[Bioperl-l] how to identify least degeneracy for a conserved region among all conserved regions in an amino acid alignment?

[gandipalem]

Hi,

I am new to this.

I am working on designing primers for a set of highly diverged  proteins.
I designed degenerate primers for all those proteins manually starting from
multiple sequence alignment to reverse translation of conserved regions. But
this process is very time taking and robust. I would like automate this work
PERL. But I am getting a problem were I am unable to getting the logic "how
to measure/find out the least degeneracy for a conserved region among all
conserved regions of a multiple sequence alignment?".

So can anybody tell about how to find out least degenerated conserved region
in PERL?

Thanking you

Suresh
NBPGR

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