[Biojava-l] Global Alignmeent: Needle vs Biojava3

[Andreas Prlic]

Hi Khalil,

I don't think you can set end gap penalties, currently.

Andreas

On Tue, May 3, 2011 at 8:56 AM, Khalil El Mazouari
<khalil.elmazouari at gmail.com> wrote:
> Hi
>
> is it possible to set an End gap penalty to false for Global alignment in biojava3.
>
> As you can see, the T in biojava3 GA is wrong.
>
> Needle gives correct result. In case of end gap penalty=true => same biojava3 result.
>
> Thanks
>
> khalil
>
>
>
> Biojava3
> query   MGWSWIFLFLLSGTAGVLSEVQLQQSGPELVKPGASVRMSCKSSGYIFDDFYMNWVRQSHGKSLDYIGYISPYSGVTGYNQKFKGKATLTVDKSSSTAYMELRSLTSEDSAVYYCAGSSGNKWAMDYWGHGASVTVSS
> target  -------------------QVQLQQPGAELVKPGASVKLSCKASGYTF-----------------------------------------------------------------------------------------T
>
>
>
> Needle (Emboss) : End gap penalty = false
> query              1 MGWSWIFLFLLSGTAGVLSEVQLQQSGPELVKPGASVRMSCKSSGYIFDD     50
>                                        :|||||.|.|||||||||::|||:|||.|.
> target             1 -------------------QVQLQQPGAELVKPGASVKLSCKASGYTFT-     30
>
> query             51 FYMNWVRQSHGKSLDYIGYISPYSGVTGYNQKFKGKATLTVDKSSSTAYM    100
>
> target            30 --------------------------------------------------     30
>
> query            101 ELRSLTSEDSAVYYCAGSSGNKWAMDYWGHGASVTVSS    138
>
> target            30 --------------------------------------     30
>
>
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