SWISS-PROT & TREMBL
THE SWISS-PROT PROTEIN SEQUENCE DATA BANK
SWISS-PROT is an annotated protein sequence database established in
1986 and maintained collaboratively, since 1987, by the group of Amos
Bairoch first at the Department of Medical Biochemistry of the
University of Geneva and now at the Swiss Institute of Bioinformatics
(SIB) and the EMBL Data Library (now the EMBL Outstation - The European
Bioinformatics Institute (EBI)). The SWISS-PROT protein sequence data
bank consists of sequence entries. Sequence entries are composed of
different lines types, each with their own format. For standardization
purposes the format of SWISS-PROT follows as closely as possible that
of the EMBL Nucleotide Sequence Database.
Organizations
Swiss Institute of Bioinformatics
The EMBL Outstation - The European Bioinformatics Institute (EBI)
FTP addresses
ftp://ftp.expasy.ch/databases/swiss-prot
ftp://ftp.ebi.ac.uk/databases/swiss-prot
WWW server: http://www.expasy.ch/, http://www.ebi.ac.uk/
Electronic mail address:: swiss-prot@expasy.ch
TREMBL - 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. Since we do not want to dilute the quality standards of SWISS-PROT
by incorporating sequences into the database without proper sequence
analysis and annotation, we cannot speed up the incorporation of new
incoming data indefinitely. But as we also want to make the sequences
available as fast as possible, we have introduced with SWISS-PROT a
computer annotated supplement. This supplement consists of entries in
SWISS-PROT-like format derived from the translation of all coding
sequences (CDS) in the EMBL nucleotide sequence database, except those
already included in SWISS-PROT.
We name this supplement TrEMBL (Translation from EMBL). It can be
considered as a preliminary section of SWISS-PROT. This SWISS-PROT release
is supplemented by TrEMBL release 6. TrEMBL is split in two main sections;
SP-TrEMBL and REM-TrEMBL:
- SP-TrEMBL (SWISS-PROT TrEMBL) contains the entries (150'329 in release
6) which should be incorporated into SWISS-PROT. SWISS-PROT accession
numbers have been assigned for all SP-TrEMBL entries.
- REM-TrEMBL (REMaining TrEMBL) contains the entries (27'428 in release
6) that we do not want to include in SWISS-PROT for a variety of
reasons (synthetic sequences, pseudogenes, translations of uncorrect
open reading frames, fragments with less than eight amino acids,
patent-derived sequences, immunoglobulins and T-cell receptors, etc.)
TrEMBL is available by FTP from the EBI server (ftp.ebi.ac.uk) in the
directory '/pub/databases/trembl'. It can be queried on WWW by the EBI SRS
server (http://www.ebi.ac.uk/). It is also available on the SWISS-PROT CD-
ROM and is searchable on the FASTA, BIC and BLAST servers of the EBI.
If you want to cite SWISS-PROT 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 1998.
Nucleic Acids Res. 26:38-42(1998).
IMPORTANT ANNOUNCEMENT
It became obvious in the last years that the tremendous increase in data
flow has created a requirement for resources which cannot be addressed in
full by public funding. This is causing databases to fall behind the
research. We believe that the only solution to the resource shortfall is
to ask commercial users to participate by paying a license fee. No fee
will be charged to academic users, nor will any restriction be imposed on
their use or reuse of the data. both SWISS-PROT and PROSITE are concerned
by these changes while this is not the case of ENZYME.
A document fully describing what will be the impact of this change for
SWISS-PROT is available with the SWISS-PROT distribution files on FTP
(SP_98.TXT). You can also access the document as well as other relevant
ones from:
http://www.expasy.ch/announce/
http://www.ebi.ac.uk/news.html
If you do not have the time to read this document, the most important
take-home message is that these changes should not have any impact on the
way SWISS-PROT or PROSITE are accessed or redistributed. Academic users
will not be affected by these changes. Industrial end-users will also not
directly be affected as long as their employer pays the license fee. The
same holds true for bioinformatics companies. Academic software or
database developers as well as providers of database distribution services
will be only minimally affected by these changes. We hope to be able to
ensure their long-term financial survival. We sincerely hope and believe
that in the next two years the only change that will matter will be the
increase in scope and timeliness of the databases.
Finally, it should be noted that release 36 of SWISS-PROT and release 15
of PROSITE are not concerned by these changes. There are no restrictions
on their use and their distribution.