Protein function retrieval

Question

[susan.klein]

Hi,

if I have a list of protein IDs, or GIs from for example a blast output, what do you all think is the best way top retrieve their full hierarchical function (obviously only for the known proteins in the data, I don't need to do prediction stuff). I've tried the stand-alone mgrast way (md5-tools.pl) but it only gives the simple description (same as the fasta file).

Thanks.

Theo

[susan.klein]

Thanks, I think they will solve my problem.

Theo

Answer 1

[Pavel Senin]

You can use KEGG. Here is the page where at the very bottom you can put a GI or other databases ids to get the functional annotation; there is an API to do that automatically too.

Answer 2

[Elisabeth Gasteiger]

You can use the ID mapping service on the UniProt web site http://www.uniprot.org to map your gi numbers to UniProtKB accessions and then look at the entries and/or download them.

You could also have a look at the new beta site, http://beta.uniprot.org/, where the ID mapping service can be found under "Upload lists".

Details regarding the REST API can be found here: http://www.uniprot.org/faq/28

If you have questions regarding these services, please contact the UniProt helpdesk, [e-mail]