[Biojava-l] Global Sequence Alignment

["Andreas Dräger"]

Hello,

I just implemented the Needleman-Wunsch-Algorithm and an object for handling
substitution matrices like BLOSSUM, PAM, GONNET and so on. It parses a
matrix file and provides a method to get the costs for changing Symbol A to
Symbol B. This is realized by two hashes and a private int[][] matrix.
If NeedlemanWunsch gets equal weights for gap opening and gap extension it
won't consider affine gap penalties, whereas otherwise it will, which needs
three times more memory. 
It would also be good to have a kind of interface to create multiple
different implementations of pairwise sequence alignment algorithms which
could be used easily then. I also attached an Interface for that purpose.
The NeedlemanWunsch already implements. The HMM algorithm from the cookbook
also implements this interface with only little effort of changes.

Andreas Dräger 


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