Quick navigation:        Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |   
Protein structure
 

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

Basic tutorials: 		 
 

CCP4bb navigation

CCP4bb <-- 2008 <-- March 2008 <-- 04 March 2008
Previous message:
Subject: Re: WM DELETE WINDOW
From: James Stroud jstroud {- at -} MBI {- dot -} UCLA {- dot -} EDU
Date: 2008-03-04 		Next message:
Subject: Re: phenix.refine and refmac
From: Savvas Savvides savvas {- dot -} savvides {- at -} UGENT {- dot -} BE
Date: 2008-03-04


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
>
ProteinCrystallography.org: Copyright 2006-2007 by Quid United Ltd