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Mercury BLASTP
ACM Transactions on Reconfigurable Technology and Systems ( IF 2.3 ) Pub Date : 2009-01-13 , DOI: 10.1145/1371579.1371581 Arpith Jacob 1 , Joseph Lancaster , Jeremy Buhler , Brandon Harris , Roger D Chamberlain
ACM Transactions on Reconfigurable Technology and Systems ( IF 2.3 ) Pub Date : 2009-01-13 , DOI: 10.1145/1371579.1371581 Arpith Jacob 1 , Joseph Lancaster , Jeremy Buhler , Brandon Harris , Roger D Chamberlain
Affiliation
Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more running time or a cluster of machines to keep pace. To address this problem, we have designed and built a high-performance FPGA-accelerated version of BLASTP, Mercury BLASTP . In this article, we describe the architecture of the portions of the application that are accelerated in the FPGA, and we also describe the integration of these FPGA-accelerated portions with the existing BLASTP software. We have implemented Mercury BLASTP on a commodity workstation with two Xilinx Virtex-II 6000 FPGAs. We show that the new design runs 11--15 times faster than software BLASTP on a modern CPU while delivering close to 99% identical results.
中文翻译:
水星爆炸
大规模蛋白质序列比较是分子生物学中一项重要但计算密集型的任务。BLASTP 是最流行的蛋白质序列比较分析工具。近年来,蛋白质序列数据库的规模呈指数增长,需要更多的运行时间或一组机器才能跟上步伐。为了解决这个问题,我们设计并构建了一个高性能的 FPGA 加速版本的 BLASTP,水星爆炸 . 在本文中,我们描述了在 FPGA 中加速的应用程序部分的架构,并且我们还描述了这些 FPGA 加速部分与现有 BLASTP 软件的集成。我们在带有两个 Xilinx Virtex-II 6000 FPGA 的商品工作站上实施了 Mercury BLASTP。我们展示了新设计在现代 CPU 上的运行速度比软件 BLASTP 快 11--15 倍,同时提供接近 99% 的相同结果。
更新日期:2009-01-13
中文翻译:
水星爆炸
大规模蛋白质序列比较是分子生物学中一项重要但计算密集型的任务。BLASTP 是最流行的蛋白质序列比较分析工具。近年来,蛋白质序列数据库的规模呈指数增长,需要更多的运行时间或一组机器才能跟上步伐。为了解决这个问题,我们设计并构建了一个高性能的 FPGA 加速版本的 BLASTP,