How to obtain a local copy of the Swiss-Prot and TrEMBL databases

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How to obtain a local copy of the Swiss-Prot and TrEMBL databases

ftp servers

Swiss-Prot and TrEMBL can be obtained by anonymous ftp from

the ExPASy servers:
China: cn.expasy.org
Canada: ca.expasy.org
Korea: kr.expasy.org
Switzerland: ftp.expasy.org
Taiwan: tw.expasy.org
USA: us.expasy.org
the EBI server: ftp.ebi.ac.uk/pub/.

Downloading Swiss-Prot, TrEMBL, TrEMBL_new (complete non-redundant database)

With every weekly update of Swiss-Prot and TrEMBL on the ExPASy and EBI web servers, we provide an updated copy of the complete non-redundant data sets for Swiss-Prot, TrEMBL and TrEMBLnew for ftp download:

ExPASy: ftp://ftp.expasy.org/databases/sp_tr_nrdb/
EBI: ftp://ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/.

The latest version of the three databases Swiss-Prot (sprot.dat.gz), TrEMBL (trembl.dat.gz) and TrEMBL_new (trembl_new.dat.gz) can be either downloaded and used separately, or the three data files can be concatenated to form a complete non-redundant protein sequence collection.

The files are also available in fasta format:

ExPASy: ftp://ftp.expasy.org/databases/sp_tr_nrdb/fasta/
EBI: ftp://ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/fasta/.

The data is further supplemented by two files containing the sequences of all additional splice isoforms annotated in Swiss-Prot and TrEMBL.

The data sets are documented in the files README and varsplic.txt.

Cumulative updates

The download approaches described in this paragraph have various disadvantages and are only listed for those users who cannot download large quantities of data by ftp. They require some amount of data processing, removing duplicates between original versions of an entry and updated versions of the same entry, and special treatment if entries have been merged and "unmerged" since the last full release. If at all possible, we recommend to download the fully updated database versions as described in the previous paragraph.

Users who do not wish to download the complete Swiss-Prot database every week, can use the latest full release and combine it with weekly updated files containg all new and updated entries since the last full release.
Swiss-Prot full release:
ExPASy: ftp://ftp.expasy.org/databases/swiss-prot/release_compressed
EBI: ftp://ftp.ebi.ac.uk/pub/databases/swissprot/release_compressed
Swiss-Prot updates:
ExPASy: ftp://ftp.expasy.org/databases/swiss-prot/updates_compressed
EBI: ftp://ftp.ebi.ac.uk/pub/databases/swissprot/updates_compressed
For TrEMBL, the latest full release can be combined with a file containing all the new entries since the last full release. Updated TrEMBL entries are not made available via this approach.
TrEMBL full release:
ExPASy: ftp://ftp.expasy.org/databases/trembl/release_compressed
EBI: ftp://ftp.ebi.ac.uk/pub/databases/trembl/sptrembl/
new TrEMBL entries:
ftp://ftp.ebi.ac.uk/pub/databases/trembl/new/cumulative.dat.gz.

CD-ROM

Swiss-Prot and TrEMBL are also distributed on CD-ROM by the EBI. The CD-ROMs also contain some database query and retrieval software for MS-DOS and Apple Macintosh computers.

For all enquiries contact:
The EMBL Outstation - The European Bioinformatics Institute,
Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, U.K.
Tel.: +44 1223 494 444;
Fax: +44 1223 494 468;
Email: datalib@ebi.ac.uk.