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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: Stephen Graham stepheng {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-03-04 		Next message:
Subject: Re: phenix.refine and refmac
From: yang li robertcatrukie {- at -} GMAIL {- dot -} COM
Date: 2008-03-04


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
I can recommend MUSTANG: http://p2p.cs.mu.oz.au/mustang/
Web server version is http://p2p.cs.mu.oz.au/mustang/php/
paper is here:
http://www.ncbi.nlm.nih.gov/pubmed/16736488?ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum

Ashley

On 05/03/2008, at 6:13 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



Ashley Buckle Ph.D
NHMRC Senior Research Fellow
The Department of Biochemistry and Molecular Biology
School of Biomedical Sciences, Faculty of Medicine &
Victorian Bioinformatics Consortium (VBC)
Monash University, Clayton, Vic 3800
Australia

http://www.med.monash.edu.au/biochem/staff/abuckle.html
iChat/AIM: blindcaptaincat
skype: ashley.buckle
Tel: (613) 9902 0269 (office)
Tel: (613) 9905 1653 (lab)

Fax : (613) 9905 4699




CCP4bb navigation

CCP4bb <-- 2008 <-- March 2008 <-- 04 March 2008
Previous message:
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 		Next message:
Subject: Re: phenix.refine and refmac
From: yang li robertcatrukie {- at -} GMAIL {- dot -} COM
Date: 2008-03-04


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