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A computer program, OligoWalk, is reported that
predicts the equilibrium affinity of complementary DNA
or RNA oligonucleotides to an RNA target. This program
considers the predicted stability of the oligonucleotide-target
helix and the competition with predicted secondary structure
of both the target and the oligonucleotide. Both unimolecular
and bimolecular oligonucleotide self structure are considered
with a user-defined concentration. The application of OligoWalk
is illustrated with three comparisons to experimental results
drawn from the literature.
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