Degenerate Primer generation from Multiple Alignments

Andy Law Andy.Law at
Thu Apr 2 05:15:15 EST 1998

In article <pGuU.1$gK.86848 at>, "Curtis R.  Altmann"
<altmanc at> wrote:

I've just (this morning) finished a program to scan a GCG sequence for
degree of degeneracy in a user defined window. It will calculate the
degeneracy score in one of 3 ways, namely multiplicative (an estimate of
the total number of possibile oligos within the window), additive (a kind
of weighted count where N is worse than S or R) or simple count (number of
ambiguous bases in the window). It will then optionally sort the output by
scores and report.

If you are interested in trying this, then mail me and we'll see what we
can do for you.


Andy Law
( Andy.Law at )
( Big Nose in Edinburgh )

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