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 alignement should be ok (The "Rascal" step should do this job).
good luck
claudine
Le 26/11/2010 15:19, Muhammed bashir Khan a écrit :
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 Frederic wrote:
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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Pr Claudine MAYER
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Université Paris Diderot - Paris 7
Dynamique structurale des Macromolécules
Département de Biologie Structurale et Chimie
Institut Pasteur
25 rue du Dr Roux
75 015 PARIS
Tel. 01 45 68 83 87
Mobil. 06 07 23 51 16
Fax. 01 45 68 89 93
Mail. [email protected]
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