Question: Does hmmsearch look at the reverse complement of the fasta?
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gravatar for uwe.menzel
2.3 years ago by
uwe.menzel0
uwe.menzel0 wrote:

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

genome • 863 views
ADD COMMENTlink modified 2.3 years ago by cryptogenomicon150 • written 2.3 years ago by uwe.menzel0

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

ADD REPLYlink written 2.3 years ago by LluĂ­s R.840

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.

ADD REPLYlink written 2.3 years ago by uwe.menzel0
0
gravatar for cryptogenomicon
2.3 years ago by
United States
cryptogenomicon150 wrote:

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

ADD COMMENTlink written 2.3 years ago by cryptogenomicon150

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

ADD REPLYlink written 2.3 years ago by uwe.menzel0
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