{"title":"gpu上Zuker算法的优化","authors":"Amik Singh, M. Miśra","doi":"10.1109/PDCAT.2017.00048","DOIUrl":null,"url":null,"abstract":"Prediction of ribonucleic acid (RNA) secondary structure is one of the most important research areas in bioinformatics. The Zuker algorithm is one of the most popular methods of free energy minimization for RNA secondary structure prediction. We present a novel algorithm to optimize Zuker Algorithm on CUDA GPUs and achieve a speedup of ∼10x for certain viruses.","PeriodicalId":119197,"journal":{"name":"2017 18th International Conference on Parallel and Distributed Computing, Applications and Technologies (PDCAT)","volume":"33 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Optimization of Zuker Algorithm on GPUs\",\"authors\":\"Amik Singh, M. Miśra\",\"doi\":\"10.1109/PDCAT.2017.00048\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Prediction of ribonucleic acid (RNA) secondary structure is one of the most important research areas in bioinformatics. The Zuker algorithm is one of the most popular methods of free energy minimization for RNA secondary structure prediction. We present a novel algorithm to optimize Zuker Algorithm on CUDA GPUs and achieve a speedup of ∼10x for certain viruses.\",\"PeriodicalId\":119197,\"journal\":{\"name\":\"2017 18th International Conference on Parallel and Distributed Computing, Applications and Technologies (PDCAT)\",\"volume\":\"33 1\",\"pages\":\"0\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2017-12-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"2017 18th International Conference on Parallel and Distributed Computing, Applications and Technologies (PDCAT)\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1109/PDCAT.2017.00048\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"2017 18th International Conference on Parallel and Distributed Computing, Applications and Technologies (PDCAT)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1109/PDCAT.2017.00048","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Prediction of ribonucleic acid (RNA) secondary structure is one of the most important research areas in bioinformatics. The Zuker algorithm is one of the most popular methods of free energy minimization for RNA secondary structure prediction. We present a novel algorithm to optimize Zuker Algorithm on CUDA GPUs and achieve a speedup of ∼10x for certain viruses.