Re: [modeller_usage] How to improve sequence alignment?!

[Modeller Caretaker <>]

On 11/13/13 8:28 AM, Amjad Farooq wrote:
> I am noticing that Modeller does not do a good job when it comes to
> sequence alignment of short peptides or DNA sequences.

You're not required to use Modeller to make modeling alignments - as 
long as you can make alignment files in the PIR format Modeller wants, 
you can use any package (including ClustalW).

That said, by default Modeller's alignment methods use global alignment 
and so try to align the termini, since this is typically what you want 
for modeling. You can adjust the overhang parameter to discourage this 
behavior, or use local alignment.

	Ben Webb, Modeller Caretaker
--
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