| Presentation | 2009-05-14 Accelerating HMMER search using FPGA Toyokazu TAKAGI, Tutomu MARUYAMA, |
|---|---|
| PDF Download Page |  PDF download Page Link |
| Abstract(in Japanese) | (See Japanese page) |
| Abstract(in English) | This paper describes an implementation of HMMER with FPGA. HMMER is one of the most used software tools for sensitive profile HMM searches of biological sequence databases. In the profile HMM, a feedback path from the end of the model to the beginning is allowed, and this loop makes it difficult to process the Viterbi algorithm in parallel. In our approach, the alignment is calculated speculatively in parallel, and when the feedback path is selected in the alignment, the alignment is recalculated from the beginning using the fedback score. Another problem for accelerating HMMER using FPGA is the large size of the score tables required for profile HMMs. By crossing the search direction in the quadratic search space and the moving direction of each processing unit in the search space, we can minimize the size of the memory banks for storing the score tables. |
| Keyword(in Japanese) | (See Japanese page) |
| Keyword(in English) | FPGA / HMMER / profile HMM / parallel computation |
| Paper # | RECONF2009-6 |
| Date of Issue |
| Conference Information | |
| Committee | RECONF |
|---|---|
| Conference Date | 2009/5/7(1days) |
| Place (in Japanese) | (See Japanese page) |
| Place (in English) | |
| Topics (in Japanese) | (See Japanese page) |
| Topics (in English) | |
| Chair | |
| Vice Chair | |
| Secretary | |
| Assistant | |
| Paper Information | |
| Registration To | Reconfigurable Systems (RECONF) |
|---|---|
| Language | JPN |
| Title (in Japanese) | (See Japanese page) |
| Sub Title (in Japanese) | (See Japanese page) |
| Title (in English) | Accelerating HMMER search using FPGA |
| Sub Title (in English) | |
| Keyword(1) | FPGA |
| Keyword(2) | HMMER |
| Keyword(3) | profile HMM |
| Keyword(4) | parallel computation |
| 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 | 2009-05-14 |
| Paper # | RECONF2009-6 |
| Volume (vol) | vol.109 |
| Number (no) | 26 |
| Page | pp.pp.- |
| #Pages | 6 |
| Date of Issue | |