Ye Weicai, Chen Ying, Zhang Yongdong, Xu Yuesheng
School of Data and Computer Science, and Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, People's Republic of China.
Professor Emeritus of Department of Mathematics, Syracuse University, Syracuse, NY 13244, USA.
Bioinformatics. 2017 Apr 15;33(8):1130-1138. doi: 10.1093/bioinformatics/btw769.
The sequence alignment is a fundamental problem in bioinformatics. BLAST is a routinely used tool for this purpose with over 118 000 citations in the past two decades. As the size of bio-sequence databases grows exponentially, the computational speed of alignment softwares must be improved.
We develop the heterogeneous BLAST (H-BLAST), a fast parallel search tool for a heterogeneous computer that couples CPUs and GPUs, to accelerate BLASTX and BLASTP-basic tools of NCBI-BLAST. H-BLAST employs a locally decoupled seed-extension algorithm for better performance on GPUs, and offers a performance tuning mechanism for better efficiency among various CPUs and GPUs combinations. H-BLAST produces identical alignment results as NCBI-BLAST and its computational speed is much faster than that of NCBI-BLAST. Speedups achieved by H-BLAST over sequential NCBI-BLASTP (resp. NCBI-BLASTX) range mostly from 4 to 10 (resp. 5 to 7.2). With 2 CPU threads and 2 GPUs, H-BLAST can be faster than 16-threaded NCBI-BLASTX. Furthermore, H-BLAST is 1.5-4 times faster than GPU-BLAST.
https://github.com/Yeyke/H-BLAST.git.
Supplementary data are available at Bioinformatics online.
序列比对是生物信息学中的一个基本问题。BLAST是为此目的经常使用的工具，在过去二十年中有超过118000次引用。随着生物序列数据库规模呈指数级增长，比对软件的计算速度必须提高。
我们开发了异构BLAST（H-BLAST），这是一种用于异构计算机的快速并行搜索工具，它结合了CPU和GPU，以加速NCBI-BLAST的BLASTX和BLASTP基本工具。H-BLAST采用局部解耦的种子扩展算法以在GPU上获得更好的性能，并提供性能调优机制以在各种CPU和GPU组合中提高效率。H-BLAST产生与NCBI-BLAST相同的比对结果，并且其计算速度比NCBI-BLAST快得多。H-BLAST相对于顺序NCBI-BLASTP（分别为NCBI-BLASTX）实现的加速比大多在4到10（分别为5到7.2）之间。使用2个CPU线程和2个GPU时，H-BLAST可以比16线程的NCBI-BLASTX更快。此外，H-BLAST比GPU-BLAST快1.5到4倍。
https://github.com/Yeyke/H-BLAST.git。
补充数据可在《生物信息学》在线获取。
