Acceleration of Ungapped Extension in Mercury BLAST.
Acceleration of Ungapped Extension in Mercury BLAST.
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DOI：
10.1016/j.micpro.2009.02.007
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发表时间：
2009-06-01
影响因子：
2.6
通讯作者：
Chamberlain, Roger D.
中科院分区：
文献类型：
--
作者：
Lancaster, Joseph;Buhler, Jeremy;Chamberlain, Roger D.
每年产生的生物序列数据量呈指数级增长。从这些海量数据中有效地提取有用的信息正成为一项越来越困难的任务。有许多可用的软件工具，分子生物学家用于比较基因组数据。本文重点介绍加速最广泛使用的此类工具，BLAST。Mercury BLAST通过将性能关键部分卸载到专用硬件来采用流式方法进行BLAST计算。然后，该硬件与主机系统的处理器结合使用，以在单独的通用处理器的一小部分时间内提供BLAST结果。本文介绍了水星鼓风机无间隙扩展级的设计。沿着描述了无帽延伸阶段的架构以及Mercury BLAST系统中该阶段的背景。该设计结构紧凑，在可用的FPGA上以100 MHz运行，使其成为加速生物序列比较的有效和强大的组件。这个阶段的性能是标准软件发行版的25倍，在完整的BLAST应用程序上产生接近50倍的性能改进。灵敏度基本上与标准分布的灵敏度相等。
The amount of biosequence data being produced each year is growing exponentially. Extracting useful information from this massive amount of data efficiently is becoming an increasingly difficult task. There are many available software tools that molecular biologists use for comparing genomic data. This paper focuses on accelerating the most widely used such tool, BLAST. Mercury BLAST takes a streaming approach to the BLAST computation by off loading the performance-critical sections to specialized hardware. This hardware is then used in combination with the processor of the host system to deliver BLAST results in a fraction of the time of the general-purpose processor alone. This paper presents the design of the ungapped extension stage of Mercury BLAST. The architecture of the ungapped extension stage is described along with the context of this stage within the Mercury BLAST system. The design is compact and runs at 100 MHz on available FPGAs, making it an effective and powerful component for accelerating biosequence comparisons. The performance of this stage is 25× that of the standard software distribution, yielding close to 50× performance improvement on the complete BLAST application. The sensitivity is essentially equivalent to that of the standard distribution.
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影响因子：
1.7
作者：
Zhang, Z;Schwartz, S;Miller, W
通讯作者：
Miller, W
影响因子：
7
作者：
Ning, ZM;Cox, AJ;Mullikin, JC
通讯作者：
Mullikin, JC
DOI：
10.1142/s0219720004000661
发表时间：
2004-09-01
影响因子：
1
作者：
Li, Ming;Ma, Bin;Tromp, John
通讯作者：
Tromp, John
影响因子：
14.9
作者：
Altschul, SF;Madden, TL;Lipman, DJ
通讯作者：
Lipman, DJ
影响因子：
5.6
作者：
ALTSCHUL, SF;GISH, W;LIPMAN, DJ
通讯作者：
LIPMAN, DJ