DNA序列匹配的优化并行无故障Aho-Corasick算法

2016 IEEE International Conference on Information and Automation for Sustainability (ICIAfS) Pub Date : 2016-12-01 DOI:10.1109/ICIAFS.2016.7946533

Vajira Lasantha Thambawita, R. Ragel, D. Elkaduwe

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引用次数: 2

摘要

ho- corasick算法是一种顺序运行的多模式搜索算法，用于在给定的大输入字符串中查找多个输入字符串，如网络入侵检测和生物信息学。Aho-Corasick算法的并行版本被称为并行无故障Aho-Corasick算法，因为它不像原来的Aho-Corasick算法那样需要故障链接。在本研究中，我们通过应用几种匹配DNA序列的缓存优化技术，在通用图形处理单元上实现了一种特定应用的并行无故障Aho-Corasick算法。我们的并行Aho-Corasick算法由于其简单性和优化的DNA序列匹配图形处理单元的缓存使用，比现有的并行Aho-Corasick算法库表现出更好的性能。

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An optimized Parallel Failure-less Aho-Corasick algorithm for DNA sequence matching

The Aho-Corasick algorithm is a multiple patterns searching algorithm running sequentially in various applications like network intrusion detection and bioinformatics for finding several input strings within a given large input string. The parallel version of the Aho-Corasick algorithm is called as Parallel Failure-less Aho-Corasick algorithm because it doesnt need failure links like in the original Aho-Corasick algorithm. In this research, we implemented an application specific parallel failureless Aho-Corasick algorithm on the general purpose graphic processing unit by applying several cache optimization techniques for matching DNA sequences. Our parallel Aho-Corasick algorithm shows better performance than the available parallel Aho-Corasick algorithm library due to its simplicity and optimized cache memory usage of graphic processing units for matching DNA sequences.

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来源期刊

2016 IEEE International Conference on Information and Automation for Sustainability (ICIAfS)

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