Software The Python program first-rna.py is available at the book website. It asks the user if they want to type in an RNA string, or read one from a file called
“randomstring.” Once an RNA string has been input (either by typing, or from a file), the
program generates the ILP formulation to solve the simple RNA folding problem for that RNA
string.
Download the program and then run it, choosing the option of typing in the RNA string.
Type in the toy string s = ACUGU. Then, issue the appropriate Gurobi command to solve the
ILP formulation and save the solution to a file. Compare the result obtained with the result stated
above. The objective value must be the same, but the selected pairs might be different.
Next, run first-rna.py again, but this time type in the RNA string shown in Figure 6.1. The
linear string is given in the caption. Then, run Gurobi to solve the ILP formulation. Is the nested
pairing shown in Figure 6.1 optimal?