Nakaya A, Yamamoto K, Yonezawa A
Department of Information Science, University of Tokyo, Japan.
Comput Appl Biosci. 1995 Dec;11(6):685-92. doi: 10.1093/bioinformatics/11.6.685.
An RNA secondary structure prediction method using a highly parallel computer is reported. We focus on finding thermodynamically stable structures of a single-stranded RNA molecule. Our approach is based on a parallel combinatorial method which calculates the free energy of a molecule as the sum of the free energies of all the physically possible hydrogen bonds. Our parallel algorithm finds many highly stable structures all at once, while most of the conventional prediction methods find only the most stable structure. The important idea in our algorithm is search tree pruning, with dynamic load balancing across the processor elements in a parallel computer. Software tools for visualization and classification of secondary structures are also presented using the sequence of cadang-cadang coconut viroid as an example. Our software system runs on CM-5.
报道了一种使用高度并行计算机的RNA二级结构预测方法。我们专注于寻找单链RNA分子的热力学稳定结构。我们的方法基于一种并行组合方法，该方法将分子的自由能计算为所有物理上可能的氢键的自由能之和。我们的并行算法能一次性找到许多高度稳定的结构，而大多数传统预测方法只能找到最稳定的结构。我们算法中的重要思想是搜索树剪枝，以及在并行计算机的处理器元素之间进行动态负载平衡。还以卡当卡当椰子类病毒的序列为例，展示了用于二级结构可视化和分类的软件工具。我们的软件系统在CM - 5上运行。
