Is there a way or a tool to compare two hmm DNA profiles?

Question

[abarcajose97]

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!

[LChart]

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?

Answer 1

[Mensur Dlakic]

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.

[abarcajose97]

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.