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.
>
>
--
Muhammad Bashir Khan
**************************************************
Department for Structural and Computational Biology
Max F. Perutz Laboratories
University of Vienna
Campus Vienna Biocenter 5
A-1030 Vienna
Austria
Austria
Phone: +43(1)427752224
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