[ssml] Structure based multiple sequence alignment

[Pankaj]

there is an option in clustalw program which allows the involvemnet of
structure into multiple sequnece alignment.
i have a downloaded version of clustalw, which allows profile/structure
alignment.
plzz try to use that.
hope it help

Pankaj Kamra
Research Scholar
National Institute of Immunology
New Delhi
India
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---------- Original Message -----------
From: sangeeta at bioinfo.ernet.in
To: rfsouza at cecm.usp.br
Sent: Tue, 17 May 2005 14:02:07 +0530 (IST)
Subject: Re: [ssml] Structure based multiple sequence alignment

> Hi Robson,
> *If* you have a large enough set of the 3D structures of the 
> proteins of your interest, you may try a structural alignment of 
> those which will give the corresponding sequence alignment also. You 
> may take a look at STRAP available at 
> http://www.charite.de/bioinf/strap/ OR CE at http://cl.sdsc.edu/ce.html
> 
> Hope this helps.
> Best wishes,
> Sangeeta Sawant
> Bioinformatics Centre
> University of Pune
> India
> 
> > Hi everybody,
> >
> > I'm trying to perform some analysis about residue variability on some
> > cell division proteins, looking for conserved sites which might be
> > involved
> > in protein-protein interactions. In order to do this, I'm using methods
> > like
> > evolutionary trace and the methods implemented on the Consurf server.
> >
> > My first round of analysis seems to indicate that such methods are very
> > sensible to differences in input multiple sequence alignments, since they
> > use the variation in an alignment column to identify highly conserved
> > residues. Therefore, hoping to improve the matching of homologous residues
> > to alignment columns, I'm looking for a tool that is able to build
> > multiple
> > protein sequence alignments using strutural information, which is
> > available
> > for some of my sequences in PDB.
> >
> > Do you know if there is any alignment program that multiply aligns
> > a set of homologous sequences while respecting the best "fit" of those
> > sequences to a 3D structure?
> >
> > Thanks for any help.
> > Best,
> > Robson
> >
> > _______________________________________________
> > ssml-general mailing list
> > ssml-general at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/ssml-general
> >
> 
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------- End of Original Message -------