Batch download UniProt proteomes with list of proteome IDs

Question

[JMac]

Is there any way to batch download UniProt proteomes based on a list of proteome IDs (e.g. UP000011712).

I have a list of about 1,000 proteome IDs from UniProt. I know it is possible to do this with taxon IDs but I do not have these.

So, is it possible to batch download proteomes based on proteome IDs, or is there any way to convert proteome ID to taxon identifier?

Thanks for any help.

Answer 1

[Elisabeth Gasteiger]

You can do this programmatically using URLs like https://www.uniprot.org/uniprot/?query=proteome:UP000005640&format=fasta (FASTA format)

Use format=txt, format=xml etc for other download formats.

There is a related FAQ for programmatic access with a code example to download the UniProt reference proteomes for all organisms below a given taxonomy node in compressed FASTA format: https://www.uniprot.org/help/api_downloading

[JMac]

Thanks, this is exactly what I was looking for. I rewrote the example code to accept proteome IDs instead of taxa IDs.

[priyajk24]

But only the index html file is getting downloaded instead of the fasta file. How can i retrieve the fasta of th ereference proteome ID ??

[Elisabeth Gasteiger]

This RESTful URL should work: https://www.uniprot.org/uniprot/?query=proteome:UP000005640&format=fasta Please contact the UniProt helpdesk if the problem persists. If you include your code, we can look into your problem in detail.

Answer 2

[Jean-Karim Heriche]

The README file for reference proteomes has UniProt ID mapping to taxon ID. You can also download files by taxonomic division. Locate the file(s) containing the species you're interested in and filter them based on species.