[Bioperl-l] Percentage Similarity

[shalabh sharma]

Hi,     Thanks for the reply. I used clustalW for the MSA.
Also i was just wondering that what if i use smith Waterman (EMBOSS' water)
and pass the same library as query sequences and reference library, then
just parse it and calculate average similarity.Is this right approach?

Thanks
Shalabh


On Wed, Aug 5, 2009 at 3:10 AM, Dan Bolser <dan.bolser at gmail.com> wrote:

> 2009/8/4 shalabh sharma <shalabh.sharma7 at gmail.com>:
> > Hi All,       thanks a lot.
> > @Khader Shameer, ALISTAT is what i was looking for. But still it gives
> you
> > the average identity, what i need exactly is the average similarity.
>
> The problem is that identity is well defined. Similarity is more
> vague, and at least depends on a particular alignment scoring matrix.
> How did you align your sequences?
>
> Dan.
>
> >> > Try asking in irc://irc.freenode.net/#bioinformatics
> >> >
>
> ;-)
>