[Biojava-l] Protein CharacterTokenization

Hi, There is something strange with the protein alphabet CharacterTokenization. It knows how to parse the ambiguity symbol 'X', but it does not contain the other way around mapping of the protein alphabet ambiguity symbol to 'X'. Is that the way it should be or is that a bug? Can someone suggest a

[Biojava-l] Psi-Blast results

Hi, I need to get Psi-Blast results for a large dataset of proteins. Does anyone know if there are any free tools or classes to do that? Thanks, Tal ___ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l

[Biojava-l] How to use AlignmentRenderer?

Hi, I am trying to show an alignment. I saw there is the class AlignmentRenderer but I couldn't figure out how to use it. Does someone know? Thanks, Tal Blum ___ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/lis

[Biojava-l] Using pairwiseDP

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