4 Sep
2014
4 Sep
'14
12:09 p.m.
Ashika,
Just to expand on what Ben said, you can use any tool to generate the alignment. Converting it into PIR format can be done with a number of programs- I have used Jalview (see jalview.org) for example.
However, you will still need to do some editing of the .pir file for Modeller to read it. The first two lines of each sequence entry need to correspond to the description in the manual: https://salilab.org/modeller/manual/node494.html#alignmentformat
Hope that helps, -Jonathan
--
Jonathan Sheehan, Ph.D.
Computational Structural Biology
Vanderbilt Univ. Ctr. for Struct. Biol.
5137 MRB3, 465 21st Avenue S.
Nashville, TN 37232-8755
615-936-2516
On Thu, Sep 4, 2014 at 7:04 AM, ashika torikora
ashika.torikora@gmail.com wrote:
> Hi,
>
> I was wondering if one could use an external multiple sequence alignment
> (instead of align2d or equivalent functions) with modeller and how I could
> go about doing that. Thanks for any help you could provide.
>
> Ashika,
>
>
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