The BioInformer nr. 6, 2000 --- InterPro Release 1.2




	A publication of EMBL - Outstation Hinxton, The European Bioinformatics Institute

InterPro Release 1.2

Introduction

The databases SWISS-PROT, TrEMBL, PROSITE, PRINTS, Pfam, and ProDom joined forces to launch an Integrated Resource of Protein Families, Domains and Sites, abbreviated InterPro. A detailed description of the project can be found in the InterPro user manual.

Contents of current release

InterPro release 1.2 (June 2000) contains 3052 entries, representing 574 domains, 2418 families, 46 repeats, and 14 post-translational modification sites. Overall, there are 1060226 InterPro hits from 384572 SWISS-PROT + TrEMBL protein sequences. A complete list is available from the ftp site.

The release was build using the following database versions:

Database	Version	Entries	Date
SWISS-PROT	38.19	86552	10-Jun-2000
TrEMBL	13.7	298020	12-Jun-2000
PROSITE	16.0	1370	01-Apr-1999
prelim. profiles	-	241	10-Feb-1999
Pfam	5.2	2128	10-Apr-2000
PRINTS	26.1	1310	05-Apr-2000
ProDom	2000.1	540	07-Feb-2000

The SWISS-PROT and TrEMBL data used includes updates of these versions.

Changes since release 1.0

The first 540 ProDom methods have been integrated into InterPro. 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.

A new relationship has been introduced which can be used to identify multi-domain proteins. This relationship, "CONTAINS/FOUND IN", is used to show that a domain can be found in more than one type of protein or family of proteins, but is not a SUBTYPE in the family sense. The domain is a functional entity, which can be found in proteins with different domain organisations. The "CONTAINS/FOUND IN" relationship does not imply that this is always the case, but suggests that a protein may contain this domain. It is useful in linking InterPro entries which are often associated, but not in a family/subfamily relationship. With the introduction of this new relationship, some of the previously existing parent/child relationships have been altered.

Forthcoming changes

The second production release 2.0 is scheduled for September 2000. For Release 2.0, we aim to integrate more of the ProDom database and incorporate the Gene Ontology (GO) classification system.

Information by: EBI´s InterPro Team

Resources and further information

European Bioinformatics Institute (EMBL-EBI)
http://www.ebi.ac.uk/

InterPro homepage
http://www.ebi.ac.uk/interpro/

InterPro User manual
http://www.ebi.ac.uk/interpro/user_manual.html

InterPro ftp site
ftp://ftp.ebi.ac.uk/pub/databases/interpro/

Stanford University
http://www.stanford.edu/

Gene Ontology (GO) classification system
http://genome-www.stanford.edu/GO/

External sites are not endorsed by EMBL-EBI

Direct questions or comments to Bioinformer Editor. This page last modified Monday, 07 August, 2000.
ISSN 1462-1363. More information about the BioInformer.