Degenerate Primers

ww40 William_D_WARREN at UMAIL.UMD.EDU
Wed Sep 22 13:20:00 EST 1993

>  The Molecular Cloning Manual (Sambrook, Fritsch, & Maniatis) discusses
>the rational of synthesizing degenerate PCR primers by hand, but I would
>like to find out if there are any computer programs available that will
>generate degenerate primers if given a set of known sequences (I have
>sequences from 10 or so other species).   I looked into Bill Engles Amplify
>program, but it doesn't seem to handle degenerate primers.  Will GCC allow
>me to do this? 

TO my knowledge there are not any programs currently available that will, if
fed a multiple sequence alignment, will spit out optimized degenerate PCR
primers. Although I have no doubt that such a program could be written, the
task is a complex one and it would be far from trivial (if it were a trivial
task then you'd not be asking for a program to do it for you).

I have designed many pairs of matched degenerate primers that have worked
successfully and I have done them all by hand. I personally wouldn't trust a
black box program to do the task for me.

If you would like some basic DO's and DON'T feel free to Email me.

Good luck


William D. WARREN, PhD
Center for Agricultural Biotechnology     Email: ww40 at
University of Maryland at College Park    Phone: (301) 405-7681 


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