基于混沌模拟退火的RNA二级结构预测的研究

【作者】 胥杰；

【导师】 刘勇国；

【作者基本信息】 电子科技大学 ， 计算机软件与理论， 2010， 硕士

【摘要】 RNA是生物遗传信息的中间载体,参与蛋白质合成,在细胞分化凋亡、生物发育、疾病发生等方面起着重要作用。RNA二级结构是由碱基配对与核苷酸链折叠而成的茎环空间结构,其茎环结构不仅可用于RNA功能分析,还可用于RNA三级结构预测。因此,RNA二级结构预测具有重要意义。RNA二级结构可通过物理实验测定,但耗时长且成本高。借助生物信息学方法预测RNA二级结构,可加速认识RNA分子空间结构及其生物学功能。本论文探讨基于混沌模拟退火的RNA二级结构预测问题,主要工作包括:1、阐述RNA二级结构的表达方式和形式化表示;2、描述RNA二级结构预测的现有主要方法并总结各方法特点;3、基于混沌映射的随机性,遍历性特点和模拟退火的优化能力,给出一个基于混沌模拟退火的RNA二级结构预测算法,通过控制混沌系统的轨道密度调节RNA序列上发生折叠的位置,以冷却进度表控制模拟退火过程,采用最小自由能作为目标函数以预测RNA二级结构。对RNA序列Asellus aquaticus, Haloarcula marismortui, Saccharomyces cerevisiae进行的仿真实验分别取得了69.12%、55.26%和89.19%的碱基对正确率,表明了基于幂函数载波的混沌退火算法应用于RNA二级结构预测的可行性。选择更长的RNA序列试验、进一步研究幂函数载波方法对预测结果的影响是下一步的研究方向。更多还原

【Abstract】 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.更多还原