Question: Protein function retrieval
0
gravatar for susan.klein
5.7 years ago by
susan.klein50
Oceania
susan.klein50 wrote:

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

ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by susan.klein50
1
gravatar for Pavel Senin
5.7 years ago by
Pavel Senin1.9k
Los Alamos, NM
Pavel Senin1.9k wrote:

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.

ADD COMMENTlink written 5.7 years ago by Pavel Senin1.9k
1
gravatar for Elisabeth Gasteiger
5.7 years ago by
Geneva
Elisabeth Gasteiger1.7k wrote:

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, help@uniprot.org

ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by Elisabeth Gasteiger1.7k
0
gravatar for susan.klein
5.7 years ago by
susan.klein50
Oceania
susan.klein50 wrote:

Thanks, I think they will solve my problem.

 

Theo

ADD COMMENTlink written 5.7 years ago by susan.klein50
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