Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment

Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment

Guang-Ming Tan;Lin Xu;Dong-Bo Bu;Sheng-Zhong Feng;Ning-Hui Sun

【期刊名称】《计算机科学技术学报（英文版）》 【年(卷),期】2006(021)006

【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. 【总页数】6页(973-978) 【

关

键

词

】

sequence

alignment;BLAST;MegaBlast;I/O

intensive;parallelization

【作者】Guang-Ming Tan;Lin Xu;Dong-Bo Bu;Sheng-Zhong Feng;Ning-

Hui Sun

【作者单位】Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, P.R. China;Graduate University of Chinese Academy of Sciences, Beijing 100039, P.R. China;Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, P.R. China;Graduate University of Chinese Academy of Sciences, Beijing 100039, P.R. China;Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, P.R. China;Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, P.R. China;Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, P.R. China 【正文语种】中文 【中图分类】TP3 【文献来源】

https://www.zhangqiaokeyan.com/academic-journal-cn_journal-computer-science-technology_thesis/0201241259673.html 【相关文献】

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