{"title":"平行位置权重矩阵算法","authors":"Mathieu Giraud, Jean-Stéphane Varré","doi":"10.1109/ISPDC.2009.31","DOIUrl":null,"url":null,"abstract":"Position Weight Matrices (PWMs) are broadly used in computational biology. The basic problem, SCAN, aims to find the occurrences of a given PWM in large sequences. Some other PWM tasks share a common NP-hard subproblem, SCOREDISTRIBUTION. The existing algorithms rely on the enumeration on a large set of scores or words, and they are mostly not suitable for parallelization.We propose a new algorithm, BUCKETSCOREDISTRIBUTION, that is both very efficient and suitable for parallelization.We bound the error induced by this algorithm. We realized a GPU prototype for SCAN and BUCKETSCOREDISTRIBUTION with the CUDA libraries, and report for the different problems speedups of 21x and 77x on a Nvidia GTX 280.","PeriodicalId":226126,"journal":{"name":"2009 Eighth International Symposium on Parallel and Distributed Computing","volume":"90 3 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2009-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"12","resultStr":"{\"title\":\"Parallel Position Weight Matrices Algorithms\",\"authors\":\"Mathieu Giraud, Jean-Stéphane Varré\",\"doi\":\"10.1109/ISPDC.2009.31\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Position Weight Matrices (PWMs) are broadly used in computational biology. The basic problem, SCAN, aims to find the occurrences of a given PWM in large sequences. Some other PWM tasks share a common NP-hard subproblem, SCOREDISTRIBUTION. The existing algorithms rely on the enumeration on a large set of scores or words, and they are mostly not suitable for parallelization.We propose a new algorithm, BUCKETSCOREDISTRIBUTION, that is both very efficient and suitable for parallelization.We bound the error induced by this algorithm. We realized a GPU prototype for SCAN and BUCKETSCOREDISTRIBUTION with the CUDA libraries, and report for the different problems speedups of 21x and 77x on a Nvidia GTX 280.\",\"PeriodicalId\":226126,\"journal\":{\"name\":\"2009 Eighth International Symposium on Parallel and Distributed Computing\",\"volume\":\"90 3 1\",\"pages\":\"0\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2009-06-30\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"12\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"2009 Eighth International Symposium on Parallel and Distributed Computing\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1109/ISPDC.2009.31\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"2009 Eighth International Symposium on Parallel and Distributed Computing","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1109/ISPDC.2009.31","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Position Weight Matrices (PWMs) are broadly used in computational biology. The basic problem, SCAN, aims to find the occurrences of a given PWM in large sequences. Some other PWM tasks share a common NP-hard subproblem, SCOREDISTRIBUTION. The existing algorithms rely on the enumeration on a large set of scores or words, and they are mostly not suitable for parallelization.We propose a new algorithm, BUCKETSCOREDISTRIBUTION, that is both very efficient and suitable for parallelization.We bound the error induced by this algorithm. We realized a GPU prototype for SCAN and BUCKETSCOREDISTRIBUTION with the CUDA libraries, and report for the different problems speedups of 21x and 77x on a Nvidia GTX 280.
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