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

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CCP4bb <-- 2008 <-- March 2008 <-- 05 March 2008
Previous message:
Subject: Re: finicky protein
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-03-05 		Next message:
Subject: BIOXHIT - Sulphur SAD Workshop - June, 18th-21st - REMINDER
From: Daniele de Sanctis de {- dot -} sanctisd {- at -} GMAIL {- dot -} COM
Date: 2008-03-05


Subject: Re: multiple sequence alignment from multiple pairwise structural alignments
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-03-05
Not so long ago someone posted this link in this bord:

http://www.charite.de/bioinf/strap/

It convinced me.

Maybe that should also be included in the CCP4wiki a collection of what
program do I use when I want to make X Y or Z

Juergen

Ashley Buckle wrote:

> 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
>
>
>


--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch

CCP4bb navigation

CCP4bb <-- 2008 <-- March 2008 <-- 05 March 2008
Previous message:
Subject: Re: finicky protein
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-03-05 		Next message:
Subject: BIOXHIT - Sulphur SAD Workshop - June, 18th-21st - REMINDER
From: Daniele de Sanctis de {- dot -} sanctisd {- at -} GMAIL {- dot -} COM
Date: 2008-03-05


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