水星BLASTP：加速蛋白质序列比对
Mercury BLASTP: Accelerating Protein Sequence Alignment.
作者信息
Jacob Arpith, Lancaster Joseph, Buhler Jeremy, Harris Brandon, Chamberlain Roger D
机构信息
Dept. of Computer Science and Engineering, Washington University in St. Louis.
出版信息
ACM Trans Reconfigurable Technol Syst. 2008 Jun;1(2):9. doi: 10.1145/1371579.1371581.
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 paper, 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.
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是蛋白质序列比较分析中最常用的工具。近年来，蛋白质序列数据库规模呈指数级增长，这要么需要指数级增长的运行时间，要么需要一组机器才能跟上。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BLASTP，即Mercury BLASTP。在本文中，我们描述了在FPGA中加速的应用程序部分的架构，还描述了这些FPGA加速部分与现有BLASTP软件的集成。我们在配备两个Xilinx Virtex-II 6000 FPGA的商用工作站上实现了Mercury BLASTP。我们表明，新设计在现代CPU上的运行速度比软件BLASTP快11至15倍，同时提供接近99%的相同结果。
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