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UniProtKB/TrEMBL - Old Release NotesN.B. From release 27, the UniProtKB/TrEMBL release notes are included in the UniProt release notes.
TrEMBL Release Notes
EMBL Outstation
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Telephone: (+44 1223) 494 400
Fax: (+44 1223) 494 468
Electronic mail address: DATALIB@EBI.AC.UK
WWW server: http://www.ebi.ac.uk/
Amos Bairoch
Medical Biochemistry Department
Centre Medical Universitaire
1211 Geneva 4
Switzerland
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/
Acknowledgements
TREMBL has been prepared by:
o Rolf Apweiler, Alain Gateau, Vivien Junker, Stephanie Kappus, Fiona
Lang, Nicoletta Mitaritonna and Claire O'Donovan at the EMBL
Outstation - European Bioinformatics Institute (EBI) in Hinxton, UK;
o Amos Bairoch at the Medical Biochemistry Department of the University
of Geneva, Switzerland.
Notes
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.
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 new
supplement TREMBL.
Nucleic Acids Res. 24:21-25(1996).
1. Introduction
TREMBL is a computer-annotated 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.
2. Why a supplement to Swiss-Prot?
The ongoing genome 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.
We name this supplement TREMBL (TRanslation from EMBL), since the tools
used to create the translations of the CDS are based on the program
'trembl' written by Thure Etzold at the EMBL.
3. The Release
This TREMBL release is created from the EMBL Nucleotide Sequence Database
release 48 and contains 104'955 sequence entries, comprising 28'061'351
amino acids. TREMBL release 1 will be distributed with Swiss-Prot release 34.
TREMBL is split into two main sections; SP-TREMBL and REM-TREMBL:
SP-TREMBL (Swiss-Prot TREMBL) contains the entries (86'033) 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:
fun.dat (Fungi): 3367 entries
hum.dat (Human): 4322 entries
inv.dat (Invertebrates): 11920 entries
mam.dat (Other Mammals): 1761 entries
mhc.dat (MHC proteins): 2050 entries
org.dat (Organelles): 6285 entries
phg.dat (Bacteriophages): 866 entries
pln.dat (Plants): 5524 entries
pro.dat (Prokaryotes): 17222 entries
rod.dat (Rodents): 4573 entries
vrl.dat (Viruses): 26042 entries
vrt.dat (Other Vertebrates): 2101 entries
REM-TREMBL (REMaining TREMBL) contains the entries (19'255) that we do
not want to include in Swiss-Prot. This section is organised in five
subsections:
1) Immunoglobulins and T-cell receptors
Most REM-TREMBL entries will be 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
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
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 sequence contains either
erroneous data or concern artificially generated sequences outside the
scope of Swiss-Prot.
4) Small fragments
Another subsection consists of fragments with less than seven amino
acids.
5) CDS not coding for real proteins
The last subsection consists of CDS translations where we have strong
evidence to believe that these CDS are not coding for real proteins.
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 PID tagged to the
corresponding CDS in the EMBL Nucleotide Sequence Database. 'PID' stands for
the "Protein IDentification" number. It is a number that you will find in
EMBL nucleotide sequence entries in a qualifier called "/db_xref" which is
tagged to every CDS in the nucleotide database. Example:
FT CDS 54..1382
FT /note="ribulose-1,5-bisphosphate carboxylase/
FT oxygenase activase precursor"
FT /db_xref="PID:g1006835"
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 are referring 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-NOV-1996 (TREMBLREL. 01, LAST ANNOTATION UPDATE)
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