We're currently working on a genome that doesn't have any GAF file for gene ontology with Ontologizer. In order to create the GAF file, for this genome, we need to generate GO annotation from either Interproscan or Blast2GO. We have a list of genes from NCBI (total of 2,000 genes) as below, I've been reading the manual of Blast2GO, but that looks like Chinese to me, How to use Blast2GO to generate GO annotation from a list of gene symbols??
5HTT A3F2 ABCC1 ACCN1 ACCN3 ACP5 ACTB ACTN3 ACVR2A ADAMTS4 ADIPOR2 ADORA2A
Also, I'm very open minded to hear if you have an alternative to gene ontology for genomes that don't have any GAF file yet.