Re: [modeller_usage] What is the difference in salign_multiple_struc among these 2 conditions

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 12/14/2011 01:01 AM, Ashish Runthala wrote:
> I am a bit confused about the utility of auto_overhang=true usage in
> salign_multiple_struc.py for MSA computation. Even if i don't use
> this line, result comes the same as _fit files are generated.

auto_overhang is designed to handle the case where the two sequences 
being aligned are of very different lengths, for example trying to align 
a single chain with a multi-chain protein. A regular global alignment 
will try to "stretch" the shorter sequence so that its termini will 
align with those of the longer sequence; auto_overhang reduces the 
global alignment penalty so that the termini need not align.

If your sequences are of similar length, auto_overhang will have no effect.

	Ben Webb, Modeller Caretaker
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