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High Performance Computing and Grid in Asia Pacific Region, International Conference on (2005)
Beijing, China
Nov. 30, 2005 to Dec. 3, 2005
ISBN: 0-7695-2486-9
pp: 176-180
Bu Dongbo , Chinese Academy of Science, Beijing, China
Sun Ninghui , Chinese Academy of Science, Beijing, China
Xu Lin , Graduate School of Chinese Academy of Science Beijing, China
Zhang Peiheng , Chinese Academy of Science, Beijing, China
Feng Shengzhong , Chinese Academy of Science, Beijing, China
ABSTRACT
Multiple sequence alignment is a fundamental and challenging problem in computational molecular biology. ClustalW, the most widely used multiple sequence alignment software, performs very slowly on hundreds of sequence. Here, we analyze the algorithm complexity of ClustalW as well as the time profile in practice, and then propose a strategy which uses the reconfigurable hardware FPGA to accelerate ClustalW. Comparison with other coarse-grained parallel strategies demonstrates a fine speedup of this strategy and savage of computing resource.
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CITATION
Bu Dongbo, Sun Ninghui, Xu Lin, Zhang Peiheng, Feng Shengzhong, "To Accelerate Multiple Sequence Alignment using FPGAs", High Performance Computing and Grid in Asia Pacific Region, International Conference on, vol. 00, no. , pp. 176-180, 2005, doi:10.1109/HPCASIA.2005.96
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