I am trying to compare two hmm profiles of DNA sequences, the idea is that the comparison will give me a “similarity” type result between the two profiles. I tried with hhblits, using hhalign but blits considers two things: 1) the creation of own profiles and 2) that it takes into consideration the aa alphabet and not ACTG.
thanks in advance!
To the best of my knowledge, there is no program that will do this from HMMs. However, tomtom from the MEME suite will compare DNA profiles in a different format and output p- and e-values indicating how likely they are to be related. There are many other tools in that suite that are useful for manipulating DNA profiles, sequence logos, etc.
I see... I already did that and the problem is that the metric provided by tomtom is related to the statistical analysis. i am rather looking for a percentage that indicates how similar both profiles are. Anyway, thanks for your comment! I will look for a way to solve this problem.
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By "hmm profile" do you mean the sequence of emission probabilities (i.e., a PWM), or do you mean a sequence of state probabilities, or do you mean the state transition matrix? Is the number of states the same or different between the HMMs?