Within the past week, I have finished my Perl program (for now) that runs Mfold and calculates and directly outputs the folding energy. Using this program, I calculated the energy of a specific sequence and got ∆G=-41. Next, I took the first 100 nucleotides and calculated the folding energy for this piece and got ∆G=-5.2. Then, I used Rfold to calculate the local base pairing probabilities for the 100 nucleotide piece and made synonymous changes that involved the nucleotides with a probability greater than 0.1. I ran this modified 100 nucleotide sequence through my Mfold Perl program and found that the folding energy changed to -13.8 now. Finally, I put this modified sequence back into the original whole sequence and recalculated the folding energy and found that ∆G=-38.4. The results are shown in the table below.
Now I plan to repeat this experiment several times (~100) to see how consistent my results are. After I do this, I will modify the threshold as well as the size of the piece and see how these changes affect my results. I also plan to repeat these experiments several times.
Now I plan to repeat this experiment several times (~100) to see how consistent my results are. After I do this, I will modify the threshold as well as the size of the piece and see how these changes affect my results. I also plan to repeat these experiments several times.