On 02/03/2010 06:43 PM, Thomas Evangelidis wrote: > Actually I used compare.py as a means to narrow down the list with the 8 > potential templates, not to generate an alignment for comparative > modelling.
That's what I figured - compare.py won't give you a useful modeling alignment. But there is no requirement to compare your templates with compare.py either.
> Certainly my option 3 (letting Modeller align the sequences) is not a > good idea as T-COFFEE's method is more sophisticated and incorporates > structural information. So I'm between 1. and 2.
Right - align() is the simplest alignment method, so will not be competitive with anything other than simple sequence-sequence alignment methods. So feel free to use T-COFFEE or one of Modeller's more powerful alignment methods, such as SALIGN.
> 1. edit my T-COFFEE-generated consensus alignment by leaving only the 4 > sequences I need, and create an alignment for Modeller > 2. generate a new structure-based alignment with T-COFFE with only the > selected 4 sequences and feed it to Modeller
Why not build both and see? (1) sounds better to me, but it's impossible to be sure.
Ben Webb, Modeller Caretaker