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.
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