Perform GO analysis on genome

Question

[a.rex]

I have a protein fasta file, for each longest ORF for an annotated locus in my genome.

Could anyone advise how best to perform a GO analysis on the this file, such that for each locus I have a GO id?

[jared.andrews07]

Need more details - what genome, do you only want it for a single/handful of genes, etc. Generally, GO analysis is as easy as throwing gene symbols/IDs at any number of programs. EnrichR, clusterProfiler, and TopGO are all R packages that come to mind, though there are many online tools as well (EnrichR also has a web server).

[a.rex]

Hello - apologies for that. It is a new genome for an obscure animal. I have annotated using mikado, and have produced a translated longest ORF file

Answer 1

[seidel]

I think you mean that you want to assign GO ids to the genes in your genome, as represented by the longest ORF at each locus. Correct? If so, it is common to use homology for the assignments. Find a genome that is closest to your organism - for which GO ids exist, then map your genes to that, and assign the GO ids. Or simply pick an organism - BLAST your genes against human and assign GOids using homologs.