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Re: [ccp4bb] multiple sequence alignment from multiple pairwise structural alignments
 

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CCP4bb <-- 2008 <-- March 2008 <-- 04 March 2008
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Subject: Re: multiple sequence alignment from multiple pairwise structural alignments
From: Joao Dias jmdias {- at -} SCRIPPS {- dot -} EDU
Date: 2008-03-04 		Next message:
Subject: Re: multiple sequence alignment from multiple pairwise structural alignments
From: Ashley Buckle ashley {- dot -} buckle {- at -} MED {- dot -} MONASH {- dot -} EDU {- dot -} AU
Date: 2008-03-04


Subject: Re: multiple sequence alignment from multiple pairwise structural alignments
From: Stephen Graham stepheng {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-03-04
Dear all,

Thanks very much to everyone who replied. A tip-off from Petr Leiman
led me towards UCSF Chimera, which was able to generate a multiple
alignment file from my 4 superposed PDB files. Protocol for the
interested:
Open up Chimera and from the menu select "Tools" -> "Structure
Comparison" -> "Match->Align"

Much easier than hand-editing the alignment!

Thanks again,

Stephen

On 3/4/08, 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
>


--
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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