Question: hmmsearch didn't work with nucleotide genome
gravatar for lbroetto
12 days ago by
lbroetto0 wrote:

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.


ADD COMMENTlink modified 12 days ago by Alex Reynolds23k • written 12 days ago by lbroetto0

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 ...

ADD REPLYlink written 11 days ago by Jean-Karim Heriche14k
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