Interpro release 2.0

Alexander Kanapin alex at ebi.ac.uk
Tue Oct 31 11:40:32 EST 2000


InterPro Release Notes

Release 2.0, October 2000

http://www.ebi.ac.uk/interpro/
ftp://ftp.ebi.ac.uk/pub/databases/interpro/

Acknowledgments
InterPro has been prepared by:

R.Apweiler (1), T.K.Attwood (4), A.Bairoch (2), A.Bateman (5), 
E.Birney (1), M.Biswas (1), P.Bucher (3), L.Cerutti (5), 
M.D.R.Croning (1,4), R.Durbin (5), W.Fleischmann (1), 
H.Hermjakob (1), N.Hulo (2) A.Kanapin (1), Y.Karavidopoulou 
(1), R.Lopez (1), B.Marx (1), N.Mulder (1), T.Oinn (1), 
F.Servant (6), C.Sigrist (2), E.Zdobnov (1).

(1) EMBL Outstation - European Bioinformatics Institute, Wellcome Trust
Genome Campus, Hinxto
n, 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; 


1. Introduction

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


2. Contents of current release

InterPro release 2.0 (October 2000) contains 3204 entries, representing
767 domains, 2372 fam
ilies, 50 repeats, and 15 post-translational modification sites.
Overall, there are 1315512 I
nterPro hits from 462483 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          39.7    88753   02-OCT-2000
   TrEMBL              15.3   373730   20-OCT-2000
   PROSITE            16.25     1424   31-AUG-2000
   prelim. profiles     -        236   25-SEP-2000
   Pfam                 5.5     2478   01-SEP-2000
   PRINTS              27.0     1356   25-AUG-2000
   ProDom             2000.1    1309   07-FEB-2000



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


3. Changes since release 1.2

A further 769 ProDom methods have been integrated into InterPro. The
protein matches have bee
n updated according to the latest updates of SWISS-PROT and TrEMBL, and
additional methods fr
om new releases of the member databases have been added. The format of
the flatfiles has chan
ged, and consist of two separate files, one for all the data and one for
the protein matches.
 An SRS-based InterProScan suite as well as a Perl-based stand-alone
InterProScan package hav
e been developed. The Perl-based InterProScan has a robust and efficient
(parallel) internal 
architecture that benefits from network distributed computing with
support of queuing systems
. It is capable of providing a pre-processed, integrated view of the
results.

The InterPro webserver has been redesigned to make the pages more
coherent and consistent. It
 also includes links to a more comprehensive help menu. Within an
InterPro entry there are li
nks to pop-up windows with explanations of terms. In addition, where a
parent/child relations
hip exists, there is a link to a view to the hierarchical tree of the
relationship. The match
 views are also improved, with legends describing symbols or colours.


4. Forthcoming changes

The third production release 3.0 is scheduled for January 2001. For
Release 3.0, we aim to in
tegrate more of the ProDom database, and the SMART database. We will
also incorporate the Gen
e Ontology (GO) classification system
(http://genome-www.stanford.edu/GO/).


5. We need your help

We welcome any feedback. If you find errors or omissions please let us 
know. You can contact
 us at: Interhelp at ebi.ac.uk.


6. Copyright Notice

InterPro - Integrated Resource Of Protein Domains And Functional Sites 
Copyright (C) 2000 The InterPro Consortium. 
This  manual and the accompanying database may be copied and
redistributed freely, without ad
vance permission, provided that this Copyright statement is reproduced
with each copy.


_______________________________________________________________________
Alexander A. Kanapin, Ph.D.         | European Bioinformatics Institute
+44 (0)1223 49 4610                 | Wellcome Trust Genome Campus,
Hinxton
+44 (0)1223 49 4468 (fax)           | Cambridgeshire CB10 1SD, United
Kingdom







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