even if I use the global alignment for aligning this sequence against itself, it aligns 100% and I don;t see the strange gap. What are the two sequences you are aligning? Otherwise I can;t reproduce the behaviour that you describe.
Andreas On Wed, Jan 19, 2011 at 1:04 PM, Khalil El Mazouari <[email protected]> wrote: > Thank Andreas, > > these 2 seq (s1 and s2) are exactly the same. Indeed, it works for 100% > identical seq. > > I have used the same code as below except, I used .GLOBAL. I am not > interested in local alignment. > > Regards, > > Khalil > > > On 19 Jan 2011, at 16:07, Andreas Prlic wrote: > >> Hi Kalil, >> >> can you send your code snipplet that you are running? I just re-ran >> the cookbook example and it works for me. Also this behaves fine: >> >> ProteinSequence s1 = new >> ProteinSequence("QVQLQQPGSELVKPGASVKLSCKASGYTFTNYLIHWVRQRPGRGLEWIGRIDPNSGGTKYSEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCATYYFGRSFFDFWGQGTTLTVSSQVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCAR"); >> ProteinSequence s2 = new >> ProteinSequence("QVQLQQPGSELVKPGASVKLSCKASGYTFTNYLIHWVRQRPGRGLEWIGRIDPNSGGTKYSEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCATYYFGRSFFDFWGQGTTLTVSSQVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCAR"); >> >> SubstitutionMatrix<AminoAcidCompound> matrix = new >> SimpleSubstitutionMatrix<AminoAcidCompound>(); >> SequencePair<ProteinSequence, AminoAcidCompound> pair = >> Alignments.getPairwiseAlignment(s1, s2, >> PairwiseSequenceAlignerType.LOCAL, new >> SimpleGapPenalty(), matrix); >> System.out.printf("%n%s vs %s%n%s", >> pair.getQuery().getAccession(), >> pair.getTarget().getAccession(), pair); >> >> System.out.println("Identicals:" + pair.getNumIdenticals()); >> System.out.println("Similars:" + pair.getNumSimilars()); >> >> Andreas >> >> >> >> On Wed, Jan 19, 2011 at 2:39 AM, Khalil El Mazouari >> <[email protected]> wrote: >>> Hi all, >>> >>> while doing PSA or MSA with default gop and gep values I obtained the >>> following alignment! >>> >>> QVQLQQPGSELVKPGASVKLSCKASGYTFTNYLIHWVRQRPGRGLEWIGRIDPNSGGTKYSEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCATYYFGRSFFDFWGQGTTLTVSS >>> QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCA---------------------R >>> >>> Expected PSA should be at least >>> QVQLQQPGSELVKPGASVKLSCKASGYTFTNYLIHWVRQRPGRGLEWIGRIDPNSGGTKYSEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCATYYFGRSFFDFWGQGTTLTVSS >>> QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCA-----R---------------- >>> >>> this expected alignment was obtained with gop=1 and gep=100 >>> >>> I can't understand while the PSA algorithm with default values always adds >>> many gaps at the end of alignment to end up with a S:R while it is obvious >>> that with less gaps we could obtain better SequencePair with R:R? >>> >>> Finally, how to get a score for PSA, that reflects the number of identical, >>> similar residues and gaps? >>> >>> Many thanks. >>> >>> Khalil >>> >>> >>> >>> _______________________________________________ >>> 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
