RNA folding algorithm based on fuzzy dynamic programming

Owing to the fact that three-dimensional structures of biological macromolecule determine their functions, the development of prediction approaches of RNA secondary structures is undoubtedly of great significance, which becomes one of the most important topics in the field of computational biology. On the basis of the analysis of dynamic programming method involved in RNA secondary structure predictions, a new RNA prediction approach was presented using fuzzy dynamic programming. The optimal fuzzy folding problem of tRNA families of the E. coli genome sequence was considered. A collection of fuzzy parameters such as fuzzy decisions, fuzzy goals, states, and fuzzy termination times were given. Based on the RNAfold module in the ViennaRNA package, the new RNA prediction algorithm was implemented, in which any possible secondary structures were generated when tRNA sequences of E. coli are used as an input. Furthermore, the alaT tRNA sequence of E. coli as a test sample was used and four fuzzy predictions of possible secondary structures were produced. All these results were visualized and analyzed.