A shell program for the design of PCR primers using genetics computer group (GCG) software (7.1) on VAX/VMS systems.
A number of software analysis packages for the design of PCR primers are available for PCs; however, software for users that depend on VAX/VMS operating systems is not available. By treating oligonucleotides as RNA molecules, I have designed an alternative means toward studying oligonucleotide interactions using software that is currently available from The Genetics Computer Group (GCG, Madison, WI). The oligonucleotide interactions with self and non-self are analyzed by the GCG FOLD program, a program which finds a secondary structure of minimum free energy for an RNA molecule. This approach allows the identification of self-priming primer pairs, and the interaction energies provide a guideline for the prediction of optimal PCR primers.
Eberhardt
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NL
Mayo Clinic, Rochester, MN 55905.
D001483:Base Sequence; D003199:Computer Systems; D004247:DNA / Q000737:chemistry / Q000235:genetics; D005069:Evaluation Studies as Topic; D015336:Molecular Probe Techniques; D008969:Molecular Sequence Data; D015345:Oligonucleotide Probes; D010957:Plasmids; D016133:Polymerase Chain Reaction / Q000379:methods*; D012984:Software; D013816:Thermodynamics
D015345:Oligonucleotide Probes; D004247:DNA