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

[Chris Friedline]

Hi Andreas,

The io should be the same, since I've used the same set of genes for testing
both.  So, I'm guessing it's either the alignment calculation or the new
biojava design contributing to the slowness.

Chris

On Tue, Oct 26, 2010 at 2:42 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

> 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
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>



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