How to obtain a local copy of the UniProt Knowledgebase (Swiss-Prot and TrEMBL)

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How to obtain a local copy of the UniProt Knowledgebase (Swiss-Prot and TrEMBL)

ftp servers

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

the ExPASy servers:
Australia: au.expasy.org
Bolivia: bo.expasy.org
Brazil: br.expasy.org
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 and TrEMBL, the UniProt Knowledgebase

With every biweekly update of UniProt, we provide an updated copy of the UniProt Knowledgebase for ftp download:

ExPASy: ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/
EBI: ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/.

The latest version of the two databases UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz) and UniProtKB/TrEMBL (uniprot_trembl.dat.gz) can be either downloaded and used separately, or the two data files can be concatenated to form a complete non-redundant protein sequence collection.

The files are also available in fasta and XML format, from the same directory.

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 file README.varsplic.

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 major 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 UniProtKB/Swiss-Prot database every two weeks, can use the latest major release and combine it with biweekly updated files containg all new and updated entries since the last major release.
UniProtKB/Swiss-Prot major release:
ftp://ftp.expasy.org/databases/uniprot/previous_major_releases/release5.0/knowledgebase
UniProtKB/Swiss-Prot updates:
ftp://ftp.expasy.org/databases/swiss-prot/updates_compressed

Old releases

Old (major) releases of Swiss-Prot can be downloaded from ftp://ftp.expasy.org/databases/swiss-prot/sw_old_releases/ (up to release 43.0)
and from ftp://ftp.expasy.org/databases/uniprot/previous_major_releases/ (starting with Swiss-Prot release 44.0/UniProt release 2.0). Old release notes are also archived.

DVD

UniProtKB/Swiss-Prot and UniProtKB/TrEMBL are also distributed on DVD by the EBI. The DVDs 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: .

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