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