Question: Generating Go Ids
gravatar for Zev.Kronenberg
5.5 years ago by
United States
Zev.Kronenberg11k wrote:

Hi everyone,

I am a Gene Ontology newbie. I have a Maker annotated GFF3 file for a non-model organism. I want to experiment with term enrichment analyses for genes in regions of the genome under positive selection. I believe the first step is generating some GO IDs from the evidence I have (blastx, blastn, genome2protein, ect...)? I have looked at blast2go, but I don't want to use software that is not free / open source.

I would also really appreciate any advice on how to be conservative in these analyses. I am often skeptical of GO enrichment analyses, but don't know what the quality metrics are.

gff3 enrichment gene-ontology • 1.5k views
ADD COMMENTlink written 5.5 years ago by Zev.Kronenberg11k
gravatar for rama.gollapudi
5.5 years ago by
rama.gollapudi60 wrote:


You can use InterPro2GO mappings to generate GO annotations for your proteins/gene products (details are listed in the URL mentioned by DK above). You can also contact the GO annotation group at EBI if you need assistance with Interpro2GO mappings ( GO term finder at Princeton or the one available via AmiGO can be used for doing enrichment analysis.

Both these sites use the same algorithm described in PMID:15297299 Please feel free to write to if you have more questions.


ADD COMMENTlink written 5.5 years ago by rama.gollapudi60
gravatar for Damian Kao
5.5 years ago by
Damian Kao14k
Damian Kao14k wrote:

Your two main options are really blast2go or a HMM database. Check the mappings to go page at gene ontology:

It contains a list of index files that'll relate other database's terms to GO IDs.

ADD COMMENTlink written 5.5 years ago by Damian Kao14k
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