{"title":"DNA序列匹配的优化并行无故障Aho-Corasick算法","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":"{\"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}","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}
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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