A special-purpose computer for exploring similar protein sequences by the dynamic programming method Original Research Article

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 Pentium4 at 1.8 GHz. BIOLER-1 showed us the effectiveness in the field of biological sequence analysis.