Xilinx FPGA Accelerated Bioinformatics Algorithm

Pico Computing used CoDeveloper C-to-FPGA compiler (Impulse Accelerated Technologies) to develop and deploy a DNA biotechnology genome search algorithm on a new, modular FPGA acceleration platform. The Xilinx FPGA-accelerated bioinformatics algorithm, written in C, performs sequence analysis and pair-match scoring of DNA runs with lengths of 25 base pairs. The algorithm is inherently parallel, making it an ideal candidate for acceleration using a large number of FPGA devices.

Within two days of powering up the EX-500 with the first Virtex-6 SX240T FPGA computing modules, Pico Computing engineers had successfully migrated and tested the C-language bioinformatics searching algorithm and demonstrated significant improvements in algorithm speed and throughput over previous generation FPGA products.

Using the new, modular EX-500 platform as the foundation, and Impulse C as the programming tool, Pico Computing software and firmware engineers were able to successfully deploy the bioinformatics algorithm with no significant changes needed to the algorithm source code. The Pico EX-500 supports up to six M-501 modules per PCI Express board. Each module can be configured with a range of FPGAs including the Xilinx Virtex-6 LX240T devices used in this first test application.

More info: Impulse Accelerated Technologies | Pico Computing