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Single Pass Streaming BLAST on FPGAs.
Parallel Computing ( IF 1.4 ) Pub Date : 2007-11-01 , DOI: 10.1016/j.parco.2007.09.003
Martin C Herbordt 1 , Josh Model , Bharat Sukhwani , Yongfeng Gu , Tom Vancourt
Affiliation  

Approximate string matching is fundamental to bioinformatics and has been the subject of numerous FPGA acceleration studies. We address issues with respect to FPGA implementations of both BLAST- and dynamic-programming- (DP) based methods. Our primary contribution is a new algorithm for emulating the seeding and extension phases of BLAST. This operates in a single pass through a database at streaming rate, and with no preprocessing other than loading the query string. Moreover, it emulates parameters turned to maximum possible sensitivity with no slowdown. While current DP-based methods also operate at streaming rate, generating results can be cumbersome. We address this with a new structure for data extraction. We present results from several implementations showing order of magnitude acceleration over serial reference code. A simple extension assures compatibility with NCBI BLAST.

中文翻译:

FPGA 上的单通道流 BLAST。

近似字符串匹配是生物信息学的基础,也是众多 FPGA 加速研究的主题。我们解决了基于 BLAST 和动态编程 (DP) 方法的 FPGA 实现问题。我们的主要贡献是一种用于模拟 BLAST 的播种和扩展阶段的新算法。这在以流速率通过数据库的单次传递中操作,并且除了加载查询字符串之外没有任何预处理。此外,它模拟参数达到最大可能的灵敏度而不会减速。虽然当前基于 DP 的方法也以流速率运行,但生成结果可能很麻烦。我们用一种新的数据提取结构来解决这个问题。我们展示了几个实现的结果,显示了串行参考代码的数量级加速。
更新日期:2019-11-01
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