Re: needleman-wunsch score problems

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 <[email protected]> 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
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