A study of architectural optimization methods in bioinformatics applications
文献类型：期刊论文
| 作者 | Tan, G.; Xu, L.; Dai, Z.; Fong, S.; Sun, N. |
| 刊名 | INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS
 |
| 出版日期 | 2007-09-01 |
| 卷号 | 21期号:3页码:371-384 |
| 关键词 | bioinformatics sequence alignment cache memory instruction level parallelism I/O overlapping |
| ISSN号 | 1094-3420 |
| DOI | 10.1177/1094342007078175 |
| 英文摘要 | Studies in the optimization of sequence alignment have been carried out in bioinformatics. In this paper, we have focused on two aspects: memory usage and execution time. Our study suggests that cache memory does not have a significant effect on system performance. Our attention then turns to optimize Smith-Waterman's algorithm. Two instruction level methods have been proposed and 2-8 fold speed improvements have been observed after the optimization has been implemented. Further improvements on system performance have been achieved by overlapping computation with system I/O usage. |
| WOS研究方向 | Computer Science |
| 语种 | 英语 |
| WOS记录号 | WOS:000248886900008 |
| 出版者 | SAGE PUBLICATIONS LTD |
| 源URL | [http://119.78.100.204/handle/2XEOYT63/10849]  |
| 专题 | 中国科学院计算技术研究所期刊论文_英文 |
| 通讯作者 | Tan, G. |
| 作者单位 | Chinese Acad Sci, Inst Comp Technol, Key Lab Comp Syst & Architecture, Beijing, Peoples R China |
| 推荐引用方式 GB/T 7714 | Tan, G.,Xu, L.,Dai, Z.,et al. A study of architectural optimization methods in bioinformatics applications[J]. INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS,2007,21(3):371-384. |
| APA | Tan, G.,Xu, L.,Dai, Z.,Fong, S.,&Sun, N..(2007).A study of architectural optimization methods in bioinformatics applications.INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS,21(3),371-384. |
| MLA | Tan, G.,et al."A study of architectural optimization methods in bioinformatics applications".INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS 21.3(2007):371-384. |
入库方式： OAI收割
来源：计算技术研究所
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