Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment
文献类型：期刊论文
| 作者 | 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
 |
| 出版日期 | 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 |
| 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. |
入库方式： OAI收割
来源：计算技术研究所
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