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使用GPU加速BLAST算法初探 被引量:3

A Preliminary Exploration on Parallelized BLAST Algorithm Using GPU
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摘要 应用GPU通用高性能编程技术实现了一种加速BLAST算法的新方法。BLAST是目前最常用的用于生物序列查询比对的算法和软件包,其处理速度受到串行化执行和磁盘I/O等因素的影响。本文通过实验分析了BLAST软件包中的典型程序BLASTN的运行热点,并选定关键热点模块,应用CUDA编程技术对其进行并行化改造。对比实验结果表明,对于平均序列长度较大的序列库,应用GPGPU并行化可明显缩短该模块的运行时间,获得超过35倍的加速比。这说明,我们可以利用GPGPU对BLAST进行并行化加速,以满足高性能生物序列查询的需求。 In this article we present a novel approach to accelerating the BLAST algorithm by using the GPGPU technology. BLAST is the most widely used algorithm and software package for biological sequence search. It is, however, limited by serial process and heavy disk I/O operation. We analyze BLASTN, a typical BLAST tool, identify the most important hotspot of BLASTN, and use CUDA to reprogram the hotspot process. Our test results show that more than 35 times speedup has been achieved in the GPU BLASTN as compared to the CPU counterpart, which demonstrates the significance of parallelizing the BLAST algorithm using the GPGPU technology.
出处 《计算机工程与科学》 CSCD 北大核心 2009年第11期98-101,共4页 Computer Engineering & Science
基金 国家973计划资助项目(2006CB910400) 中国科学院重大科研装备研制项目(YZ200823)
关键词 BLAST BLASTN 序列查询比对 GPU GPGPU CUDA 并行计算 BLAST BLASTN Sequence query and alignment GPU GPGPU CUDA parallel computing
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参考文献14

  • 1Altsehul S F, Gish W, Miller W, et al. Basic Local Alignment Search Tool[J]. Journal of Moleeular Biology, 1990, 215(3) :403-410.
  • 2Altschul S F, Madden T L, Sehaffer A A, et al. Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs[J]. Nucleic Acids Research, 1997,25 (17) : 3389-3402.
  • 3http://blast. wustl. edu.
  • 4http://www. mpiblast. org.
  • 5Lin H,Ma X, Chandramohan P, et al. Effcient Data Access for Parallel Blast[C]//Proc of Int'l Parallel and Distributed Processing Symp, 2005:726-726.
  • 6Rangwala H, Lantz E, Musselman R, et al. Massively Parallel BLAST for the Blue Gene/L[C]//Proc of High Availability and Performance Workshop, 2005.
  • 7谭光明,徐琳,周幼英,冯圣中,孙凝晖.基于曙光4000A的BLAST并行算法[J].计算机工程,2006,32(10):45-46. 被引量:2
  • 8http://www. timelogic. com/decypher_blast. htmt.
  • 9http://www. clearspeed. com/.
  • 10http://www. amd. com/US/PRODUCTS/TECHNOLOGIES/STREAM-TECHNOLOGY/Pages/stream-technology. aspx.

二级参考文献5

  • 1Altschul S F,Gish W,Miller W,et al.Basic Local Alignment Search Tool[J].Journal of Molecular Biology,1990,215(3):403-410.
  • 2Darling A E,Carey L,Feng Wuchun.The Design,Implementation,and Evaluation of MpiBlast[C].Cluster World Conference & Expo in Conjunction with the 4th International Conference on Linux Clusters:The HPC Revolution,2003-06.
  • 3Tao Jiang,Xu Ying,Zhang M Q.Current Topics in Computational Molecular Biology[D].Beijing:Tsinghua University,2002.
  • 4Grama A,Gupta A,Karypis G,et al.Introduction to Parallel Computing(Second Edition)[M].Addison Wesley,2003.
  • 5Galison F.The Fasta and Blast Programs[Z].http://bioweb.pasteur.fr/seqanal/blast/,2000.

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同被引文献42

  • 1谭光明,徐琳,周幼英,冯圣中,孙凝晖.基于曙光4000A的BLAST并行算法[J].计算机工程,2006,32(10):45-46. 被引量:2
  • 2林皎,陈文光,栗强,郑纬民,张益民.基于图划分的全基因组并行拼接算法[J].计算机研究与发展,2006,43(8):1323-1329. 被引量:5
  • 3Blackstock W P, Weir M P. Proteomics: quantitative and physi- cal mapping of cellular proteins I-J]. Trends Biotechnology, 1999,17(3) : 121-127.
  • 4Leptos K C, Sarracino D A, Jaffe J D, et al. MapQuant: open- source software for large-scale protein quantitation I-J]. Pro- teomics, 2006,6(6) .. 1770-1782.
  • 5Mueller L N, Rinner O, Schmidt A, et al. SuperHim-a novel tool for high resolution LC-MS based peptide/protein profiling[J]. Proteomics, 2007,7(19) : 3470-3480.
  • 6Sturm M, Bertsch A, Groepl C, et al. OpenMS-An open-source software framework for mass spectrometry[-J]. BMC Bioinfor- matics, 2008,9(1) : 163-173.
  • 7Park S K, Venable J D, Xu T, et al. A quantitative analysis soft- ware tool for mass spectrometry-based proteomics [-J ]. Nat Methods, 2008,5 .. 319-322.
  • 8Top500 supercomputer sites[-EB/OL, http://www, topS00, org.
  • 9Smith TF, Waterman MS. Identification of common molecular subsequences [J]. J Mol Biol, 1981, 147(1):195 -197.
  • 10Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool [J]. J Mol Biol, 1990, 215(3) :403 -410.

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