After 4000 iterations of mRNA Optimiser on my input sequence, the maximized output sequence generated a maximum folding energy of -23.865 using Mfold. After 4000 iterations of my program on the same input sequence, the maximized output sequence generated a maximum folding energy of -22.7 (also using Mfold). The results and sequences can be summarized in the diagram below: Although my program takes more time than mRNA Optimiser, it can generate synonymous maximized sequences with higher folding energies. It can also minimize the folding energy and allows the user to specify the size of the selected window and Rfold threshold.
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JAY VillariUndergraduate student studying Computer Science and Biology at The College of New Jersey Archives
May 2016
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