UniProtKB/TrEMBL - Old Release Notes
N.B. From release 27, the UniProtKB/TrEMBL release notes are included in the UniProt release notes.
TrEMBL Release Notes
Release 6, June 1998
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Cambridge CB10 1SD
Telephone: (+44 1223) 494 400
Fax: (+44 1223) 494 468
Electronic mail address: DATALIB@EBI.AC.UK
WWW server: http://www.ebi.ac.uk/
Medical Biochemistry Department
Centre Medical Universitaire
1211 Geneva 4
Telephone: (+41 22) 784 40 82
Fax: (+41 22) 702 55 02
Electronic mail address: BAIROCH@CMU.UNIGE.CH
WWW server: http://www.expasy.ch/
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 6.0 OF TREMBL
This TREMBL release is created from the EMBL Nucleotide Sequence Database
release 54 and contains 177'757 sequence entries, comprising 48'796'878
TREMBL is split in two main sections; SP-TREMBL and REM-TREMBL:
SP-TREMBL (Swiss-Prot TREMBL) contains the entries (150'329) 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): 5556 entries (new section)
fun.dat (Fungi): 4781 entries
hum.dat (Human): 6312 entries
inv.dat (Invertebrates): 20364 entries
mam.dat (Other Mammals): 2450 entries
mhc.dat (MHC proteins): 3524 entries
org.dat (Organelles): 11685 entries
phg.dat (Bacteriophages): 1240 entries
pln.dat (Plants): 11217 entries
pro.dat (Prokaryotes): 32000 entries
rod.dat (Rodents): 5913 entries
unc.dat (Unclassified): 88 entries
vrl.dat (Viruses): 41882 entries
vrt.dat (Other Vertebrates): 3317 entries
REM-TREMBL (REMaining TREMBL) contains the entries (27'428) that we do
not want to include in Swiss-Prot. REM-TrEMBL entries have no accession
numbers. This section is organised in five subsections:
1) Immunoglobulins and T-cell receptors (Immuno.dat)
Most REM-TrEMBL entries are immunoglobulins and T-cell receptors. We
stopped entering immunoglobulins and T-cell receptors into Swiss-Prot,
because we only want to keep the germ line gene derived translations
of these proteins in Swiss-Prot and not all known somatic recombinated
variations of these proteins. We would like to create a specialised
database dealing with these sequences as a further supplement to
Swiss-Prot and keep only a representative cross-section of these
proteins in Swiss-Prot.
2) Synthetic sequences (Synth.dat)
Another category of data, which will not be included in Swiss-Prot are
synthetic sequences. Again, we do not want to leave these entries in
TrEMBL. Ideally one should build a specialised database for artificial
sequences as a further supplement to Swiss-Prot.
3) Patent application sequences (Patent.dat)
A third subsection consists of coding sequences captured from patent
applications. A thorough survey of these entries have shown that
apart from a rather small minority (which in most cases have already
been integrated in Swiss-Prot), most of these sequences contain either
erroneous data or concern artificially generated sequences outside the
scope of Swiss-Prot.
4) Small fragments (Smalls.dat)
Another subsection consists of fragments with less than eight amino
5) CDS not coding for real proteins (Pseudo.dat)
The last subsection consists of CDS translations where we have strong
evidence to believe that these CDS are not coding for real proteins.
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.
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, Christian Desaintes, 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.
This manual and the database it accompanies may be copied and redistributed
freely, without advance permission, provided that this statement is reproduced
with each copy.
If you want to cite TREMBL in a publication please use the following
Bairoch A., and Apweiler R.
The Swiss-Prot protein sequence data bank and its
supplement TREMBL in 1998.
Nucleic Acids Res. 26:38-42(1998).