Re: [modeller_usage] Question about gap_penalties_1d and gap_penalties_2d

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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