An optimized Parallel Failure-less Aho-Corasick algorithm for DNA sequence matching
D.R.V.L.B Thambawita, Roshan G. Ragel, Dhammike Elkaduwe · 2016
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.