{"title":"gpu上超长序列的成对序列对齐。","authors":"Junjie Li, Sanjay Ranka, Sartaj Sahni","doi":"10.1109/ICCABS.2012.6182641","DOIUrl":null,"url":null,"abstract":"<p><p>We develop novel single-GPU parallelizations of the Smith-Waterman algorithm for pairwise sequence alignment. Our algorithms, which are suitable for the alignment of a single pair of very long sequences, can be used to determine the alignment score as well as the actual alignment. Experimental results demonstrate an order of magnitude reduction in run time relative to competing GPU algorithms.</p>","PeriodicalId":89933,"journal":{"name":"IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences","volume":" ","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/ICCABS.2012.6182641","citationCount":"22","resultStr":"{\"title\":\"Pairwise Sequence Alignment for Very Long Sequences on GPUs.\",\"authors\":\"Junjie Li, Sanjay Ranka, Sartaj Sahni\",\"doi\":\"10.1109/ICCABS.2012.6182641\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>We develop novel single-GPU parallelizations of the Smith-Waterman algorithm for pairwise sequence alignment. Our algorithms, which are suitable for the alignment of a single pair of very long sequences, can be used to determine the alignment score as well as the actual alignment. Experimental results demonstrate an order of magnitude reduction in run time relative to competing GPU algorithms.</p>\",\"PeriodicalId\":89933,\"journal\":{\"name\":\"IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2012-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://sci-hub-pdf.com/10.1109/ICCABS.2012.6182641\",\"citationCount\":\"22\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1109/ICCABS.2012.6182641\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1109/ICCABS.2012.6182641","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Pairwise Sequence Alignment for Very Long Sequences on GPUs.
We develop novel single-GPU parallelizations of the Smith-Waterman algorithm for pairwise sequence alignment. Our algorithms, which are suitable for the alignment of a single pair of very long sequences, can be used to determine the alignment score as well as the actual alignment. Experimental results demonstrate an order of magnitude reduction in run time relative to competing GPU algorithms.
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