TY - GEN
T1 - Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs
AU - Jacob, Arpith
AU - Buhler, Jeremy
AU - Chamberlain, Roger D.
PY - 2008
Y1 - 2008
N2 - 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 39x on a Xilinx Virtex-II 6000 FPGA over a modern x86 CPU.
AB - 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 39x on a Xilinx Virtex-II 6000 FPGA over a modern x86 CPU.
UR - https://www.scopus.com/pages/publications/51649129789
U2 - 10.1109/ASAP.2008.4580177
DO - 10.1109/ASAP.2008.4580177
M3 - Conference contribution
AN - SCOPUS:51649129789
SN - 9781424418985
T3 - Proceedings of the International Conference on Application-Specific Systems, Architectures and Processors
SP - 191
EP - 196
BT - ASAP08, Conference Proceedings - IEEE 19th International Conference on Application-Specific Systems, Architectures and Processors
PB - Institute of Electrical and Electronics Engineers Inc.
T2 - ASAP08 - IEEE 19th International Conference on Application-Specific Systems, Architectures and Processors
Y2 - 2 July 2008 through 4 July 2008
ER -