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
Hi there,
Ages ago, for this type of work (fine-tuning sequence alignments), I was
loading pre-aligned (or not pre-aligned) sequences and was editing the
alignment "by hand" using a sequence alignment editor. This editor was
working on VAX/VMS systems, which no-one uses anymore (I haven't touched
VMS in many many years).
So I had a look at what sequence alignment editors are available today
using google, and I came across this: Jalview (http://www.jalview.org ).
Unfortunately, it seems it does not wish to install on my Linux box so I
don't know if the software does what you want it to do. And it is not
clear to me exactly what you mean by "extending the sequence only at the
c-terminus".
Fred.
