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Re: [ccp4bb] multiple sequence alignment from multiple pairwise structural alignments
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
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Subject: Re: multiple sequence alignment from multiple pairwise structural alignments
From: Sophia Tsai sophiats {- at -} USC {- dot -} EDU
Date: 2008-03-04

Hi Stephen,

Fun question! A quick google search with "structure based sequence
alignment" gave me this site which looks promising:

http://www.cgl.ucsf.edu/home/meng/grpmt/structalign-content.html

Let me know how it turns out!
Sophia

On Tue, Mar 4, 2008 at 11:13 AM, Stephen Graham
wrote:

> Hi all,
>
> I would like to generate a structure-based multiple sequence alignment
> using 4 structures. I have already generated pairwise alignments for
> each 'pair' of structures (6 alignments in all). Is there a program
> out there that can take a number of aligned structures (or even just a
> number of pairwise sequence alignments) and calculate the 'best'
> multiple sequence alignment? Please note that there is absolutely no
> sequence conservation between these structures, making standard
> sequence-based alignment tools pretty useless.
>
> Thanks,
>
> Stephen
>
> --
> Dr Stephen Graham
> Nuffield Medical Fellow
> Division of Structural Biology
> Wellcome Trust Centre for Human Genetics
> Roosevelt Drive
> Oxford OX3 7BN
> United Kingdom
> Phone: +44 1865 287 549
>
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