How to perform GO enrichment for non-model species

Question

[Kumar]

Hi, I am trying to perform GO enrichment analysis for a non-model species. I tried BiNGO at Cytoscape but it did not work for me (please see my post here How to perform GO enrichment using BiNGO at Cytoscape).

I have prepared my input file in the following manner. It will be appreciated if anyone can recommend me any other software or pipeline for GO enrichment analysis.

Input file example:

**Gene name     GO terms**
SE_09257    GO:0008152
SE_09257    GO:0003824
SE_29669    GO:0050896
SE_13594    GO:0008152
SE_13576    GO:0009987

Answer 1

[shelkmike]

I had a good experience with goatools

[chasem]

I like gprofilr quite a bit -- the site is easy to use, and they have a great API for programmatic access. It is part of the EU "Elixr infrastructure" and is actively maintained and updated, too.

They also list quite a number of organisms for which they have some functional annotations -- maybe you'll get lucky and yours will be there: https://biit.cs.ut.ee/gprofiler/page/organism-list

[Kumar]

Thank you for your reply. It works.