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.
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 (http://www.ebi.ac.uk/GOA/). GO term finder at Princeton or the one available via AmiGO can be used for doing enrichment analysis. http://amigo.geneontology.org/cgi-bin/amigo/term_enrichment?session_id= http://go.princeton.edu/cgi-bin/GOTermFinder/GOTermFinder
Both these sites use the same algorithm described in PMID:15297299 Please feel free to write to email@example.com if you have more questions.
Your two main options are really blast2go or a HMM database. Check the mappings to go page at gene ontology: http://www.geneontology.org/GO.indices.shtml.
It contains a list of index files that'll relate other database's terms to GO IDs.