Question: Methodological process for GO functional annotation of my positively selected candidate genes
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gravatar for ishengomae
5.2 years ago by
ishengomae100
Tanzania, United Republic Of
ishengomae100 wrote:

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?

blast gene • 3.0k views
ADD COMMENTlink modified 4.0 years ago by Biostar ♦♦ 20 • written 5.2 years ago by ishengomae100
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gravatar for chefer
5.1 years ago by
chefer280
Pretoria, ZA
chefer280 wrote:

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

ADD COMMENTlink written 5.1 years ago by chefer280

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.

ADD REPLYlink written 5.1 years ago by ishengomae100
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