After a great, albeit short, spring break, I have continued with my research. This week, I have furthered my research by performing 5 times the amount of iterations as previously performed and comparing my results to an existing mRNA Optimiser. My results are shown in the graph below. Using a bioinformatics tool called, "mRNA Optimiser", which optimizes mRNA secondary structure, I entered my sequence (after changing Thymine to Uracil) to compare results. After altering the setting to retain the GC content, it found that the initial pseudo-energy (after 4000 iterations) was -8256.7 and the final pseudo-energy was -7076.67. Currently, I am trying to interpret this results as I have found (using Mfold) that the initial folding energy of my sequence is -41 and the optimized energy (after 500 iterations) is -56.
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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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