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 > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
