[BiO BB] checking conservation of short sequences

[manoj yadav]

first u have to done multiple sequence alignment using any available
software.In output u will get the evolutionary similar sequences according
to the e-values.

On 12/9/08, T Joshi <tejalonline at gmail.com> wrote:
>
> Hi,
> I have some small short sequences of less than 40nt. I want to check
> if they are evolutionarily conserved across some species.
>
> One way I could do so is to download conservation track from UCSC in
> .aln format and use that with clustalw or clustalx for alignment  with
> my query sequences. Blastn also doesn't have any database containing
> information on conservation.
>
> Could you suggest some other way by which I could do so without
> downloading the conservation track ?
>
> Thanks a lot..
>
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-- 
Manoj Kumar Yadav
Research Scholar,
Center for Bioinformatics
BHU,Varanasi
+91 9838016500