please try with the following sequences >seq1 QVQLQQPGSELVKPGASVKLSCKASGYTFTNYLIHWVRQRPGRGLEWIGRIDPNSGGTKYSEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCATYYFGRSFFDFWGQGTTLTVSS >seq2 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCAR
thanks, khalil On 19 Jan 2011, at 22:35, Andreas Prlic wrote: > 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
