[Biojava-l] Needleman-Wunsch implemented in Java

[Heather Trumbower]

Greetings:   I recently implemented Needleman-Wunsch for global alignment of 2 protein sequences in Java (1.3.1).   The part I found a bit tricky (and therefore possibly valuable to share) was deducing the alignment from the backtrace, but I think I've got it working -- at least it works right on all of my test data. :-)  I didn't build a GUI, just a command line interface.  I'm using BLOSUM50 for the scoring matrix.   I also made the easy modifications to calculate Smith Waterman (the scoring matrix and the backtrace directions), but I didn't build the sequence alignment for Smith Waterman (yet).   I'm wondering whether this is something already in Biojava, or if it might be interesting to put it out for discussion/review.  I'm not sure exactly how the Biojava working group actually works.    Thanks for any feedback,   Heather Trumbower [EMAIL PROTECTED]