Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs

RNA structure prediction, or folding, is a computeintensive task that lies at the core of several search applications in bioinformatics. We begin to address the need for high-throughput RNA folding by accelerating the Nussinov folding algorithm using a 2D systolic array architecture. We adapt classic results on parallel string parenthesization to produce efficient systolic arrays for the Nussinov algorithm, elaborating these array designs to produce fully realized FPGA implementations. Our designs achieve estimated speedups up to 39× on a Xilinx Virtex-II 6000 FPGA over a modern x86 CPU.

• Type: Conference
• Year: 2008
• Where: ASAP
• Authors: Arpith C. Jacob, Jeremy Buhler, Roger D. Chamberlain
• Keywords: ASAP 2008, Distributed And Parallel Computing, Nussinov Folding Algorithm, Systolic Array Architecture, Systolic Arrays