On May 18, 2019, at 10:10 PM, Carson Hinton Holt <[hidden email]> wrote:
I’ve CC’d my reply to the devel list as well. MAKER can annotate gene positions on prokaryotes although it’s best suited for eukaryotic genomes. It does only support canonical codon usage though (so would not be usful if the prakaryote you are
interested has any other codon table). You need to train a predictor like genemark first, although the protein2genome prediction option works relatively well in prokaryotes.
Output is in fasta and GFF3 format. If you need GeneBank format (what you have below) you will need to convert. There are tools out there like GAG that can help convert MAKER output for GenBank submission.