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!