Optimizations of Sequence Alignment on FPGA: A Case Study of Extended Sequence Alignment (Abstact Only)

Zheming Jin, Kazutomo Yoshii
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Abstract

Detecting similarities between sequences is an important part of Bioinformatics. In this poster, we explore the use of high-level synthesis tool and a field-programmable gate array (FPGA) for optimizing a sequence alignment algorithm. We demonstrate the optimization techniques to improve the performance of the extended sequence alignment algorithm in the BWA software package, a tool for mapping DNA sequences against a large reference sequence. Applying the optimizations to the algorithm using Xilinx SDAccel OpenCL-to-FPGA tool, we reduce the kernel execution time from 62.8 ms to 0.45 ms while the power consumption is approximately 11 Watts on the ADM-PCIE-8K5 FPGA platform.
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基于FPGA的序列对齐优化:以扩展序列对齐为例(仅摘要)
序列间相似性检测是生物信息学的重要组成部分。在这张海报中,我们探索了使用高级合成工具和现场可编程门阵列(FPGA)来优化序列对齐算法。我们演示了优化技术,以提高BWA软件包中的扩展序列比对算法的性能,BWA软件包是一个针对大型参考序列进行DNA序列比对的工具。使用Xilinx SDAccel OpenCL-to-FPGA工具对算法进行优化,我们将内核执行时间从62.8 ms减少到0.45 ms,而在ADM-PCIE-8K5 FPGA平台上功耗约为11瓦。
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