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

[Andreas Prlic]

Hi Chris,

about your comment that the biojava3-alignment is slower than the 1.7
one: Do you have any data if this is coming from the io or is the
actual alignment calculation slower?

Andreas

On Sun, Oct 24, 2010 at 7:57 AM, Chris Friedline <cfriedline at vcu.edu> wrote:
> 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
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-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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