Hi Shahab, Sounds like you want to use an identity matrix for the alignment..
Andreas On Sat, Sep 17, 2011 at 3:28 PM, Shahab Kamali <[email protected]> wrote: > Thanks Andreas, > I want two components that have different names to have 0 alignment score. > My application is not about bio-compounds,so I can use anything else rather > than ProteinSequence and AminoAcidCompound. I just need to align sequences > of arbitrary alphabets. Could you suggest me a solution please? > Thanks a lot, > Shahab > > Quoting Andreas Prlic <[email protected]>: > >> 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 <[email protected]> >> 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 >>> >>> >>> >>> _______________________________________________ >>> biojava-dev mailing list >>> [email protected] >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>> >> > > > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
