[modeller_usage] Are gap in target and template same.

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