| Article ID: | iaor2006155 |
| Country: | Netherlands |
| Volume: | 157 |
| Issue: | 1 |
| Start Page Number: | 1 |
| End Page Number: | 8 |
| Publication Date: | Feb 2004 |
| Journal: | Computer Physics Communications |
| Authors: | Ito T., Sugie T., Horita K., Hosono S., Ebisuzaki T. |
| Keywords: | programming: dynamic |
We built a special-purpose computer for exploring similar protein sequences by the dynamic programming method, BIOLER-1 (BIOLogical sequence explorER). It can compute a complete similarity between two protein sequences which have less than 1024 amino acids. We integrated the system on a PLD (Programmable Logic Device) chip, APEX EP20K300EQC240-1 (300,000 gates) by Altera Corporation. It is mounted on the 32 bit PCI (Peripheral Component Interconnect) bus board which is connected to a personal computer. The performance is 3564 MIPS (Million Instructions Per Second) which is three times faster than a personal computer with Pentium 4 at 1.8 GHz. BIOLER-1 showed us the effectiveness in the field of biological sequence analysis.