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TrEMBL 7.0

Introduction

TrEMBL is the 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

TrEMBL release 7.0  is created from the EMBL Nucleotide Sequence Database release 55 and contains 193'860 sequence entries, comprising 53'601'062 amino acids.

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

SP-TrEMBL (SWISS-PROT TrEMBL) contains the entries (165'420), 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:

arc.dat

(Archea)

7434 entries

fun.dat

(Fungi):

5261 entries

hum.dat

(Human)

6976 entries

inv.dat

(Invertebrates)

21991 entries

mam.dat

(Other Mammals)

2684 entries

mhc.dat

(MHC proteins)

3601 entries

org.dat

(Organelles)

12699 entries

phg.dat

(Bacteriophages)

1604 entries

pln.dat

(Plants)

12668 entries

pro.dat

(Prokaryotes)

35857 entries

rod.dat

(Rodents)

6346 entries

unc.dat

(Unclassified)

88 entries

vrl.dat

(Viruses)

44561 entries

vrt.dat

(Other Vertebrates)

3650 entries

REM-TrEMBL (REMaining TrEMBL) contains the entries (28'440) that we do not want to include in SWISS-PROT.

Weekly updated 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

TrEMBL is available on the EBI´s web and ftp services, and  is also included on the SWISS-PROT CD-ROM. SWISS-PROT + TrEMBL is searchable on a number of the computational services, which are listed at the end of this article.

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 Swiss Institute of Bioinformatics in Geneva, Switzerland.

Information by: EBI´s TrEMBL team

 

Resources and further information

  • European Bioinformatics Institute (EMBL-EBI)
    http://www.ebi.ac.uk/
    • Full TrEMBL 7 release notes
      http://bioinformer.ebi.ac.uk/newsletter/archives/4/trembl7-rel notes.txt
    • FTP access to latest TrEMBL release
      ftp://ftp.ebi.ac.uk/pub/databases/trembl/
    • SRS access to latest TrEMBL release
      http://srs.ebi.ac.uk/
    • SWISS-PROT + TrEMBL searchable services
      • FASTA3
        http://www2.ebi.ac.uk/fasta3/
      • BLAST2 
        http://www2.ebi.ac.uk/blast2/
      • Bic_sw 
        http://www2.ebi.ac.uk/bic_sw/
      • Scanps 
        http://www2.ebi.ac.uk/scanps/
      • SSearch
        http://www2.ebi.ac.uk/ssearch3/
  • Swiss Institute of Bioinformatics (SIB)
    http://www.isb-sib.ch/

 

External sites are not endorsed by EMBL-EBI

 
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