Hi Piyush,
On Fri, 11 Jun 2010 17:00:39 +0100 Piyush Diyora <>
wrote:
>
> > HI,
> > I performed multiple sequence alignment using salign. When I analysed the
> > result output (.pap output), there was some improper alignment at 400th
> > position. Because of that, entire alignment after that error was
> > improper. How can I improve the alignment and what is the reason for such
> > mistakes.
> >
> > I have attached the file containing sequence of the protein, salign code
> > and the pap output file.
If you look at the structures, you'll notice that there is one domain,
starting from about residue 400 and ending at about residue 710 that is
shifted in the different structures. The structures before and after that
domain align well. Perhaps you have to create your alignment through other
means?
Cheers,
Rob
--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Botterell Hall Rm 644
Department of Biochemistry, Queen's University,
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821 Fax: 613-533-2497
<> http://pldserver1.biochem.queensu.ca/~rlc