Name
Title | ||
|---|---|---|
Optimizations of Sequence Alignment on FPGA: A Case Study of Extended Sequence Alignment (Abstact Only). |
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.
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Year | Venue | Field |
|---|---|---|
2018 | FPGA | Sequence alignment,Kernel (linear algebra),Computer science,Parallel computing,Field-programmable gate array,Software,Gate array,Execution time,Reference genome,Power consumption |
DocType | ISBN | Citations |
Conference | 978-1-4503-5614-5 | 0 |
PageRank | References | Authors |
0.34 | 0 | 2 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Zheming Jin | 1 | 17 | 11.95 |
| Kazutomo Yoshii | 2 | 249 | 18.53 |