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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