TrEMBL release 19.0
Published December 1, 2001
TrEMBL Release Notes
Release 19, December 2001
EMBL Outstation
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Telephone: (+44 1223) 494 444
Fax: (+44 1223) 494 468
Electronic mail address: DATALIB@EBI.AC.UK
WWW server: http://www.ebi.ac.uk/
Swiss Institute of Bioinformatics (SIB)
Centre Medical Universitaire
1, rue Michel Servet
1211 Geneva 4
Switzerland
Telephone: (+41 22) 702 50 50
Fax: (+41 22) 702 58 58
Electronic mail address: Amos.Bairoch@isb-sib.ch
WWW server: http://www.expasy.org/
Acknowledgements
TrEMBL has been prepared by:
o Rolf Apweiler, Kirsty Bates, Margaret Biswas, Sergio Contrino,
Daniel Barrell, Kirill Degtyarenko, Wolfgang Fleischmann, Gill Fraser,
Henning Hermjakob, Kati Laiho, Alexander Kanapin, Youla Karavidopoulou,
Paul Kersey, Minna Lehvaslaiho, Michele Magrane, Maria Jesus Martin,
Virginie Mittard, Nicola Mulder, Claire O'Donovan, John F. O'Rourke,
Eleanor Whitfield and Allyson Williams at the EMBL Outstation -
European Bioinformatics Institute (EBI) in Hinxton, UK;
o Amos Bairoch, Alain Gateau, Isabelle Phan and Sandrine Pilbout at the
Swiss Institute of Bioinformatics in Geneva, Switzerland.
Copyright Notice
TrEMBL copyright (c) 2000 EMBL-EBI
This manual and the database it accompanies may be copied and
redistributed freely, without advance permission, provided
that this copyright statement is reproduced with each copy.
Citation
If you want to cite TrEMBL in a publication please use the
following reference:
Bairoch A., and Apweiler R.
The SWISS-PROT protein sequence data bank and its supplement
TrEMBL in 2000.
Nucl. Acids Res. 28:45-48(2000).
1. Introduction
TrEMBL is a computer-annotated protein sequence database supplementing the
SWISS-PROT Protein Knowledgebase. 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.
2. Why a supplement to SWISS-PROT?
The ongoing gene sequencing and mapping projects have dramatically
increased the number of protein sequences to be incorporated into SWISS-PROT.
We do not want to dilute the quality standards of SWISS-PROT by incorporating
sequences without proper sequence analysis and annotation, but we do want to
make the sequences available as fast as possible. TrEMBL achieves this second
goal, and is a major step in the process of speeding up subsequent
upgrading of annotation to the standard SWISS-PROT quality.
To address the problem of redundancy, the translations of all coding
sequences (CDS) in the EMBL Nucleotide Sequence Database already included
in SWISS-PROT have been removed from TrEMBL.
3. The Release
This TrEMBL release was created from the EMBL Nucleotide Sequence Database
release 68 and updates until 16.11.01 and contains 636'825 entries
and 184'332'036 amino acids. To minimize redundancy, the translations of all
coding sequences (CDS) in the EMBL Nucleotide Sequence Database already
included in SWISS-PROT release 40 and updates until 13.12.01 have been
removed from TrEMBL release 19
TrEMBL is split in two main sections: SP-TrEMBL and REM-TrEMBL:
SP-TrEMBL (SWISS-PROT TrEMBL) contains the entries (562'222) 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 (Archaea): 1692 entries
arp.dat (Complete Archaeal proteomes): 19590 entries
fun.dat (Fungi): 13339 entries
hum.dat (Human): 29064 entries
inv.dat (Invertebrates): 60611 entries
mam.dat (Other Mammals): 9724 entries
mhc.dat (MHC proteins): 7434 entries
org.dat (Organelles): 50792 entries
phg.dat (Bacteriophages): 4368 entries
pln.dat (Plants): 58841 entries
pro.dat (Prokaryotes): 69426 entries
prp.dat (Complete Prokaryote Proteomes): 74477 entries
rod.dat (Rodents): 24185 entries
unc.dat (Unclassified): 252 entries
vrl.dat (Viruses): 60309 entries
vrt.dat (Other Vertebrates): 11003 entries
vrv.dat (Retroviruses): 67115 entries
80'772 new entries have been integrated in SP-TrEMBL. The sequences of
1388 SP-TrEMBL entries have been updated and the annotation has been
updated in 321'110 entries.
In the document deleteac.txt, you will find a list of all accession numbers
which were previously present in TrEMBL, but which have now been deleted from
the database.
REM-TrEMBL (REMaining TrEMBL) contains the entries (74'603) that we do
not want to include in SWISS-PROT. REM-TrEMBL entries have no accession
numbers. This section is organized in six 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 specialized
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 specialized 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
acids.
5) CDS not coding for real proteins (Pseudo.dat)
This subsection consists of CDS translations where we have strong
evidence to believe that these CDS are not coding for real proteins.
6) Truncated proteins (Truncated.dat)
The last subsection consists of truncated proteins which result from
events like mutations introducing a stop codon leading to the truncation
of the protein product.
4. Format Differences Between SWISS-PROT and TrEMBL
The format and conventions used by TrEMBL follow as closely as possible
that of SWISS-PROT. Hence, it is not necessary to produce an additional
user manual and extensive release notes for TrEMBL. The information given
in the SWISS-PROT release notes and user manual are in general valid for
TrEMBL. The differences are mentioned below.
The general structure of an entry is identical in SWISS-PROT and TrEMBL.
The data class used in TrEMBL (in the ID line) is always 'PRELIMINARY',
whereas in SWISS-PROT it is always 'STANDARD'.
Differences in line types present in SWISS-PROT and TrEMBL:
The ID line (IDentification):
The entry name used in SP-TrEMBL is the same as the Accession Number of the
entry. The entry name used in REM-TrEMBL is the stable part of the protein_id
tagged to the corresponding CDS in the EMBL Nucleotide Sequence Database.
'protein_id' stands for the "Protein Identification" number. It is a number
that you will find in the feature table of the EMBL nucleotide sequence
entries in a qualifier called "/protein_id" which is tagged to every CDS.
Example:
FT CDS 339..1514
FT /codon_start=1
FT /db_xref="PID:g1256015"
FT /product="dystrobrevin-epsilon"
FT /protein_id="AAC50431.1"
The protein_id is defined as follows in the The DDBJ/EMBL/GenBank Feature Table
Definition documentation
Qualifier /protein_id
Definition Protein Identifier, issued by International collaborators.
This qualifier consists of a stable ID portion (3+5 format
with 3 position letters and 5 numbers) plus a version
number after the decimal point.
Value format <identifier>
Example /protein_id="AAA12345.1"
Comment When the protein sequence encoded by the CDS changes, only
the version number of the /protein_id value is incremented.
The stable part of the /protein_id remains unchanged and
as a result will permanently be associated with a given
protein. This qualifier is valid only on CDS features
which translate into a valid protein.
The DT line (DaTe)
The format of the DT lines that serve to indicate when an entry was
created and updated are identical to that defined in SWISS-PROT; but the
DT lines in TrEMBL refer to the TrEMBL release. The difference is
shown in the example below.
DT lines in a SWISS-PROT entry:
DT 01-JAN-1988 (Rel. 06, Created)
DT 01-JUL-1989 (Rel. 11, Last sequence update)
DT 01-AUG-1992 (Rel. 23, Last annotation update)
DT lines in a TrEMBL entry:
DT 01-NOV-1996 (TrEMBLrel. 01, Created)
DT 01-NOV-1996 (TrEMBLrel. 01, Last sequence update)
DT 01-FEB-1997 (TrEMBLrel. 02, Last annotation update)
5. 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 and in databases/sp_tr_nrdb
on the ExPASy server): sprot.dat.gz, trembl.dat.gz and trembl_new.dat.gz.
This set of non-redundant files is especially important for two types of
users:
(i) Managers of similarity search services. They can now provide what is
currently the most comprehensive and non-redundant data set of protein
sequences.
(ii) Anybody wanting to update their full copy of SWISS-PROT + TrEMBL to
their own schedule without having to wait for full releases of SWISS-PROT
or of TrEMBL.
We also recently introduced Varsplic Expand which is a program to generate
"expanded" sequences from SWISS-PROT records i.e. sequences including the
variants specified by the varsplic, variant and conflict annotations. New
records are produced in either pseudo-SWISS-PROT or FASTA format for each
specified variant. More information and the data is available at
ftp://ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/
6. 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 following servers at the EBI:
FASTA3 (http://www.ebi.ac.uk/fasta33/)
BLAST2 (http://www.ebi.ac.uk/blast2/)
Bic_sw (http://www.ebi.ac.uk/bic_sw/)
Scanps (http://www.ebi.ac.uk/scanps/)
MPSrch (http://www.ebi.ac.uk/MPsrch/)
7. Description of changes made to TrEMBL since release 18
7.1 Changes concerning cross-references (DR line)
We have added crossreferences from TrEMBL to a number of new databases.
7.1.1 MEROPS, the protease database, available at http://www.merops.co.uk
7.1.2 ANU-2DPAGE, the Australian National University Two-Dimensional
Polyacrylamide Gel Electrophoresis Database, available at
http://semele.anu.edu.au/2d/2d.html
7.1.3 PHCI-2DPAGE, the two-dimensional polyacrylamide gel electrophoresis
database at Universidad Complutense de Madrid, available at
http://babbage.csc.ucm.es/2d/2d.html
7.1.4 PMMA-2DPAGE, the Purkyne Military Medical Academy 2D-PAGE database,
available at http://www.pmma.pmfhk.cz/2d/2d.html
7.1.5 Siena-2DPAGE, the 2D-PAGE database from the Department of Molecular
Biology, University of Siena, Italy, available at
http://www.bio-mol.unisi.it/2d/2d.html
A list of all crossreferences in TrEMBL to other databases is provided below:
EMBL
PIR
PDB
HSSP
MEROPS
REBASE
TRANSFAC
Aarhus/Ghent-2DPAGE
ANU-2DPAGE
COMPLUYEAST-2DPAGE
PHCI-2DPAGE
PMMA-2DPAGE
Siena-2DPAGE
FlyBase
Leproma
MIM
MGD
MypuList
SGD
SubtiList
TIGR
TubercuList
WormPep
ZFIN
InterPro
Pfam
PRINTS
ProDom
SMART
PROSITE
7.2 New database divisions:
Three new database divisions were created as previously announced
to reflect the specialised attention we are giving to complete
proteomes and the HAMAP project. The new viral division is for
operational reasons:
7.2.1 New database division 'arp'
It will contain archaeal complete proteome entries.
7.2.2 New database division 'prp'
It will contain bacterial complete proteome entries.
7.2.3 New database division 'vrv'
It will contain retrovirus entries.
8. Planned changes
8.1 Evidence tags:
We are continuing with the introduction of evidence tags to SWISS-PROT and
TrEMBL entries. The aim of this is to allow users to see where data items
came from and to enable SWISS-PROT staff to automatically update data if
the underlying evidence changes. This is ongoing internally and we hope
to provide a public version early in 2002. For more information,
please see
ftp://ftp.ebi.ac.uk/pub/databases/trembl/evidenceDocumentation.html
We would welcome any feedback from the user community.
8.2 Conversion of TrEMBL to mixed case:
Most of the DE (DEscription), GN (Gene Name) and RC (Reference Comment)
lines is being converted to mixed case internally. The conversion is
ongoing and will be made public when ready.
8.3 Version of SWISS-PROT/TrEMBL in XML format:
A distribution version of SWISS-PROT and TrEMBL in XML format is
being developed. The specifications of this new format will be described
when it will be first implemented in TrEMBL.
8.4 Multiple RP lines:
In the workreleases from release 19 onwards, there can be more than one
RP (Reference Position) line per reference in a TrEMBL entry. For more
information on this development, please read SWISS-PROT Protein
Knowledgebase Release Notes 40 at http://www.expasy.org/sprot/relnotes