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 <[email protected]> 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 > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
