I need to create a GAF file for a non model organism. Currently I have a reference.fa and a gff3 with predicted genes. How can I map those to GO terms and create a GAF file according to these specifications:
Google only brought up Blast2Go, a non-free software suite, where I am not even completely sure whether it can do what I need. Do you know where I can get the corresponding GO terms for each predicted gene, so I can write script that joines these infos, as for example asked here or here? I think I am lost somewhere in the ontology world.