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
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
Disclaimer: I'm a co-author of one of meta-server methods. Karsten Suhre [karsten.suhre@igs.cnrs-mrs.fr] wrote: > > before attacking an alignment by hand, I would try some more sophisticated > alignment programs, i.e. those that can include structure information. This is true and tcoffee is highly recommended but please do not recommend a single threading-based methods on their own to newcomers. No single structure prediction method is able to match performance of combined approach which includes following steps: - target protein class discovery - prediction of primary (family membership) and secondary structure (including disordered regions) - structure prediction itself - approaching the consensus I highly appreciate Fugue method as such but what was outlined above should be kept in mind. Of course in a simple cases a 'naive' structural alignment, for example produced by tcoffe in a structural mode might be just in case. Cheers, -- Michal Kurowski <michal@genesilico.pl>
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 -- Open WebMail Project (http://openwebmail.org) ---------- 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 -------
Hi, I must add an errata: > (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...) > thats false, what I wanted to say is: You coud have a very bad stereochem (and that is measured in a baaaad ramachandran plot) an a good seq alignment.... Sorry for my mistake... L.
participants (4)
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Karsten Suhre -
Luis Rosales -
Michal Kurowski -
rajesh rengaraj