Re: [modeller_usage] Automatically find gaps in the alignment

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