Release 11 of TREMBL, a protein sequence database supplementing SWISS-PROT

Maria Jesus Martin martin at ebi.ac.uk
Wed Aug 4 04:19:13 EST 1999


INTRODUCTION
============

TrEMBL is a protein sequence database supplementing the SWISS-PROT
Protein Sequence Data Bank. TrEMBL contains the translations of all
coding sequences (CDS) present in the EMBL Nucleotide Sequence
Database not yet integrated in SWISS-PROT. TrEMBL can be considered
as a preliminary section of SWISS-PROT. For all TrEMBL entries
which should finally be upgraded to the standard SWISS-PROT
quality, SWISS-PROT accession numbers have been assigned.


RELEASE 11.0 OF TrEMBL
=====================

The goal of this TrEMBL release is to achieve synchronization with
SWISS-PROT release 38.0. Therefore, all sequence entries present in
SWISS-PROT release 38.0 have been removed from TrEMBL release 11,
further upgrading of existing TrEMBL entries was achieved and
only a very few new entries were incorporated.

TrEMBL is split in two main sections; SP-TrEMBL and REM-TrEMBL:

SP-TrEMBL (SWISS-PROT TrEMBL) contains the entries (199'794),
which should be eventually incorporated into SWISS-PROT.
SWISS-PROT accession numbers have been assigned for all SP-TrEMBL
entries.

SP-TrEMBL is organized in subsections:

arc.dat (Archea):               7383 entries
fun.dat (Fungi):                6656 entries
hum.dat (Human):                7880 entries
inv.dat (Invertebrates):       23594 entries
mam.dat (Other Mammals):        3094 entries
mhc.dat (MHC proteins):         4210 entries
org.dat (Organelles):          16227 entries
phg.dat (Bacteriophages):       1963 entries
pln.dat (Plants):              17250 entries
pro.dat (Prokaryotes):         45908 entries
rod.dat (Rodents):              7348 entries
unc.dat (Unclassified):           44 entries
vrl.dat (Viruses):             53911 entries
vrt.dat (Other Vertebrates):    4326 entries


REM-TrEMBL (REMaining TrEMBL) contains the entries (45'967) that we do
not want to include in SWISS-PROT.


WEEKLY UPDATES OF TrEMBL AND NON-REDUNDANT DATA SETS
====================================================
Weekly cumulative updates of TrEMBL are available by anonymous FTP and
from the EBI SRS server.
We also produce every week a complete non-redundant protein sequence
collection by providing three compressed files (these are in the
directory /pub/databases/sp_tr_nrdb on the EBI FTP server):
sprot.dat.Z, trembl.dat.Z and trembl_new.dat.Z.


ACCESS/DATA DISTRIBUTION
========================

FTP server:     ftp.ebi.ac.uk/pub/databases/trembl
SRS server:     http://srs.ebi.ac.uk/

TREMBL is also available on the SWISS-PROT CD-ROM.
SWISS-PROT + TREMBL is searchable on the FASTA3, BLAST2 and Bic_sw
servers of the EBI.



TrEMBL HAS BEEN PREPARED BY:
============================

Rolf Apweiler, Kirsty Bates, Margaret Biswas, Sergio Contrino,
Wolfgang Fleischmann, Gill Fraser, Henning Hermjakob, Vivien Junker,
Youla Karavidopoulou, Fiona Lang,  Minna Lehvaslaiho, Michele Magrane,
Maria Jesus Martin, Steffen Moeller, Nicoletta Mitaritonna,
Nicola Mulder, Claire O'Donovan, Lucia Rodriguez-Monge and
Eleanor Whitfield at the EMBL Outstation - European Bioinformatics
Institute (EBI) in Hinxton, UK;
Amos Bairoch and Alain Gateau at the Swiss Institute of Bioinformatics
in Geneva, Switzerland.


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Maria Jesus Martin                     email:martin at ebi.ac.uk
EMBL Outstation EBI
(European Bioinformatics Institute)    URL: http://www.ebi.ac.uk
Wellcome Trust Genome Campus           Tel: +44 (1223) 494408
Hinxton                                fax: +44 (1223) 494468
Cambridge
CB10 1SD UK
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