基于动态规划的DNA二级结构预测算法  

Dynamic programming algorithm for DNA secondary structure prediction

作　　者：黄鑫泉[1] 张凯[1] 陈建勋[1] 

机构地区：[1]武汉科技大学计算机科学与技术学院,湖北武汉430065

出　　处：《计算机工程与设计》2014年第9期3080-3084,3223,共6页Computer Engineering and Design

基　　金：国家自然科学基金项目(61100055;61033003;60974112;91130034);湖北省自然科学基金项目(2011CDB233)

摘　　要：基于DNA分子二级结构的结构稳定性和热力学稳定性,提出一种预测DNA分子二级结构的算法。利用基于矩阵的动态规划算法求解DNA分子最大碱基对匹配的所有二级结构;利用Nearest-Neighbor热力学模型计算所有结构的自由能,自由能在阈值范围内的即为DNA分子可能的二级结构。将实验结果与RNA structure软件结果进行对比,对比结果表明,该方法具有较高的准确率和覆盖范围。Based on the structural and thermodynamic stability of the DNA molecule, a new algorithm was proposed to predict the secondary structure of the DNA molecule. First, the matrix dynamic programming algorithm was employed to generate the secondary structure of the DNA molecule with the largest base pair match. Then, Nearest-Neighbor thermodynamic model was used to calculate all of the free energies of the structures, those were within the scope of the threshold value might be the secondary structure of the DNA molecule. Comparing with the results of RNA structure software, experiment results show that the new method has higher accuracy and wider coverage.

关 键 词：生物信息学 结构稳定性 热力学稳定性 DNA二级结构 最大碱基对匹配 Nearest-Neighbor热力学模型 

分 类 号：TP301.6[自动化与计算机技术—计算机系统结构]