Retrieve all proteomes from UniProt by taxid
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Entering edit mode
10 months ago

Greetings!

I am trying to obtain reference proteomes of UniProt from taxids or taxon names. So far have tried with BioPython and biomart(r), but the former only allows this for Entrez, and the latter only searches for species (using the standard "getProteome", or kingdoms or phyla (with "meta.retrieval"). I want to be able to get for whole genus and/or other taxa level.

Is there any tool or methodology for querying UniProt and obtaining this information?

taxid uniprot • 447 views
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2
Entering edit mode
10 months ago

You may want to have a look at this UniProt help page https://www.uniprot.org/help/api_downloading

Reference proteomes are also available for download from our FTP server, at https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/

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

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Entering edit mode
10 months ago

Well, just realized it's as simple as requests.get('https://www.uniprot.org/uniprot/?query=taxonomy:taxid&format=fasta')

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