| Presentation | 2010-09-16 Accelerating HMMER search using FPGA Grid Toyokazu TAKAGI, Tutomu MARUYAMA, |
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| PDF Download Page |  PDF download Page Link |
| Abstract(in Japanese) | (See Japanese page) |
| Abstract(in English) | HMMER is one of the most used software tools for sensitive profile HMM (Hidden Markov Model) searches of biological sequence databases. HMMER can be accelerated by comparing a profile HMM with N sequences in parallel using a computing grid with N nodes. HMMER is, however, still a cpu-intensive program. In HMMER, the Viterbi algorithm, which is a quadratic dynamic programming algorithm, is used to align a profile HMM and a sequence. Using a dedicated hardware, the search by the Viterbi algorithm can be accelerated by processing several nodes in the search space in parallel. In this paper, we describe an approach for accelerating HMMER search using an FPGA grid. |
| Keyword(in Japanese) | (See Japanese page) |
| Keyword(in English) | FPGA / HMMER / profile HMM / parallel computation / grid computing |
| Paper # | RECONF2010-23 |
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| Conference Information | |
| Committee | RECONF |
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| Conference Date | 2010/9/9(1days) |
| Place (in Japanese) | (See Japanese page) |
| Place (in English) | |
| Topics (in Japanese) | (See Japanese page) |
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| 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) | Accelerating HMMER search using FPGA Grid |
| Sub Title (in English) | |
| Keyword(1) | FPGA |
| Keyword(2) | HMMER |
| Keyword(3) | profile HMM |
| Keyword(4) | parallel computation |
| Keyword(5) | grid computing |
| 1st Author's Name | Toyokazu TAKAGI |
| 1st Author's Affiliation | Systems and Information Engineering, University of Tsukuba() |
| 2nd Author's Name | Tutomu MARUYAMA |
| 2nd Author's Affiliation | Systems and Information Engineering, University of Tsukuba |
| Date | 2010-09-16 |
| Paper # | RECONF2010-23 |
| Volume (vol) | vol.110 |
| Number (no) | 204 |
| Page | pp.pp.- |
| #Pages | 6 |
| Date of Issue | |