How to download viral subset of the UniProt Reference Clusters?
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6 months ago

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?

swissprot database uniprot • 464 views
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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.

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That looks reasonable. I will go ahead and move your comment to an answer.

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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

https://www.uniprot.org/uniref/?query=taxonomy:%22Viruses%20(9VIRU)%20[10239]%22&fil=identity:0.9&sort=score

Please don't hesitate to contact the UniProt helpdesk in case of doubts.

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