FPGA-accelerated seed generation in Mercury BLASTP

Shinohara, Hiroshi; Monji, Hideaki; Iida, Masahiro; Sueyoshi, Toshinori

doi:10.1109/fccm.2007.11

Cited by 24 publications

(24 citation statements)

References 11 publications

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“…活的算法适应性和较低的硬件代价成为理想的算法加速平台。为了提高搜索效率，基于 FPGA 平台的并行 BLAST 算法成为研究热点。近年来备受关注的研究成果有 Mercury BLASTn [9]- [11]、 Mercury BLASTp [12]、RC-BLAST [13]、Tree-BLAST [14]、FPGA/FLASH [15]、Multi-engine BLASTn [16] …”

Section: Fpga (Field Programmable Gate Array)器件以其可编程特性、细粒度并行能力、丰富的计算资源、灵unclassified

The Research on BLAST Accelerator with Parallel Multi-Seeds Detection and Extension

夏飞¹,

金国庆²,

张春雷³

2015

HJCB

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BLAST adopts index-based approach to detect the matches between two substrings by looking up a large table and processing one match per query. In this paper, we propose a systolic array approach to detect string matches without using looking up tables. The pipelining systolic array is implemented as a multi-seeds detection and parallel extension engine to accelerate the first two stages of NCBI BLAST algorithm. Different from the index-based approach, our implementation consumes little memory resources and eliminates redundant string extensions. Our FPGA implementation achieves superior performance results in both of processing element number and clock frequency over related works in the area of FPGA BLAST accelerators. The experimental results show a speedup factor of more than 20× over the NCBI BLAST software running on a current mainstream PC platform.

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Section: Fpga (Field Programmable Gate Array)器件以其可编程特性、细粒度并行能力、丰富的计算资源、灵unclassified

The Research on BLAST Accelerator with Parallel Multi-Seeds Detection and Extension

夏飞¹,

金国庆²,

张春雷³

2015

HJCB

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“…Although the subsequent algorithms can be even faster BLAST is mostly used. Many attempts have been made in the last decade to design and develop new BLAST software tools for specific hardware (Fei et al, 2008;Jacob et al, 2007;Sotiriades and Dollas, 2007;Zhang et al, 2000) or even for parallel supercomputers (Lin et al, 2008). Unfortunately, most of the researchers do not have access to these hardware platforms.…”

Section: Issn: 2320-5407mentioning

confidence: 99%

Protein Sequence Alignment Analysis Using Gpu Accelerated Based Tools for Human Genome.

Mary¹,

Babu²

2016

IJAR

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“…Word Matching is accelerated in [56] and Gapped Extension is accelerated with Smith-Waterman in [57]. Finally, [58] presents a full acceleration of BLASTp where all the previous efforts are combined to deliver a full implementation.…”

Section: B Database Searchmentioning

confidence: 99%

Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts

Liu

Luk

2017

2017 27th International Conference on Field Programmable Logic and Applications (FPL)

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Abstract-Genetic sequence alignment has always been a computational challenge in bioinformatics. Depending on the problem size, software-based aligners can take multiple CPUdays to process the sequence data, creating a bottleneck point in bioinformatic analysis flow. Reconfigurable accelerator can achieve high performance for such computation by providing massive parallelism, but at the expense of programming flexibility and thus has not been commensurately used by practitioners. Therefore, this paper aims to provide a thorough survey of the proposed accelerators by giving a qualitative categorization based on their algorithms and speedup. A comprehensive comparison between work is also presented so as to guide selection for biologist, and to provide insight on future research direction for FPGA scientists.

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FPGA-accelerated seed generation in Mercury BLASTP

Cited by 24 publications

References 11 publications

The Research on BLAST Accelerator with Parallel Multi-Seeds Detection and Extension

The Research on BLAST Accelerator with Parallel Multi-Seeds Detection and Extension

Protein Sequence Alignment Analysis Using Gpu Accelerated Based Tools for Human Genome.

Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts

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