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.
@article{arxiv.1811.10498,
title = {An optimized Parallel Failure-less Aho-Corasick algorithm for DNA sequence matching},
author = {Vajira Thambawita and Roshan G. Ragel and Dhammike Elkaduwe},
journal= {arXiv preprint arXiv:1811.10498},
year = {2018}
}
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6 pages, 3 figures, 4 tables, 5 graphs, 2016 IEEE International Conference on Information and Automation for Sustainability (ICIAfS)