> 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.
Hi Piyush,
On Fri, 11 Jun 2010 17:00:39 +0100 Piyush Diyora yellow_piyu46@yahoo.co.in 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
On 6/11/10 6:00 PM, Piyush Diyora wrote: >> I performed multiple sequence alignment using salign. When I >> analysed the result output (.pap output), there was some improper >> alignment at 400th position.
If you think you know what the alignment should look like at the 400th position, you can offset the dynamic programming matrix to force it. See http://salilab.org/modeller/9v8/manual/node294.html#SECTION00111525600000000... for an example.
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Piyush Diyora -
Robert Campbell