11 days ago by
The HMMER software (which is well documented) can be used to produce HMMs from alignments.
As for searching DNA with protein HMMs:
- nhmmer can be used to build nHMMs from nucleotide alignments. They can be used to query DNA.
- hmmer can be used to build HMMs from amino acid alignments. They can be used to query proteins.
The current HMMER manual (2015, version 3.1) states:
"Still missing: Translated comparisons. We’d of course love to have the HMM equivalents of BLASTX, TBLASTN, and
TBLASTX. They’ll come."
(Of course, you could always translate your genome in all frames , chop it up, and then screen it using protein HMMs. It is a bit ugly, you might run into some frameshift trouble, but maybe it works?)