Chaotic Simulated Annealing Of Rna Secondary Structure Prediction

RNA is the intermediate carrier of genetic information, participates in the synthesis of proteins, plays an important role in apects of cell differentiation and apoptosis, biological development, disease triggering etc. RNA secondary structure is a kind of stem-loop space structure which forms by base pairing and nucleotide chain self-folding. The stem-loop structures in RNA secondary structure not only on the analysis of RNA function but also can be used to predict RNA tertiary structure, therefore, RNA secondary structure prediction is a significant work. RNA secondary structure can be determined by the method of physical experiments, but it is time-consuming and costly. So, researchers predict RNA secondary structure with bioinformatics methods to accelerate understanding of the spatial structure of RNA molecules and their biological functions.This thesis discusses simulated annealing-based RNA secondary structure prediction problem, including:1. Elaborates the expression method of RNA secondary structure and formal representation;2. Describes the existing RNA secondary structure prediction methods and summarizes their characteristics;3. Based on the stochastic, ergodicity characteristics of chaos mapping and the optimal capacity of simulated annealing, this thesis proposed an algorithm based on chaotic simulated annealing algorithm through the technical of controling chaotic systems track density to adjust the position where folding occurs, using cooling schedule to regulate the annealing process, taking RNA secondary structure free energy as the objective function to predict RNA secondary structure.The simulation obtains 69.12%, 55.26% 89.19% base pair correct rate for predicting RNA sequence Aquaticus Asellus , Haloarcula Saccharomyces and Cerevisiae Marismortui respectively. It shows the feasibility of appling the CSA algorithm based on power function carrier to predict RNA secondary structure. Further work will be done in apects of testing for longer RNA sequence and studing of the affects of power function carrier to the base pair correct rate.