How can I retrieve the most recent release of uniprot protein sequences for any organism?

Sandeep Singh

Uniprot gets updated every 4 weeks

http://www.uniprot.org/downloads

to get notified about updations refer to

http://www.uniprot.org/faq/20

for the set of complete proteome of any organism refer to

http://www.uniprot.org/taxonomy/complete-proteomes

Julian Gough

You may also find the SUPERFAMILY database a useful source of proteome sequences. It is the most comprehensive collection of proteomes anywhere (nearly 2,500 organisms at the time of writing); it also includes all the UniProt proteomes. You can search for the genome in the search box here:

supfam.org

or find it on either of these two pages:

http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/taxonomic_gen_list.cgi

http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/gen_list.cgi

Then just click on your genome of choice and select the "FASTA format sequences" link under the "Downloads" heading near the top. For information on the source check the "Genome Information" tab near the top. UniProt genomes can be found here:

http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/gen_list.cgi?genome=up;subgenome=all

And there are other useful sets such as hundreds of meta-genomes, thousands of viruses, plasmids, and even pseudo-gene collections (would that be called a pseudo-genome?).

For updates on when new genomes are added please follow @SUPERFAMILY on twitter.

Can anyone suggest an alternative website for archiving theoretical protein structures other than PMDB?

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