Hi, Im trying to use hmmsearch to identify genes coding for a protein family. To achieve this Im using a hidden Markov model made from an Pfam alignment against a genome (a nucleotide not a predicte proteome). But It is returning no hits.
This is the command Im using:
hmmsearch --domtblout BbassianaXCutinase_domE1e-03_E1 -E 1 --domE 1 --max PF01083_uniprot_cutinase.hmm GCF_000280675.1_ASM28067v1_genomic.fna
Im using this genome and this HMM as a positive reference. I have made this analysis using the same HMM against the same predicted genome and it returned a lot of hits, so there is something going wrong.
And I have tryied another genomes and HMMs also, all resulting no hits.