HMMSearch on 6-frame translated genome vs protein sequences yields different results
Hi Experts,
I have noticed that when I run hmmsearch of - say a PFAM hmm - on a whole genome that was translated into all 6 possible reading frames and then concatenated I don't get hits. However, when I call genes on the same genomes (e.g. with prodigal) and run hmmsearch on their protein sequences I do get hits.
I've used the same trusted cutoffs and all the same setting for the two runs.
It is puzzling to me why the 6-frame translated genome should not yield the same (or more) hits than searching the translated genes.
Do you have an idea why this could happen?
Thanks,
Loddi
I have noticed that when I run hmmsearch of - say a PFAM hmm - on a whole genome that was translated into all 6 possible reading frames and then concatenated I don't get hits. However, when I call genes on the same genomes (e.g. with prodigal) and run hmmsearch on their protein sequences I do get hits.
I've used the same trusted cutoffs and all the same setting for the two runs.
It is puzzling to me why the 6-frame translated genome should not yield the same (or more) hits than searching the translated genes.
Do you have an idea why this could happen?
Thanks,
Loddi