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arXiv · 1811.10498

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

Vajira Thambawita·Roshan G. Ragel·Dhammike Elkaduwe
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Abstract

The Aho-Corasick algorithm is 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 doesn't need failure links like in the original Aho-Corasick algorithm. In this research, we implemented an application specific parallel failureless Aho-Corasick algorithm to the general purpose graphics 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 graphics processing units for matching DNA sequences.

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Vajira Thambawita, Roshan G. Ragel, Dhammike Elkaduwe. 2018-11-26. An optimized Parallel Failure-less Aho-Corasick algorithm for DNA sequence matching. https://doi.org/10.1109/iciafs.2016.7946533

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