Improvement of performance of megablast algorithm for dna sequence alignment
文献类型：期刊论文
| 作者 | Tan, Guang-Ming; Xu, Lin; Bu, Dong-Bo; Feng, Sheng-Zhong; Sun, Ning-Hui |
| 刊名 | Journal of computer science and technology
 |
| 出版日期 | 2006-11-01 |
| 卷号 | 21期号:6页码:973-978 |
| 关键词 | Sequence alignment Blast Megablast I/o intensive Parallelization |
| ISSN号 | 1000-9000 |
| 通讯作者 | Tan, guang-ming(tgm@ncic.ac.cn) |
| 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. |
| WOS研究方向 | Computer Science |
| WOS类目 | Computer Science, Hardware & Architecture ; Computer Science, Software Engineering |
| 语种 | 英语 |
| WOS记录号 | WOS:000242640200014 |
| 出版者 | SCIENCE CHINA PRESS |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2379234 |
| 专题 | 中国科学院大学 |
| 通讯作者 | Tan, Guang-Ming |
| 作者单位 | 1.Chinese Acad Sci, Comp Technol Inst, Beijing 100080, Peoples R China 2.Grad Univ Chinese Acad Sci, Beijing 100039, Peoples R China |
| 推荐引用方式 GB/T 7714 | Tan, Guang-Ming,Xu, Lin,Bu, Dong-Bo,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 | Tan, Guang-Ming,Xu, Lin,Bu, Dong-Bo,Feng, Sheng-Zhong,&Sun, Ning-Hui.(2006).Improvement of performance of megablast algorithm for dna sequence alignment.Journal of computer science and technology,21(6),973-978. |
| MLA | Tan, Guang-Ming,et al."Improvement of performance of megablast algorithm for dna sequence alignment".Journal of computer science and technology 21.6(2006):973-978. |
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来源：中国科学院大学
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