The Ensemble_Calc.pl script by Chikako Ragan & Michael Zuker computes equilibrium concentrations and free energy change when an oligo(ribo)nucleotide binds to a target nucleic acid. Although written for a specific application, the binding of a miRNA to a mRNA, it can be used for the binding of a short DNA oligo to a long(er) DNA target.
If called as 'Ensemble_Calc_Full.pl', the script runs in 'full
mode'. Input must be specified using appropriate flags. Read the
source code and run as
for detailed information.