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Primer design II

Christoph Gartmann GARTMANN at IMMUNBIO.MPG.DE
Sat Jan 22 05:46:20 EST 1994


In <2hpmomINNaqn at newsstand.cit.cornell.edu> douglas writes:

> Regarding PCR primer design and GCG...
> Is there a way to search for PCR primers using any of the available GCG
> programs? I have heard that there was a program developed to use the RNA
> fold algorithms, but have not been able to access it. 

Here we use

   PRIMER: A Computer Program for Automatically Selecting PCR Primers
           Version 0.5, May 1991

   by Stephen E. Lincoln, Mark J. Daly, and Eric S. Lander
      MIT Center for Genome Research and
      Whitehead Institute for Biomedical Research
      Nine Cambridge Center
      Cambridge, Massachusetts 02142

in conjunction with

  !***  ToPrimer  **************************************************************
  !*
  !*	translates a GCG sequence file into Primer sequence file
  !*	Old name: ToStaden
  !*				Copyright John Devereux 1983
  !* 				Modified by Rodrigo Lopez 1991
  !******************************************************************************

and a self-made DCL-command file (yes, on VMS; but it should be very simple
to convert the DCL into a UNIX script). All this together fits perfcetly into
the GCG environment and people are quite content with it.

Regards
   Christoph Gartmann

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