基于并行的同源RNA序列快速搜索算法  

A Parallel Algorithm for Rapid RNA Homology Search

作　　者：严繁妹[1] 骆志刚[1] 管乃洋[1] 丁凡[1] 王金华[1] 

机构地区：[1]国防科技大学并行与分布处理国家重点实验室,湖南长沙410073

出　　处：《微电子学与计算机》2006年第9期1-3,9,共4页Microelectronics & Computer

摘　　要：cmsearch程序是目前最流行的同源RNA搜索工具之一,其最大的缺陷在于搜索速度过慢,严重影响了其应用范围。文章基于序列划分策略采用两级工作池方式实现同源RNA的并行搜索,并对其中所涉及的通信和负载平衡问题进行了优化。测试结果表明,此文方法具有良好的可扩展性,在120个处理器时,并行效率可达86.3%,能够用于全基因组范围内的大规模同源RNA序列搜索。Cmsearch program is one of the most popular tools for searching homologous RNA. However, its speed is too slow, which seriously limits its application. In this paper, we present a method for parallel searching which employs sequence partition strategy and two-level work pool approach. Then, we optimized the communication and load balance involved in our method. As experiments shown, our parallel method has good scalability, which achieves 86.3% efficiency at 120 CPUs, and can be used in solving large-scale homologous RNA search problem in genomic region.

关 键 词：同源RNA序列 两级工作池 并行化 

分 类 号：TP31[自动化与计算机技术—计算机软件与理论]