On 10/11/10 10:46 AM, Knut J Bjuland wrote: > I am writing a master thesis where I am describing how I aligned > protein sequence with template sequence. I use Modellers Saling's > align2d protocol. How should I described /gap_penalties_1d/ and > /gap_penalties_2d/ and what is the difference between them.

See the reference cited in the manual for this protocol, Madhusudhan et al, 2006 (PEDS 19, p129): http://salilab.org/modeller/9v8/manual/node469.html#MadSal05

Executive summary: 1D gap penalties are the regular affine gap opening and extension from regular dynamic programming; 2D gap penalties are the additional terms used to add structural information to the alignment process - e.g. to penalize gaps in regions of known secondary structure or in core regions.

Ben Webb, Modeller Caretaker