Re: [modeller_usage] using an external multiple sequence alignment
To:
Subject: Re: [modeller_usage] using an external multiple sequence alignment
From: Jonathan Sheehan <>
Date: Thu, 4 Sep 2014 14:09:30 -0500
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
<> 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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