Release 5 of TREMBL, a protein sequence database supplementing SWISS-PROT

Rolf Apweiler apweiler at ebi.ac.uk
Thu Feb 19 11:54:21 EST 1998


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 5.0 OF TREMBL
=====================

This TREMBL release is created from the EMBL Nucleotide Sequence
Database release 53 and contains 166'361 sequence entries, comprising
45'671'684 amino acids.

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

SP-TREMBL (SWISS-PROT TREMBL) contains the entries (140'555) 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:

fun.dat (Fungi):                4694 entries
hum.dat (Human):                6101 entries
inv.dat (Invertebrates):       18423 entries
mam.dat (Other Mammals):        2444 entries
mhc.dat (MHC proteins):         3336 entries
org.dat (Organelles):          10561 entries
phg.dat (Bacteriophages):       1111 entries
pln.dat (Plants):               9871 entries
pro.dat (Prokaryotes):         34832 entries
rod.dat (Rodents):              5976 entries
unc.dat (Unclassified):          109 entries
vrl.dat (Viruses):             39943 entries
vrt.dat (Other Vertebrates):    3154 entries

REM-TREMBL (REMaining TREMBL) contains the entries (25'806) 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:5000/

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, Sergio Contrino, Wolfgang Fleischmann, Henning Hermjakob,

Vivien Junker, Stephanie Kappus, Fiona Lang, Michele Magrane, Maria
Jesus
Martin, Steffen Moeller, Nicoletta Mitaritonna and Claire O'Donovan at
the
EMBL Outstation - European Bioinformatics Institute (EBI) in Hinxton,
UK;
Amos Bairoch and Alain Gateau at the Medical Biochemistry Department of
the University of Geneva, Switzerland.


=======================================================================
Rolf Apweiler                           | SWISS-PROT Coordinator
EMBL Outstation                         | Email:apweiler at ebi.ac.uk
European Bioinformatics Institute (EBI) | URL:  http://www.ebi.ac.uk
Wellcome Trust Genome Campus, Hinxton   | Tel:  +44 (1223) 494435
Cambridge CB10 1SD, UK                  | Fax:  +44 (1223) 494968
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