A simulation program to display specific digestion products of predicted RNA foldings

A parameterizable program in Pascal was developed for VAX/VMS computers to simulate the autoradiograms of gel-separated RNA fragments generated by partial cleavage of a folded RNA molecule using five specific RNases. Each screen displays the results of cleavage by either one enzyme or all five, with the RNA molecule labeled at either of its ends (5′ or 3′); each run is performed with three different lengths and against a ladder containing alkaline hydrolysis products of the same RNA molecule as size markers. The program should be useful for comparing actual results with predicted functional foldings of RNA molecules.