基于图形硬件加速的生物序列比对算法研究  

Biological Sequence Alignment Algorithm Research Based on Graphics Hardware Acceleration

作　　者：张林[1] 柴惠[1] 沃立科[1] 袁小凤[1] 黄燕芬[1] 

机构地区：[1]浙江中医药大学生命科学学院,杭州310053

出　　处：《生物信息学》2011年第2期146-150,154,共6页Chinese Journal of Bioinformatics

基　　金：浙江省自然科学基金(Y2080844);浙江省医药卫生科学研究基金(2009B112);浙江省教育厅资助项目(Y200906336)

摘　　要：生物序列比对是生物信息学的基础,是当今功能基因组学研究中最常用、最重要的研究方法之一。本文对各类序列比对算法优缺点进行分析,对图形硬件的优势进行挖掘。在此基础上,将各类序列比对算法中准确性最高的动态规划算法予以实现,并将其映射到图形硬件上,以实现算法加速。通过实例进行性能评测,结果表明该加速算法在保证比对准确性的同时,能较大地提高比对速度。Biological sequence alignment is the basis of bioinformatics,and is also one of the most popular methods for functional genomics research.We analyzed the advantage and disadvantage of various types of sequence alignment algorithms and mined the advantages of graphics hardware.Then we achieved the dynamic programming algorithm which is the most accurate algorithms of all,and mapped it to the graphics hardware to speed up the algorithm.The evaluation of the example performance showed that the accelerated algorithm can greatly improve the alignment ratio while ensure alignment accuracy.

关 键 词：序列比对 动态规划算法 图形硬件 

分 类 号：Q332[生物学—遗传学] R318[医药卫生—生物医学工程]