噬菌体基因文库控制元件测定的并行处理方法  

Parallel processing technology on a regulatory element detection method of bacteriophage genomes

作　　者：孙伟东[1,2] 王微微[2] 马宗民[1] 

机构地区：[1]东北大学信息科学与工程学院,辽宁沈阳110004 [2]沈阳航空航天大学计算机学院,辽宁沈阳110136

出　　处：《沈阳航空工业学院学报》2010年第5期63-67,共5页Journal of Shenyang Institute of Aeronautical Engineering

摘　　要：在噬菌体基因文库的研究中,理解基因的表达机制占有重要的地位,其中最为重要的一个环节是控制元件的测定,目前大部分控制元件测定方法都是基于基因结构的概率模型。介绍了一种不依赖于任何实验数据和先验数据的噬菌体基因文库控制元件测定方法,采用字符串模式匹配算法扫描噬菌体基因序列,发现并提取出重复频度高的子序列(可能的控制元件),但该方法计算复杂度为O(N2)。为了提高对基因序列的控制元件测定效率,进一步提出了该算法在局域网环境下的并行处理解决方案,实验表明这种基于数据分割的并行处理方法极大的加快了序列处理速度,进而扩大了算法的应用范围。A major challenge in sequence analysis of bacteriophage genomes is to understand the mechanism of genes expression,the most important step to overcome is the ability to identify regulatory elements,a number of such regulatory element detection programs developed are based on probabilistic models of gene structure,in this paper,a detection method introduced which provide a systematic string（or pattern） searching method on bacteriophage genome sequences to discover and extract high occurrence subsequence（conserved regulatory elements） without any prior experimental or predictive knowledge,but the computation complexity is about O（N2）.To improve the efficiency of regulatory element detection process,this paper further proposed a parallel implementation approach using data segmentation methodology on LAN environment.The experiment result shows that the parallel implementation can significantly accelerates the sequence processing speed,which is quite important to extend the algorithm application scope.

关 键 词：噬菌体基因文库 并行处理 控制元件测定 序列分析 

分 类 号：TP311[自动化与计算机技术—计算机软件与理论]