We’ve had a few helpdesk tickets in the last few months asking how to download all of the Pfam-A domains for a particular species. This information can be quite difficult to obtain: getting it requires either downloading and installing a sub-set of the tables in our MySQL database, or else searching all of the sequences from the species of interest against Pfam, probably using our batch search.
We thought it would be useful to simplify the process and add the domain information directly to our proteome pages, so we’ve just done exactly that.
If you go to the proteome page for a particular species, for example Plasmodium falciparum, and click on the ‘Domain Composition‘ tab, you’ll now find a link above the table that will let you download a text file with the list of all regions for that proteome. We’ve only added these links in the Pfam website at Sanger so far but they’ll appear in the other Pfam sites soon. The data files are all available directly from our FTP site too, indexed by NCBI taxonomy ID.
We hope you’ll find this feature useful.
Posted by Jaina and John.