[Biojava-l] Global Alignmeent: Needle vs Biojava3

[Khalil El Mazouari]

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