Calculate base pair probability differences between Wild type and mutant sequences

Question

[RK]

Hello

I am trying to check whether the change in base pair probabilities is higher for mutations in a set of cancer genes vs mutations in non-cancer genes. I used RNAfold to calculate the mfe changes which also outputs a dp.ps file, I calculated the structural change by taking the difference of the rows with 'lbox' to quantify how many bases were newly formed or removed. I also tried rnaplfold for the same, and the output file generated is of the format id_basepairs file, which again has some base pair probabilities. I am not which one to use to compare change in base pair probabilities in wt and mutated sequences.

Any help is appreciated