| 基于多核流处理器的BLAST并行化算法研究 |
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| 引用本文： | 裴颂文,王心怡,韦刚,吴百锋.基于多核流处理器的BLAST并行化算法研究[J].系统仿真学报,2011,23(10):2065-2069. |
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| 作者姓名： | 裴颂文 王心怡 韦刚 吴百锋 |
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| 作者单位： | 1. 上海理工大学计算机科学与工程系,上海,200093
2. 复旦大学计算机科学技术学院,上海,200433 |
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| 基金项目： | 上海市教委优秀青年教师基金(SLG10005); 上海理工大学教师创新基金(GDCX-Y-102) |
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| 摘 要： | 序列比对是生物信息学中最基本、最重要的操作，通过序列比对可以发现生物序列中的功能、结构和进化的信息。BLAST算法是序列比对中应用广泛的算法之一。基于多核流处理器GPU和CPU的异构乎台，提出了BLAST算法构造单词表和单词匹配扩展的并行化实现方法。实验证明构造单词表的计算性能获得3倍以上的加速比；单词匹配扩展采用的混合并行方式可以获得7倍左右的加速比，内部并行方式可取得3～4倍的加速比。
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| 关 键 词： | 序列比对 BLAST算法 生物信息学 多核流处理器 |
Research on Parallel BLAST Algorithm Based on Multi-core Stream Processors |
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| PEI Song-wen,WANG Xin-yi,WEI Gang,WU Bai-feng.Research on Parallel BLAST Algorithm Based on Multi-core Stream Processors[J].Journal of System Simulation,2011,23(10):2065-2069. |
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| Authors: | PEI Song-wen WANG Xin-yi WEI Gang WU Bai-feng |
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| Institution: | PEI Song-wen1,WANG Xin-yi1,WEI Gang2,WU Bai-feng2(1.Department of Computer Science and Engineering,University of Shanghai for Science and Technology,Shanghai 200093,China,2.School of Computer Science,Fudan University,Shanghai 200433,China) |
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| Abstract: | Sequence alignment is one of the most fundamental and important operation in bioinformatics.In terms of sequence alignment,we can find the sequence's information of function,structure and evolution.BLAST is one of the most popular algorithms in the field of sequence alignment.A parallel BLAST algorithm was proposed and implemented based on a mixed multi-core stream processors with GPUs and CPUs.The main task is to parallel the construction of words lists procedure and the match-expansion procedure.As for ma... |
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| Keywords: | sequence alignment BLAST algorithm bioinformatics multi-core stream processors |
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