On 02/23/2011 11:24 PM, Ashish Runthala wrote: > I want to generate iterative sequence alignment of Templates before > being integrated with the target sequence. How to use salign for > optimal iterative alignment only based on sequences, with no > consideration of overhang folds.

SALIGN's iterative alignment uses structural information. If you want to use only sequence information, you could certainly write your own Python loop to do it. But you'd have to figure out how to determine your alignment is 'optimal' so you can terminate the loop.

Ben Webb, Modeller Caretaker