, 20 binding sites and 20 post translational modifications. Overall, there are 5211420 InterPro hits from 1152185 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 42.5 138922
PRINTS 37.0 1850
TrEMBL 25.5 1013263
Pfam 11.0 7255
PROSITE patterns 18.10 1659
PROSITE preprofiles N/A 131
ProDom 2002.1 1021
InterPro 7.1 10403
Smart 3.4 654
TIGRFAMs 3.0 1977
PIR SuperFamily 2.3 219
SUPERFAMILY 1.63 552

Forthcoming changes

The next release of InterPro will be release 7.2 scheduled for March 2004. This will include new data from the member databases. It will also include further improvements to the taxonomy servlet, and incorporation of MEROPS database peptidase inhibitor classification.