Does hmmsearch look at the reverse complement of the fasta?

Question

[uwe.menzel]

Hi, does anybody know if hmmsearch of the HHMER software suite considers the reverse complement of the fasta file (nucleotide sequence)?

I created a profile HMM and made two searches: a) fasta file versus profile HMM b) reverse complement of this fasta file versus the same profile HMM

Both searches do not yield the same results.

I should conclude that I always have to search the reverse complement of a fasta file in a separate step.
I'm quite surprised by this, because I can't find any hint in the HMMer User Guide. Does anybody have similar experience? Thanks Uwe

[Lluís R.]

Why should hmmsearch look for something you didn't provide? It doesn't make sense. Maybe it is not explained in the User Guide but it certainly says it search for the HMM of the input sequence, and as you only introduce one sequence and not the inverse, it does precisely that

[uwe.menzel]

Hi Lluis, thanks for your answer. Maybe I was too much influenced by Blast, where you don't provide the revcomp either, but it is considered anyway.

Answer 1

[cryptogenomicon]

hmmsearch doesn't, but nhmmer (which is meant for DNA/DNA comparison) does. Pretty sure this is documented, too.

[uwe.menzel]

Thanks a lot, cryptogenomicon, perfect hint! I'll use nhmmer in the future.