Degenerate Primers

[ww40]

>  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? 
>
Karl,

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

BILL


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

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