| Presentation | 2003/6/19 A special-purpose computer for exploring similar bio-sequences Takashige SUGIE, Tomoyoshi ITO, Toshikazu EBISUZAKI, |
|---|---|
| PDF Download Page | PDF download Page Link |
| Abstract(in Japanese) | (See Japanese page) |
| Abstract(in English) | We built a special-purpose computer for exploring similar bio-sequences by the dynamic programming method. It can compute a complete similarity between two protein or DNA sequences which have less than 10,000 characters. We integrated the system on two FPGA (Field Programmable Gate Array) chips, Vertex2 xc2v6000-4 (6 Mgates) by Xilinx. It is mounted on the 32 bit PCI (Peripheral Component Interconnect) bus board which is connected to a personal computer. The performance is 1,404,000 MIPS (Million Instructions Per Second) about 1,200 times faster than a personal computer with Pentium4 at 1.8 GHz. It showed us the effectiveness in the field of biological sequence analysis. |
| Keyword(in Japanese) | (See Japanese page) |
| Keyword(in English) | Bioinformatics / Similarity search / Dynamic programming / Pairwise alignment / Special-purpose computer |
| Paper # | PRMU2003-35 |
| Date of Issue |
| Conference Information | |
| Committee | PRMU |
|---|---|
| Conference Date | 2003/6/19(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 | Pattern Recognition and Media Understanding (PRMU) |
|---|---|
| Language | JPN |
| Title (in Japanese) | (See Japanese page) |
| Sub Title (in Japanese) | (See Japanese page) |
| Title (in English) | A special-purpose computer for exploring similar bio-sequences |
| Sub Title (in English) | |
| Keyword(1) | Bioinformatics |
| Keyword(2) | Similarity search |
| Keyword(3) | Dynamic programming |
| Keyword(4) | Pairwise alignment |
| Keyword(5) | Special-purpose computer |
| 1st Author's Name | Takashige SUGIE |
| 1st Author's Affiliation | Department of Electronics and Mechanical Engineering, Chiba University() |
| 2nd Author's Name | Tomoyoshi ITO |
| 2nd Author's Affiliation | Department of Electronics and Mechanical Engineering, Chiba University |
| 3rd Author's Name | Toshikazu EBISUZAKI |
| 3rd Author's Affiliation | The Institute of Physical and Chemical Research |
| Date | 2003/6/19 |
| Paper # | PRMU2003-35 |
| Volume (vol) | vol.103 |
| Number (no) | 150 |
| Page | pp.pp.- |
| #Pages | 4 |
| Date of Issue | |