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. > > ________________________________________________________________________ > Yahoo! India Matrimony: Find your life partner online > Go to: http://yahoo.shaadi.com/india-matrimony > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage

Hi all,

Mmmm...

Let me kow if I am wrong about this, but as far as I can say the problem with stereochemistry (Ramachandran plot) is not necessarily related to a bad sequence alignment...

(You could have a very bad stereochem [maybe as a result of a bad/poorly refined model] and a good rama plot. Modeller is more suceptible to give you the inverse scenario: a really good stereochem, without regard of the quality of your alignment...)

there are several tools more suited to evaluate your alignment and as a result, your coordinate asssignment (they evaluate the coordinates of your final model).

I think that Prosa2003 and profile3D are a couple of examples.

Hope this helps,

Luis

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---------- Original Message ----------- From: rajesh rengaraj rajesh_rengaraj@yahoo.co.in To: inbios groups inbios@yahoogroups.com, modeller modeller_usage@salilab.org, groups mtech biopearls@yahoogroups.com Sent: Tue, 15 Mar 2005 09:00:59 +0000 (GMT) Subject: [modeller_usage] Regarding manual protein sequence alignment

> 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. > > ________________________________________________________________________ > Yahoo! India Matrimony: Find your life partner online > Go to: http://yahoo.shaadi.com/india-matrimony > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage ------- End of Original Message -------