A reconfigurable accelerator for Smith-Waterman algorithm
文献类型：期刊论文
| 作者 | Jiang, Xianyang1,2; Liu, Xinchun1; Xu, Lin1; Zhang, Peiheng1; Sun, Ninghui1 |
| 刊名 | IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS II-EXPRESS BRIEFS
 |
| 出版日期 | 2007-12-01 |
| 卷号 | 54期号:12页码:1077-1081 |
| 关键词 | bioinformatics computational complexity field-programmable gate array (FPGA) reconfigurable accelerator Smith-Waterman (SW) algorithm |
| ISSN号 | 1549-7747 |
| DOI | 10.1109/TCSII.2007.909857 |
| 英文摘要 | Scanning bio-sequence database and finding similarities among DNA and protein sequences is basic and important work in bioinformatics field. To solve this problem, Needleman-Wunschh (NW) algorithm is a classical and precise tool, and Smith-Waterman (SW) algorithm is more practical for its capability to find similarities between subsequences. Such algorithms have computational complexity proportional to the length product of both involved sequences, hence processing time becomes insufferable due to exponential growth speed and great amount of bio-sequence database. To alleviate this serious problem, a reconfigurable accelerator for SW algorithm is presented. In the accelerator, a modified equation is proposed to improve mapping efficiency of a processing element (PE), and a special floor plan is applied to a fine-grain parallel PE array and interface components to cut down their routing delay. Basing on the two techniques, the proposed accelerator can reach at 82-MHz frequency in an Altera EP1S30 device. Experiments demonstrate the accelerator provides more than 330 speedup as compared to a standard desktop platform with a 2.8-GHz Xeon processor and 4-GB memory and has 50% improvement on the peak performance of a transferred traditional implementation without using the two special techniques. Our implementation is also about 9% faster than the fastest implementation in a most recent family of SW algorithm accelerators. |
| WOS研究方向 | Engineering |
| 语种 | 英语 |
| WOS记录号 | WOS:000251944900011 |
| 出版者 | IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC |
| 源URL | [http://119.78.100.204/handle/2XEOYT63/11010]  |
| 专题 | 中国科学院计算技术研究所期刊论文_英文 |
| 通讯作者 | Jiang, Xianyang |
| 作者单位 | 1.Chinese Acad Sci, Inst Comp Technol, Key Lab Comp Syst & Architecture, Beijing 100080, Peoples R China 2.Wuhan Univ, Inst Microelect & Informat Technol, Wuhan 430072, Peoples R China |
| 推荐引用方式 GB/T 7714 | Jiang, Xianyang,Liu, Xinchun,Xu, Lin,et al. A reconfigurable accelerator for Smith-Waterman algorithm[J]. IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS II-EXPRESS BRIEFS,2007,54(12):1077-1081. |
| APA | Jiang, Xianyang,Liu, Xinchun,Xu, Lin,Zhang, Peiheng,&Sun, Ninghui.(2007).A reconfigurable accelerator for Smith-Waterman algorithm.IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS II-EXPRESS BRIEFS,54(12),1077-1081. |
| MLA | Jiang, Xianyang,et al."A reconfigurable accelerator for Smith-Waterman algorithm".IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS II-EXPRESS BRIEFS 54.12(2007):1077-1081. |
入库方式： OAI收割
来源：计算技术研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。