[Bioperl-l] Percentage Similarity

[shalabh sharma]

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.

Thanks
Shalabh Sharma


On Tue, Aug 4, 2009 at 12:43 PM, K. Shameer <shameer at ncbs.res.in> wrote:

> Hello Shalabh,
>
> You may try ALISTAT. Available as a part of SQUID library from Prof. Sean
> Eddy. Make an alignment of your 100 sequences and use alignment as input
> of ALISTAT. ftp://selab.janelia.org/pub/software/squid/
>
> Best,
> Khader Shameer
>
> > 2009/7/28 shalabh sharma <shalabh.sharma7 at gmail.com>:
> >> Hi All,          I have some protein sequences (around 100) i need to
> >> find
> >> overall percentage similarity between them.
> >> How i can do that?
> >
> > Tried using blast?
> >
> > You can download that.
> >
> >
> > Try asking in irc://irc.freenode.net/#bioinformatics
> >
> > Dan.
> >
> >
> >>
> >> Thanks
> >> Shalabh
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