[Biojava-l] unwanted gap in alignments

[Khalil El Mazouari]

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