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