Khalil You can change the GAP penalty and see what happens. I think there is also a way to specify a pre-alignment of sequence positions but haven't used it.
Thanks Scooter On Fri, Jan 14, 2011 at 5:32 AM, Khalil El Mazouari < [email protected]> wrote: > Hi All, > > I am testing the PSA and MSA examples from Cookbook3. > > Sometimes, gaps were introduced in "unwanted" places in the alignments. Ex. > below: > > > EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEKGLEWIGRIDPASGNTKYDPKFQDKATITADTSSNTAYLQLSSLTSEDTAVYYCAGYDYGNFDYWGQGTTLTVSS > > EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCA-------------------R > > expected PSA was: > > EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEKGLEWIGRIDPASGNTKYDPKFQDKATITADTSSNTAYLQLSSLTSEDTAVYYCAGYDYGNFDYWGQGTTLTVSS > > EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCAR------------------- > > > the same for MSA > > DVQLVESGGGLVKPGGSLRLSCAASGFTFSTAWMKWVRQAPGKGLEWVVWRVEQVVEKAFANSVNGRFTISRNDSKNTLYLQMISVTPZBTAVYYCARVVVSTSMDVWGQGTPVT > > EVQLVESGGGLVQPGGSLKLSCAASGFTFS-----WVRQASGKGLEWV-----------------GRFTISRDDSKNTAYLQMNSLKTEDTAVYYCTR----------------- > > EVQLVESGGGLVQPGGSLRLSCAASGFTFS-----WVRQAPGKGLEWV-----------------GRFTISRDDSKNSLYLQMNSLKTEDTAVYYCAR----------------- > > QVQLVESGGGVVQPGRSLRLSCAASGFTFS-----WVRQAPGKGLEWVA-----------------RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAR----------------- > > QVQLVESGGGVVQPGRSLRLSCAASGFTFS-----WVRQAPGKGLEWVA-----------------RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAR----------------- > > expected MSA > > DVQLVESGGGLVKPGGSLRLSCAASGFTFSTAWMKWVRQAPGKGLEWVVWRVEQVVEKAFANSVNGRFTISRNDSKNTLYLQMISVTPZBTAVYYCARVVVSTSMDVWGQGTPVT > > EVQLVESGGGLVQPGGSLKLSCAASGFTFS-----WVRQASGKGLEWVG-----------------RFTISRDDSKNTAYLQMNSLKTEDTAVYYCTR----------------- > > EVQLVESGGGLVQPGGSLRLSCAASGFTFS-----WVRQAPGKGLEWVG-----------------RFTISRDDSKNSLYLQMNSLKTEDTAVYYCAR----------------- > > QVQLVESGGGVVQPGRSLRLSCAASGFTFS-----WVRQAPGKGLEWVA-----------------RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAR----------------- > > QVQLVESGGGVVQPGRSLRLSCAASGFTFS-----WVRQAPGKGLEWVA-----------------RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAR----------------- > > > I have tested different gop/gep and LOCAL/GLOBAL PSA . No success! > > How can I force or avoid the gap creation at specific positions? > > 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
