{"title":"基于FPGA的序列对齐优化:以扩展序列对齐为例(仅摘要)","authors":"Zheming Jin, Kazutomo Yoshii","doi":"10.1145/3174243.3174958","DOIUrl":null,"url":null,"abstract":"Detecting similarities between sequences is an important part of Bioinformatics. In this poster, we explore the use of high-level synthesis tool and a field-programmable gate array (FPGA) for optimizing a sequence alignment algorithm. We demonstrate the optimization techniques to improve the performance of the extended sequence alignment algorithm in the BWA software package, a tool for mapping DNA sequences against a large reference sequence. Applying the optimizations to the algorithm using Xilinx SDAccel OpenCL-to-FPGA tool, we reduce the kernel execution time from 62.8 ms to 0.45 ms while the power consumption is approximately 11 Watts on the ADM-PCIE-8K5 FPGA platform.","PeriodicalId":164936,"journal":{"name":"Proceedings of the 2018 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays","volume":"17 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2018-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Optimizations of Sequence Alignment on FPGA: A Case Study of Extended Sequence Alignment (Abstact Only)\",\"authors\":\"Zheming Jin, Kazutomo Yoshii\",\"doi\":\"10.1145/3174243.3174958\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Detecting similarities between sequences is an important part of Bioinformatics. In this poster, we explore the use of high-level synthesis tool and a field-programmable gate array (FPGA) for optimizing a sequence alignment algorithm. We demonstrate the optimization techniques to improve the performance of the extended sequence alignment algorithm in the BWA software package, a tool for mapping DNA sequences against a large reference sequence. Applying the optimizations to the algorithm using Xilinx SDAccel OpenCL-to-FPGA tool, we reduce the kernel execution time from 62.8 ms to 0.45 ms while the power consumption is approximately 11 Watts on the ADM-PCIE-8K5 FPGA platform.\",\"PeriodicalId\":164936,\"journal\":{\"name\":\"Proceedings of the 2018 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays\",\"volume\":\"17 1\",\"pages\":\"0\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2018-02-15\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Proceedings of the 2018 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1145/3174243.3174958\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Proceedings of the 2018 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1145/3174243.3174958","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Optimizations of Sequence Alignment on FPGA: A Case Study of Extended Sequence Alignment (Abstact Only)
Detecting similarities between sequences is an important part of Bioinformatics. In this poster, we explore the use of high-level synthesis tool and a field-programmable gate array (FPGA) for optimizing a sequence alignment algorithm. We demonstrate the optimization techniques to improve the performance of the extended sequence alignment algorithm in the BWA software package, a tool for mapping DNA sequences against a large reference sequence. Applying the optimizations to the algorithm using Xilinx SDAccel OpenCL-to-FPGA tool, we reduce the kernel execution time from 62.8 ms to 0.45 ms while the power consumption is approximately 11 Watts on the ADM-PCIE-8K5 FPGA platform.