This week, I have been very busy with finals and end-of-semester projects, so I have not had much time to advance my research progress. However, with the time I did have, I integrated my two programs into one. Currently, it takes a FASTA and Rfold file as input, and uses the local base-pairing probabilities to make synonymous changes at the sites that are above a specified threshold.
In the coming weeks, I plan to modify the program to take only a piece of the sequence (with a parametrized length) and make synonymous changes on that piece only. Then, if the changes reduce the folding energy, the program will keep that change and if it does not it will not. I also plan to improve the algorithm that makes the synonymous changes to make it more efficient.
In the coming weeks, I plan to modify the program to take only a piece of the sequence (with a parametrized length) and make synonymous changes on that piece only. Then, if the changes reduce the folding energy, the program will keep that change and if it does not it will not. I also plan to improve the algorithm that makes the synonymous changes to make it more efficient.