Uniprot canonical and splicing variants FTP download

Question

[Bohdan Khomtchouk]

I'm looking for a quick ftp-based solution to downloading FASTA canonical and splicing variants data from Uniprot:

Go to uniprot.org, type in Homo sapiens, click Download, select the format "FASTA (canonical & isoform)", click Go.

Can I automate this process for all organisms in the Uniprot database using ftp in one nice command line utility?

Answer 1

[Elisabeth Gasteiger]

You can download precomputed reference proteomes by ftp. They include canonical and fasta sequences:

ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/reference_proteomes/

( see also http://www.uniprot.org/help/reference_proteome )

If this is not what you want, you can indeed automate the http download, as described in the UniProt help page for programmatic access, in particular Retrieving entries via queries

e.g. http://www.uniprot.org/uniprot/?query=organism:9606&format=fasta&include=yes&compress=yes

Please note that large http downloads are much more vulnerable and likely to fail than ftp downloads.

Please don't hesitate to contact the UniProt helpdesk if you have any additional questions.

[Bohdan Khomtchouk]

Btw, the second link is broken...

[Elisabeth Gasteiger]

Thanks, just fixed it (it was just a display problem, the closing parenthesis was being added to the URL).