Re: [modeller_usage] Regarding manual protein sequence alignment
To:
Subject: Re: [modeller_usage] Regarding manual protein sequence alignment
From: Karsten Suhre <>
Date: Tue, 15 Mar 2005 12:51:03 +0100
Cc:
Organization: IGS
Dear Rajesh,
before attacking an alignment by hand, I would try some more sophisticated
alignment programs, i.e. those that can include structure information.
T-Coffee can do this for example. The best protocol would be to include your
target sequence together with the templates and a number of homologues of
your target sequence and to use the 3DCoffee structure-sequence alignment
option:
http://igs-server.cnrs-mrs.fr/Tcoffee/tcoffee_cgi/index.cgi
Alternatively, I like very much the Fugue threader :
It only requires input of a sequence, and identifies template and homologuous
sequences itself:
http://www-cryst.bioc.cam.ac.uk/~fugue/prfsearch.html
Note that T-Coffee includes the Fugue threadder in its alignment process.
I hope this helps,
Kind regards,
Karsten.
PS: should you REALLY want to align things by hand, try the seaview program
that comes with ClustalW.
On Tuesday 15 March 2005 10:00, rajesh rengaraj wrote:
> Hi friends.
>
> I need help from our groups regarding the Protein
> manual sequence alignment.I modelled a protein which
> shows low Ramachandran plot validatity in order to
> increase this i have to do the manual alignment.I dont
> know what are the procedure for this and how to do
> this, whether it is depends upon the physico-chemical
> properties of amino acids or any other else.
>
>
> So Kindly do the needful.
>
> Take care.
>
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