Batch convert gene numbers (ordered locus names) to protein IDs

Question

[Qroid]

I asked the same question on stack exchange.

I have a list of >1000 "ordered locus names" from the STRING database (also called gene numbers, ORF numbers, or CDS numbers by uniprot). They're in the form of 'b0014', 'b0015', etc. I'd like to convert them all to protein IDs.

I know how to do it in a non-batch way, since searching Uniprot for 'b0014' returns what (I think) is a protein ID. However I'd like an automated solution, since I might need to repeat this in the future and manually searching even 1000 would take forever.

[Ram]

Please do not cross-post.

Answer 1

[GenoMax]

Uniprot ID converter tool is generally the best way of mapping names in bulk. Are the b* numbers STRING ID's? If I select STRING as the source they are not mapping to Uniprot.

[Qroid]

Thanks, Uniprot ID converter looks good. As far as I know, 'b0014' etc. are 'ordered locus names', ‘ORF numbers’, ‘CDS numbers’ or ‘Gene numbers’ (http://www.uniprot.org/help/gene_name ). If I choose "gene name" in the first drop down everything appears to work! So thank you!

[GenoMax]

Indeed. Glad that worked for you.