[Biojava-l] hmm profile comparison

Kirill Petrov KPetrov at ics.uci.edu
Sat Nov 1 20:12:40 EST 2003

> 	is there a way to compare 2 existing hmm profiles using biojava api?
> 	Or probably there is another type of profiling system that allows
> 	comparisons of the profiles rather than sequences?

On Sun, 2003-11-02 at 02:29, Schreiber, Mark wrote:
> If you want to see if two profiles have the same parameters you can
> get the Distributions from each state and use the 
> DistributionTools.areEmissionSpectraEqual() method to tell you if 
> they are the same. You should also test that the Distribution that
>  holds the transitions is equal.
As far as I understand that would let me know if two profiles are equal
or not. The problem, however, is identifying the distance between 2
profiles. Basically, I would want to use the HMM for separtion of a
group of sequences into 2 distinct groups. Is that possible?



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