| Presentation | 2011-05-13 Acceleration of Smith-Waterman Algorithm on FPGAs Akira FUKUI, Masahiro FUJITA, |
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| PDF Download Page |  PDF download Page Link |
| Abstract(in Japanese) | (See Japanese page) |
| Abstract(in English) | Smith-Waterman Algorithm is utilized for alignment of DNA and protein sequences. When an unknown sample of DNA or protein was aquired, in order to detect its fuction, researchers see the similarity of the unknown sample against the database of known DNA or protein and this process needs a long calculation time. In this paper, an efficient implementation of Smith-Waterman Algoirthm on FPGA is introduced. This implementation on Virtex-5 SX240T aquired 138 times speed up compared to SSEARCH on CPU (Xeon X5570) and also more than 2 times speed up against GPU (NVidia Tesla 1.15GHz, 448core). The speed up was aquired with an implementation of pipelining, parallelizing and other optimizations. This speed shows us the FPGA's superiority to deal with Smith-Waterman Algorithm. |
| Keyword(in Japanese) | (See Japanese page) |
| Keyword(in English) | FPGA / Smith-Waterman Algorithm / acceleration / high-level synthesis |
| Paper # | RECONF2011-12 |
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| Conference Information | |
| Committee | RECONF |
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| Conference Date | 2011/5/5(1days) |
| Place (in Japanese) | (See Japanese page) |
| Place (in English) | |
| Topics (in Japanese) | (See Japanese page) |
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| Paper Information | |
| Registration To | Reconfigurable Systems (RECONF) |
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| Language | JPN |
| Title (in Japanese) | (See Japanese page) |
| Sub Title (in Japanese) | (See Japanese page) |
| Title (in English) | Acceleration of Smith-Waterman Algorithm on FPGAs |
| Sub Title (in English) | |
| Keyword(1) | FPGA |
| Keyword(2) | Smith-Waterman Algorithm |
| Keyword(3) | acceleration |
| Keyword(4) | high-level synthesis |
| 1st Author's Name | Akira FUKUI |
| 1st Author's Affiliation | Dept. of Electrical Engineering and Information Systems, The University of Tokyo() |
| 2nd Author's Name | Masahiro FUJITA |
| 2nd Author's Affiliation | VLSI Design and Education Center, University of Tokyo |
| Date | 2011-05-13 |
| Paper # | RECONF2011-12 |
| Volume (vol) | vol.111 |
| Number (no) | 31 |
| Page | pp.pp.- |
| #Pages | 6 |
| Date of Issue | |