Subject: Re: [modeller_usage] Multiple Alignment Problem
From: Modeller Caretaker <>
Date: Thu, 30 Apr 2009 12:54:46 -0700
•·.·´¯`·.·• Iƒƒ¥ •·.·´¯`·.·• wrote:
> I have done alignment through salign as mentioned in advance tutorial
> but i think it dosent gives good alignment.File AIRE_mult.ali and
> align2d_mult are attached.
> Thats why I separately aligned template sequences with protien sequence
> using align2d.py one by one and then wrote the result in one file by
> myself i-e. Mannual_Alignment.ali.
> Is this the rite way ? or M doing wrong?
> Which way should I use ?
There is no one "right way" to make an alignment. In your case you have
huge regions of the sequence with no aligned template. Modeller is not
going to be able to build an accurate model. So you would be better off
only building models of the parts of the sequence for which you do have
Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage