[Biojava-dev] A question about multiple alignment

[Andreas Prlic]

Hi Shahab,

did you take a look at the substitution matrix, if it is scoring your
sequences according to your expectation? Looks like in your
theoretical example the alignment of B and D is favorable, i.e. it has
a positive alignment score..

Andreas


On Fri, Sep 16, 2011 at 10:56 AM, Shahab Kamali <skamali at cs.uwaterloo.ca> wrote:
> Hi,
> I am using BioJava in a pattern mining project. I want to align a set of
> relatively short sequences. For example to align {"ABCE", "ABCE", "ADE",
> "ADE").
>
> This is a part of my code:
>
> SubstitutionMatrix<AminoAcidCompound> matrix = new
>                    SimpleSubstitutionMatrix<AminoAcidCompound>();
> GuideTree<ProteinSequence, AminoAcidCompound> gt = new
> GuideTree<ProteinSequence,
> AminoAcidCompound>(lst,Alignments.getAllPairsScorers(lst,
>                   Alignments.PairwiseSequenceScorerType.GLOBAL,  new
>                   SimpleGapPenalty((short)0,(short)0), matrix));
>            Profile<ProteinSequence, AminoAcidCompound> profile =
> Alignments.getProgressiveAlignment(gt,Alignments.ProfileProfileAlignerType.GLOBAL,
> new SimpleGapPenalty((short)0,(short)0),matrix);
>
> The result of the above code is:
> ABCE
> ABCE
> AD-E
> AD-E
>
> But what I need is
> A-BCE
> A-BCE
> AD--E
> AD--E
> or
> ABC-E
> ABC-E
> A--DE
> A--DE
>
> Do you have any suggestion?
> Thanks,
> Shahab
>
>
>
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