A special-purpose computer for exploring similar biological sequences: Bioler-2 with multi-pipeline and multi-sequence architecture Original Research Article

We developed a special-purpose computer for exploring similar biological sequences by Smith–Waterman method, Bioler-2 (BIOLogical sequence explorER). It can compute a complete similarity score between two biological sequences which have less than 10,000 characters. We integrated the system on two FPGA (Field Programmable Gate Array) chips, XC2V6000 (6M gates) by Xilinx corporation. They are mounted on the 32 bit PCI (Peripheral Component Interconnect) bus card which is connected to the host computer. The performance of Bioler-2 is 142 times faster than a general-purpose computer installed the Linux kernel version 2.4.25 compiled by gcc (Gnu Compiler Collection) version 3.3.3 with Pentium4 enabled hyper threading technology at 3.2 GHz. Bioler-2 is effective in the biological sequence analysis.