[Biojava-l] needleman-wunsch score problems

[Andreas Prlic]

Hi Eric,

Did you compare the alignments, i.e which pairs of amino acids are
getting aligned? There might be subtle differences..

Andreas


On Thu, Apr 14, 2011 at 7:41 PM, Erik C <erikclarke at gmail.com> wrote:
> Hi all,
> I'm having some trouble reconciling the scores from the NeedlemanWunsch
> sequence alignment object in BioJava with the scores I'm getting from the
> EMBL-EBI command-line tool 'needle'. Specifically, for the same sequences,
> matrix, and penalties, BioJava returns 274 (in one case), while `needle'
> returns 163.
> Does anybody have any ideas as to why this might be happening? Is there a
> parameter or setting I'm missing? My implementation of the n.w. code in
> biojava is below:
>
>    public long alignTwoSequences(ProteinSequence subject,
>            ProteinSequence target) {
>
>        SubstitutionMatrix<AminoAcidCompound> blosum62 =
> SubstitutionMatrixHelper.getBlosum62();
>        GapPenalty penalties = new SimpleGapPenalty();
>        penalties.setExtensionPenalty((short) .5);
>        penalties.setOpenPenalty((short) 10);
>        NeedlemanWunsch<ProteinSequence, AminoAcidCompound> nw = new
> NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(subject, target,
> penalties, blosum62);
>        return nw.getScore();
>
>    }
>
> Thanks,
> Erik
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>