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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
Previous message:
Subject: Re: phenix.refine and refmac
From: Savvas Savvides savvas {- dot -} savvides {- at -} UGENT {- dot -} BE
Date: 2008-03-04 		Next message:
Subject: Re: phenix.refine and refmac
From: Partha Chakrabarti ppchak {- at -} GMAIL {- dot -} COM
Date: 2008-03-04


Subject: Re: multiple sequence alignment from multiple pairwise structural alignments
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-03-04
On Tuesday 04 March 2008 11:13, 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.

My preference is for the CE-MC server. There are several sites that
offer this, or you can install it locally. Here's one:
bioinformatics.albany.edu/~cemc

Another one is Tcoffee:
http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi

When I've done head-to-head comparisons, I have found the output from
CE-MC to be preferable. In particular, in cases where you have two
structures A and B that have the same length but have an area in which
the structures differ, CE-MC will favor the alignment
AAAAAAaaa...AAAA
BBBBBB...bbbBBBB
whereas Tcoffee will report
AAAAAAaaaAAAA
BBBBBBbbbBBBB

For my purposes, the first is correct, even if aaa and bbb are
sequence-homologous.


--
Ethan A Merritt Courier Deliveries: 1959 NE Pacific
Dept of Biochemistry
Health Sciences Building
University of Washington - Seattle WA 98195-7742

CCP4bb navigation

CCP4bb <-- 2008 <-- March 2008 <-- 04 March 2008
Previous message:
Subject: Re: phenix.refine and refmac
From: Savvas Savvides savvas {- dot -} savvides {- at -} UGENT {- dot -} BE
Date: 2008-03-04 		Next message:
Subject: Re: phenix.refine and refmac
From: Partha Chakrabarti ppchak {- at -} GMAIL {- dot -} COM
Date: 2008-03-04


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