[Biojava-l] unwanted gap in alignments

[Khalil El Mazouari]

Hi Andreas,

local alignment doesn't help:

GLOBAL:
EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEKGLEWIGRIDPASGNTKYDPKFQDKATITADTSSNTAYLQLSSLTSEDTAVYYCAGYDYGNFDYWGQGTTLTVSS
EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCA-------------------R

LOCAL:
EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEKGLEWIGRIDPASGNTKYDPKFQDKATITADTSSNTAYLQLSSLTSEDTAVYYCA
EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCA

The last R is gone. This not what I expect.

Regards,

Khalil







On 14 Jan 2011, at 16:45, Andreas Prlic wrote:

> looks a bit like an end-gap issue to me. I think the global alignment
> algorithm does not penalize end gaps. Try a local alignment (smith
> waterman) instead.
> 
> Andreas
> 
> 
> 
> On Fri, Jan 14, 2011 at 2:32 AM, Khalil El Mazouari
> <khalil.elmazouari at gmail.com> 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
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