> I want to do the sequence alignment of these two proteins from all
> species in such a way that the structure based sequence remain constant
> while extending the sequence only at the c-terminus.
IIUC :
profile 1 = *structure-based* sequence alignment i.e. from STAMP (THESEUS?)
profile 2 = a hu
Hello Bashir,
If I understand your question correctly, Expresso and 3D-Coffee from the
T-coffee people will do just what you want. They align sequences while
utilizing any available structural information.
http://www.tcoffee.org/Projects_home_page/expresso_home_page.html
hope that is what yo
Hi Bashir,
You can use Pipealign
http://bips.u-strasbg.fr/PipeAlign/
it will do for you all the steps from the sequence search (one sequence
as a query) to the multiple alignement of the complete sequence. It
should be able to manage sequences of different length and the structure
based ali
Dear Fred;
Thanks for the reply! extending at the c-terminus means that this
protein only N-terminus structure has been solved and I want to include
the residues as well in the sequence alignment which are not in the
structure.
Regards;
Bashir
On Fri, November 26, 2010 13:38, Vellieux Fred
Muhammed bashir Khan wrote:
Dear All;
I have structures of two protein one full-length while the other truncated
at the c-terminus(one from prokaryote while the other from eukaryotes).
Now I want to do the sequence alignment of these two proteins from all
species in such a way that the structure
Dear All;
I have structures of two protein one full-length while the other truncated
at the c-terminus(one from prokaryote while the other from eukaryotes).
Now I want to do the sequence alignment of these two proteins from all
species in such a way that the structure based sequence remain constan
