Re: [modeller_usage] Automatically find gaps in the alignment

[Modeller Caretaker <>]

On 2/4/15 7:35 AM, Edelmiro Moman wrote:
> The question is: can Modeller identify and/or report those gaps
> (position and length) in order to help us to automatise the task?

Of course! See model.get_insertions()
http://salilab.org/modeller/9.14/manual/node174.html

Given an alignment object, you can also step through its 'positions' member:
http://salilab.org/modeller/9.14/manual/node290.html

Insertions relative to a given sequence are simply those where 
aln.positions[x].get_residue(seq) returns None (i.e. sequence seq has a 
gap at position x).

	Ben Webb, Modeller Caretaker
--
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