Is there a way to allow hmmsearch to search a .gbff file for protein hits? I'm trying HMMs that should have multiple hits in a particular genome, but the search keeps coming back with zero hits.
My guess would be that hmmsearch is searching just the genomic nucleotide sequence, whereas what I would want is for it to search all of the CDS feature sequences. Thoughts? I obtained the gbff from NCBI, and if I download the corresponding Protein FASTA, I'm able to find sequences. However, there's some information that I want from the gbff file that doesn't exist in the protein FASTA, so I'd rather not have to download both, if that makes sense?