hmmsearch didn't work with nucleotide genome

Question

[lbroetto]

Hi, I'm trying to use hmmsearch to identify genes coding for a protein family. To achieve this I'm 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 I'm using:

hmmsearch --domtblout BbassianaXCutinase_domE1e-03_E1 -E 1 --domE 1 --max PF01083_uniprot_cutinase.hmm GCF_000280675.1_ASM28067v1_genomic.fna 

I'm 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 tried another genomes and HMMs also, all resulting no hits.

Thanks

[Jean-Karim Heriche]

If you don't get the same result as before using what you think is the same command and the same data then something is actually not the same. Look for what could possibly have changed, e.g. software version, name and format of data files, changes in your OS environment ...