Produce Multiple Sequence Alignments using Profile HMMs
I have a few multiple sequence alignments and a few groups (let's say N) of unaligned sequences. I would like to learn the emission and transition probabilities from the multiple sequence alignments, to build with these distributions a profile HMM and then to produce with the Viterbi algorithm N multiple sequence alignments from the groups of unaligned sequences.
I have a known profile HMM structure, I have a Viterbi implementation but I am having trouble figuring out how to estimate emission distributions and transition distributions from the available multiple sequence alignments. Any ideas?
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bordieszter •
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