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 you are looking for,
Eric
__________________________
Eric Larson, PhD
Biomolecular Structure Center
Department of Biochemistry
Box 357742
University of Washington
Seattle, WA 98195
On Fri, 26 Nov 2010, 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 based sequence remain constant
| while extending the sequence only at the c-terminus. Remember the
| structure are known only for the two proteins.
|
| Any suggestion will be highly appreciated!!!!!
|
| Regards and have a nice weekend.
|
| Bashir
|
