I've got a list of proteins of interest in FASTA format and am trying to assign major GO annotations to these candidates. Normally I would use BLAST2GO, but the software appears to be having issues. Are there any worthwhile alternatives?
Dear all - thanks for the comments, much appreciated. To answer your questions:
@Martin - these are all known proteins from a mouse iTRAQ experiment
@Bjoern - Keep getting issues with database connection during the mapping step. Have reinstalled and reconfigured which seemed to help, although I just came in to error messages. If your machine is running OK it would suggest our server is having issues. Will try from home/
@Sahil - Will bear DAVID in mind if I can't rectify the situation.
Cheers chaps
Joe
Hi Joseph, the thing is, you don't really need the sequence to assign GO terms, the name of the protein will be enough. Now if the proteins' identities are unknown is a little more complicated and then you need a sequence. Using the gene symbols is the best way in your case. As Sahil suggested, using the David tool will be a good solution http://david.abcc.ncifcrf.gov/
Hi Joseph,
If they are known proteins and you have either UniProt accessions or identifiers, you can use the UniProt-GOA DAS service to retrieve the GO annotations. For instance http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot-goa/features?segment=A4_MOUSE or http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot-goa/features?segment=Q4JIM5. You can also download all GO annotations in UniProt for mouse here http://www.ebi.ac.uk/GOA/mouse_release.html, I have not use that one but the other, DAS.
If you do not have a UP accession, but the gene id for instance, you can use UniProt mapping service to find out the UP accession (http://www.uniprot.org/, mapping tab)
You can try STRAP. It's a free tool, very easy to use, and all you need is a list with the GI of your proteins/genes.
Cheers all for the suggestions. Managed to get B2GO working over the weekend - I thought computers were meant to make life more simple??
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