Currently, I have developed a perl program that prompts the user for a GenBank, EMBL, FASTA or IntelliGenetics file name and proceeds to predict the global folding energy of the resulting RNA molecule, by invoking Mfold, from the sequence. To continue my research, I plan to determine the global folding energy of a sequence and then take a 100-nucleotide long section of that sequence and use a different program called Rfold to calculate the local base pairing probabilities. Next, I will make synonymous substitutions based on a designated threshold that will substitute high probability positions with low probability positions to maximize the folding energy. Then, I will put this "improved" section back into the sequence and run mfold again to determine it's affect on the global folding energy.
|
JAY VillariUndergraduate student studying Computer Science and Biology at The College of New Jersey Archives
May 2016
Categories |