The BioInformer nr. 3, 1998 -- TREMBL Release 5




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

TREMBL Release 5

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.

This release

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. To minimise redundancy, the translations of all coding sequences (CDS) in the EMBL Nucleotide Sequence Database already included in SWISS-PROT Release 35 have been removed from TREMBL release 5.

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 organised in subsections:

Filename

Organism

Entries

fun.dat

hum.dat

inv.dat

mam.dat

mhc.dat

org.dat

phg.dat

pln.dat

pro.dat

rod.dat

unc.dat

vrl.dat

vrt.dat

Fungi

Human

Invertebrates

Other Mammals

MHC proteins

Organelles

Bacteriophages

Plants

Prokaryotes

Rodents

Unclassified

Viruses

Other Vertebrates


4694
6101
18423
2444
3336
10561
1111
9871
34832
5976
109
39943
3154

30'007 new entries have been integrated in SP-TREMBL. 1'860 sequences of SP-TREMBL entries have been updated and in 26'093 cases the annotation has been updated.

REM-TREMBL (REMaining TREMBL) contains the entries (25'806) that we do not want to include in SWISS-PROT.REM-TREMBL entries have no accessionnumbers.

Availability

Weekly cumulative updates of TREMBL are available by anonymous FTP and from the EBI SRS server. TREMBL is also available on the SWISS-PROT CD-ROM. SP-TREMBL is searchable on the FASTA server of the EBI and will be soon searchable on the BLITZ server of the EBI.

TREMBL has been prepaired by:

Rolf Apweiler, Sergio Contrino, Vivien Junker, Stephanie Kappus, Fiona Lang, Michele Magrane, Maria Jesus Martin, 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.

Written by: Viv Junker

Resources and further information

European Bioinformatics Institute
http://www.ebi.ac.uk/

SWISS-PROT Homepage
http://www.ebi.ac.uk/ebi_docs/swissprot_db/swisshome.html

TREMBL latest release ftp site
ftp://ftp.ebi.ac.uk/pub/databases/trembl/

EBI's SRS server
http://srs.ebi.ac.uk/

University of Geneva
http://www.unige.ch/e-welcome.html

Medical Bichemistry Department (French only)
http://www.hcuge.ch/

External sites are not endorsed by EMBL-EBI

Direct questions or comments to Bioinformer Editor. This page last modified Friday, 16 July, 1999.
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