We did something like this with esprit.
You get the sequence alignments from Psiblast or whatever you fancy,
then edit in the structural alignment into the txt file it generates.
Messy but successful..
Eleanor
On 12/01/2010 03:44 PM, Gerard DVD Kleywegt wrote:
This was one of the things that Indonesia was written for (a long time
ago, in a galaxy far, far away), although I'm not sure if it will still
run. If you're desperate, see http://xray.bmc.uu.se/~dennis/
--Gerard
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
Best wishes,
--Gerard
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Gerard J. Kleywegt
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[email protected]
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