Question: Should I use DNA or Protein sequence to build a HMM profile?
gravatar for liuyifan2014
4.7 years ago by
United States
liuyifan201470 wrote:

Hello my friends,

I want to build a HMM profile to search against a DNA fasta file. I use the hmmbuild to build the HMM and hmmsearch to search.

However, I am not sure should I use DNA sequence or protein sequence to construct the HMM ? Since the fasta files is composed of DNA sequence, I am afraid that the protein HMM profile do not work on it. If I construct a DNA HMM profile, there are also problems like the orientation of the protein-encoding genes and the degenerate codon.

Do you have any idea? Thank you for any help!

dna protein hmm gene genome • 2.7k views
ADD COMMENTlink modified 4.7 years ago by oli4morelle20 • written 4.7 years ago by liuyifan201470
gravatar for Devon Ryan
4.7 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:

If you want a model for proteins then build it using protein sequences. If you want to model some sort of ORF finding process that's dependent on the resulting protein sequence (enjoy dealing with splicing) then use the DNA sequence.

ADD COMMENTlink written 4.7 years ago by Devon Ryan98k
gravatar for oli4morelle
4.7 years ago by
oli4morelle20 wrote:

hmmer does not support searching DNA with a protein query. This is possible with Blast.

You could translate your fasta in all 6 reading frames. Than you can search with a protein HMM. Nevertheless if you get partial Hits I would check the corresponding DNA sequences for inserts, deletions and introns.

nhmmer is also an option. It is maybe less sensitive, but the orientation is not a problem. The subject sequences are searched in both directions. The advantage is that inserts and deletions have less effect on the hit length.

ADD COMMENTlink written 4.7 years ago by oli4morelle20
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