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
On 03/31/2011 09:27 PM, Ashish Runthala wrote: > 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.
No. Case I is an insertion. The inserted region in the target (loop) will be modeled using just the CHARMM forcefield. Case II is a deletion - the template residues aligned with the deleted region won't be used. Case III is just a regular 1:1 alignment - since the gaps are in both target and template they are ignored.
> How will the gap penalties be incorporated in these three cases, when > the modeller calculates the alignment score.
Modeller does not use gap penalties in the modeling process, nor does it calculate an alignment score.
Ben Webb, Modeller Caretaker
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Ashish Runthala -
Modeller Caretaker