A reconfigurable index FLASH memory tailored to seed-based genomic sequence comparison algorithms
文献类型：期刊论文
| 作者 | Lavenier, D.; Georges, G.; Liu, X. |
| 刊名 | JOURNAL OF VLSI SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY
 |
| 出版日期 | 2007-09-01 |
| 卷号 | 48期号:3页码:255-269 |
| 关键词 | bioinformatics genomics sequence comparison reconfigurable architecture FLASH memory index indexing seed-based algorithm |
| ISSN号 | 0922-5773 |
| DOI | 10.1007/s11265-007-0073-6 |
| 英文摘要 | Genomic sequence comparison algorithms represent the basic toolbox for processing large volume of DNA or protein sequences. They are involved both in the systematic scan of databases, mostly for detecting similarities with an unknown sequence, and in preliminary processing before advanced bioinformatics analysis. Due to the exponential growth of genomic data, new solutions are required to keep the computation time reasonable. This paper presents a specific hardware architecture to speed-up seed-based algorithms which are currently the most popular heuristics for detecting alignments. The architecture regroups FLASH and FPGA technologies on a common support, allowing a large amount of data to be rapidly accessed and quickly processed. Experiments on database search and intensive sequence comparison demonstrate a good cost/performance ratio compared to standard approaches. |
| WOS研究方向 | Computer Science ; Engineering |
| 语种 | 英语 |
| WOS记录号 | WOS:000249211900006 |
| 出版者 | SPRINGER |
| 源URL | [http://119.78.100.204/handle/2XEOYT63/10918]  |
| 专题 | 中国科学院计算技术研究所期刊论文_英文 |
| 通讯作者 | Lavenier, D. |
| 作者单位 | 1.INRISA CNRS, F-35042 Rennes, France 2.CAS, Comp Technol Inst, Key Lab Comp Syst & Architect, Beijing, Peoples R China |
| 推荐引用方式 GB/T 7714 | Lavenier, D.,Georges, G.,Liu, X.. A reconfigurable index FLASH memory tailored to seed-based genomic sequence comparison algorithms[J]. JOURNAL OF VLSI SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY,2007,48(3):255-269. |
| APA | Lavenier, D.,Georges, G.,&Liu, X..(2007).A reconfigurable index FLASH memory tailored to seed-based genomic sequence comparison algorithms.JOURNAL OF VLSI SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY,48(3),255-269. |
| MLA | Lavenier, D.,et al."A reconfigurable index FLASH memory tailored to seed-based genomic sequence comparison algorithms".JOURNAL OF VLSI SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY 48.3(2007):255-269. |
入库方式： OAI收割
来源：计算技术研究所
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