I have a software that translates DNA and searches the translation product for matches to profile HMMs. The idea is to search these DNA sequences for matches to HMMs in PfamA (version 30, which is the latest one)
However, for my purpose, there is a better curated set of proteins found as fasta sequences.
I was recently told that fasta sequences can ALSO be used as HMMER queries, they'll just be converted to HMM on the fly. That is fine.
What I seek help with is figuring out, if I have one set of queries as HMMs from PfamA and another set of queries as plain fasta sequences, is it possible to combine them into one *.hmm file in some way?