Methodological process for GO functional annotation of my positively selected candidate genes

Question

[ishengomae]

I did my homework first here and elsewhere but still find it difficult to fit pieces of information I get that would weave a standard methodological workflow enabling me analyze my candidate genes following positive selection scan to GO enrichment analysis.

So if I have positive selection candidates, about 150 genes say, from a non model species, and just want to get Gene Ontology information about these genes and then conduct a statistical approach for GO terms enriched aoout these genes, how do I proceed?

What I initially did was to download Swissprot database from NCBI, made a local blast database from its sequences and then performed blastX search with my candidate genes as Query. I had hoped to find a GO id and the terms associated from the fasta definition line of the resulting subject hits. But I don't see this approach getting me anywhere. What is the standard methodology?

Answer 1

[chefer]

Have to tried to use BLAST2GO? If you have the blast results in xml format, this might be useful.

[ishengomae]

Oh, thanks. Will try the tool. I also just found out the Ensembl BioMart tool can make direct conversion between Gene ids and GO ids.