[Biojava-l] Using pairwiseDP

Tal Blum blum+ at cs.cmu.edu
Wed Feb 2 12:59:26 EST 2005


I am trying to use BioJava for doing alignment between two sequences. I 
tried to use the pairwiseDP class, but it is not clear to me how to 
construct a MarkovModel for it. The problem, I think, is specifying the 
emission distributions for pair symbols with gaps. How can you create a 
pairDistribution with with a gap as an element of the distribution for 
use in the pairwiseDP? If anyone can refer me to example that uses 
pairwiseDP I would be grateful.
Another question I have is why is there no BaumWelch algorithm for 
MarkovModels with two heads?

Many thanks,
Tal Blum

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