[Biojava-l] Global alignment problem (bug?) in NeedlemanWunsch

[Chris Friedline]

Hello,

I am getting a weird problem with protein alignment using
NeedlemanWunsch in 1.7.1, in that the alignment does not span the
entire length of the proteins.  I've verified that this should not
happen with needle (from EMBOSS), neobio, BioJava3, and NW on NCBI.
I'm reluctant to switch to BioJava3 at this time, since performance is
about 2-3x slower than 1.7.1 for the alignments, and I'm doing about
350,000 of them.

An example of this alignment error, is shown here: http://pastebin.com/mdX516R6

Notice that the alignment stops 1 amino acid short of the end in both
cases.  The parameters for the alignment are: BLOSUM50, gapOpen=10,
gapExtend=2.

Thanks,
Chris

-- 
PhD Candidate, Integrative Life Sciences
Virginia Commonwealth University
Richmond, VA