计算机技术与发展2017，Vol.27Issue(9)：1-6,6.DOI:10.3969/j.issn.1673-629X.2017.09.001
基于OpenCL的RNA二级结构预测算法
Secondary Structure Prediction of RNA Based on OpenCL
摘要
Abstract
Predicting RNA secondary structure is an important field in computational molecular biology especially including pseudoknots. However,predicting RNA secondary structure with all kinds of pseudoknots has been proven to be an NP-complete problem. To solve it, an improved genetic algorithm is proposed in CPU platform,which can predict two kinds of pseudoknots. Its sensitivity can reach 0. 775 and its positive predictive value can reach 0. 8225. The prediction of RNA secondary structure with pseudoknots based on genetic algo-rithm is inefficient. To solve it,an accelerated algorithm based on OpenCL is presented,which accelerates the period of individual evolu-tion according to the analysis of parallelizability of serial prediction algorithm. Then the algorithm established with GPU based on OpenCL is promoted. The contrast experiments with the same test set have been conducted compared with other algorithms. The experimental re-sults show that the improved heterogeneous parallel algorithm has acquired 2. 72 times faster average operation rate than others,reducing the computing time effectively and improving the efficiency of prediction.关键词
RNA二级结构预测/假结/OpenCL/异构计算Key words
RNA secondary structure/pseudoknots/OpenCL/heterogeneous computing分类
信息技术与安全科学引用本文复制引用
汪方良,施慧彬..基于OpenCL的RNA二级结构预测算法[J].计算机技术与发展,2017,27(9):1-6,6.基金项目
国家"973"重点基础研究发展计划项目(2014CB744900) （2014CB744900）
