{"title":"An optimized Parallel Failure-less Aho-Corasick algorithm for DNA sequence matching","authors":"Vajira Lasantha Thambawita, R. Ragel, D. Elkaduwe","doi":"10.1109/ICIAFS.2016.7946533","DOIUrl":null,"url":null,"abstract":"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.","PeriodicalId":237290,"journal":{"name":"2016 IEEE International Conference on Information and Automation for Sustainability (ICIAfS)","volume":"7 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"2","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"2016 IEEE International Conference on Information and Automation for Sustainability (ICIAfS)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1109/ICIAFS.2016.7946533","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 2
Abstract
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.
京公网安备 11010802042870号
京ICP备2023020795号-1
分享
求助内容：
应助结果提醒方式：
扫码关注我们
