Degenerate Primer generation from Multiple Alignments

Andy Phillips andy.phillips at
Thu Apr 2 08:20:42 EST 1998

Curtis R. Altmann wrote:
> I am looking for software which can take multiple sequence alignments in a
> standard format such as the output from clustalw, GCG or DNAstar Megalign
> and identify least and most degenerate oligos.  In searches of the web, I
> have found one such program called Primegen.  I have not been able to obtain
> this software (from University of Washington in Seattle).  It was written by
>  Patrick J. O'Hara and Domenick Venezia.
> Any help in either obtaining this program or similar programs would be
> greatly appreciated.
> Curtis R. Altmann, Ph.D.
> The Rockefeller University

I'm not sure why you'd want to identify the _most_ degenerate oligos,
but there are a few web sites (eg GeneFisher, Simple Primer Design) that
will identify the least degenerate primers from an alignment. See the
PCR section of my Web page below.


 Email : andy.phillips at  : University of Bristol           
 Phone : +44-1275-549257            : IACR Long Ashton Research Station 
 Fax   : +44-1275-394281            : Long Ashton, Bristol, BS18 9AF, UK 
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