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 <[log in to unmask]> 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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