[modeller_usage] Are gap in target and template same.

[Ashish Runthala <>]

Dear Modellers,
I am facing an interesting problem. Are gaps in target and template same, as shown below. 

Target        AAAAA               AA--A             AA--A
Template      AA--A               AAAAA             AA--A
              CaseI               CaseII            CaseIII

Are these three cases I,II, & III modelled the same way. How will the gap penalties be incorporated in these three cases, when the modeller calculates the alignment score. 

PLEASE PROVIDE ME COMPLETE DETAILS ABOUT GAP PENALTIES IN THESE THREE CASES.

Thanks
Ashish



Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA