There are options to download the whole dataset (https://www.uniprot.org/downloads). I want to download only the viral subset. Is there any way?
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written
by
traditionalGuy •
1 answer
GenoMax What do you think of this search in UniRef database: "uniref 90" taxonomy:"Viruses [10239]" https://www.uniprot.org/uniref/?query=%22uniref+90%22+taxonomy%3a%22Viruses+%5b10239%5d%22&columns=id%2creviewed%2cname%2ccount%2cmembers%2corganisms%2clength%2cidentity&offset=0&sort=score
The UniRef query returns the correct result. However the following one is the one supported by the UniProt API and therefore stable and robust:
taxonomy:"Viruses [10239]" AND identity:0.9
Please don't hesitate to contact the UniProt helpdesk in case of doubts.
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SwissProt viral entries (LINK) and Trembl viral entries (LINK)
You could see if you are able to parse entries from clusters based on the viral ID's but otherwise there does not seem to be a way to download pre-computed viral clusters. You can use the entries above and then create your own using
CD-HIT.