Re: [modeller_usage] Regarding manual protein sequence alignment

[Karsten Suhre <>]

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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