Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment

CORC > 计算技术研究所 > 中国科学院计算技术研究所 > 中国科学院计算技术研究所期刊论文 > 2006年英文

	Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment
	Guang-Ming Tan（谭光明）; Ning-Hui Sun（孙凝晖）; Sheng-Zhong Feng（冯圣中）; Dong-Bo Bu（卜东波）; Lin Xu（徐琳）
刊名	Journal of Computer Science and Technology
	2006
卷号	21 期号:6 页码:973-978
关键词	Sequence Alignment Blast Megablast I/o Intensive Parallelization
英文摘要	MegaBlast is one of the most important programs in NCBI BLAST (Basic Local Alignment Search Tool) toolkits. However, MegaBlast is computation and I/O intensive. It consumes a great deal of memory which is proportional to the size of the query sequences set and subject (database) sequences set of product. This paper proposes a new strategy for optimizing MegaBlast. The new strategy exchanges the query and subject sequences sets, and builds a hash table based on new subject sequences. It overlaps I/O with computation, shortens the overall time and reduces the cost of memory, since the memory here is only proportional to the size of subject sequences set. The optimized algorithm is suitable to be parallelized in cluster systems. The parallel algorithm uses query segmentation method. As our experiments shown, the parallel program which is implemented with MPI has fine scalability.
语种	英语
公开日期	2010-11-04
内容类型	期刊论文
源URL	[http://ictir.ict.ac.cn/handle/311040/845]
专题	中国科学院计算技术研究所期刊论文_2006年英文
推荐引用方式 GB/T 7714	Guang-Ming Tan,Ning-Hui Sun,Sheng-Zhong Feng,et al. Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment[J]. Journal of Computer Science and Technology,2006,21(6):973-978.
APA	Guang-Ming Tan,Ning-Hui Sun,Sheng-Zhong Feng,Dong-Bo Bu,&Lin Xu.(2006).Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment.Journal of Computer Science and Technology,21(6),973-978.
MLA	Guang-Ming Tan,et al."Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment".Journal of Computer Science and Technology 21.6(2006):973-978.