Trade-offs between the sensitivity and the speed of the FPGA-based sequence aligner

Peng Chen; Chao Wang; Xi Li; Xuehai Zhou; Aili Wang; Ray C.C. Cheung

doi:10.1109/ISICIR.2014.7029587

Trade-offs between the sensitivity and the speed of the FPGA-based sequence aligner

Peng Chen
, Chao Wang
, Xi Li
, Xuehai Zhou
, Aili Wang
, Ray C.C. Cheung

Department of Electrical Engineering

Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

Abstract

Sequence alignment has attracted many attentions from various aspects of research domains, including architectures, algorithms, and applications. However, due to the tremendous computing and engineering efforts, it is reasonable and acceptable to reduce the sensitivity of the methodology, in order to maintain a satisfying speed. In this paper, we propose a PC-FPGA hybrid system to evaluate and analyze the trade-offs between the sensitivity and the speed of the FPGA-based sequence aligner. With respect to the reconfiguration and adaptation abilities, the FPGA board is able to provide fast prototyping system with different configurations. Experimental results on the FPGA prototype depicts the quantitative analysis of the trade-offs between the sensitivity and the speed.

Original language	English
Title of host publication	Proceedings of the 14th International Symposium on Integrated Circuits, ISIC 2014
Publisher	IEEE
Pages	280-283
ISBN (Print)	9781479948338
DOIs	https://doi.org/10.1109/ISICIR.2014.7029587
Publication status	Published - 2 Feb 2015
Event	14th International Symposium on Integrated Circuits, ISIC 2014 - Singapore, Singapore Duration: 10 Dec 2014 → 12 Dec 2014

Conference

Conference	14th International Symposium on Integrated Circuits, ISIC 2014
Place	Singapore
City	Singapore
Period	10/12/14 → 12/12/14

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 9 Industry, Innovation, and Infrastructure

Research Keywords

Genome Alignment
Sensitivity
Trade-off

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10.1109/ISICIR.2014.7029587

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title = "Trade-offs between the sensitivity and the speed of the FPGA-based sequence aligner",

abstract = "Sequence alignment has attracted many attentions from various aspects of research domains, including architectures, algorithms, and applications. However, due to the tremendous computing and engineering efforts, it is reasonable and acceptable to reduce the sensitivity of the methodology, in order to maintain a satisfying speed. In this paper, we propose a PC-FPGA hybrid system to evaluate and analyze the trade-offs between the sensitivity and the speed of the FPGA-based sequence aligner. With respect to the reconfiguration and adaptation abilities, the FPGA board is able to provide fast prototyping system with different configurations. Experimental results on the FPGA prototype depicts the quantitative analysis of the trade-offs between the sensitivity and the speed.",

keywords = "Genome Alignment, Sensitivity, Trade-off",

author = "Peng Chen and Chao Wang and Xi Li and Xuehai Zhou and Aili Wang and Cheung, \{Ray C.C.\}",

year = "2015",

month = feb,

day = "2",

doi = "10.1109/ISICIR.2014.7029587",

language = "English",

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pages = "280--283",

booktitle = "Proceedings of the 14th International Symposium on Integrated Circuits, ISIC 2014",

publisher = "IEEE",

address = "United States",

note = "14th International Symposium on Integrated Circuits, ISIC 2014 ; Conference date: 10-12-2014 Through 12-12-2014",

}

Chen, P, Wang, C, Li, X, Zhou, X, Wang, A & Cheung, RCC 2015, Trade-offs between the sensitivity and the speed of the FPGA-based sequence aligner. in Proceedings of the 14th International Symposium on Integrated Circuits, ISIC 2014., 7029587, IEEE, pp. 280-283, 14th International Symposium on Integrated Circuits, ISIC 2014, Singapore, Singapore, 10/12/14. https://doi.org/10.1109/ISICIR.2014.7029587

Trade-offs between the sensitivity and the speed of the FPGA-based sequence aligner. / Chen, Peng; Wang, Chao; Li, Xi et al.
Proceedings of the 14th International Symposium on Integrated Circuits, ISIC 2014. IEEE, 2015. p. 280-283 7029587.

Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

TY - GEN

T1 - Trade-offs between the sensitivity and the speed of the FPGA-based sequence aligner

AU - Chen, Peng

AU - Wang, Chao

AU - Li, Xi

AU - Zhou, Xuehai

AU - Wang, Aili

AU - Cheung, Ray C.C.

PY - 2015/2/2

Y1 - 2015/2/2

N2 - Sequence alignment has attracted many attentions from various aspects of research domains, including architectures, algorithms, and applications. However, due to the tremendous computing and engineering efforts, it is reasonable and acceptable to reduce the sensitivity of the methodology, in order to maintain a satisfying speed. In this paper, we propose a PC-FPGA hybrid system to evaluate and analyze the trade-offs between the sensitivity and the speed of the FPGA-based sequence aligner. With respect to the reconfiguration and adaptation abilities, the FPGA board is able to provide fast prototyping system with different configurations. Experimental results on the FPGA prototype depicts the quantitative analysis of the trade-offs between the sensitivity and the speed.

AB - Sequence alignment has attracted many attentions from various aspects of research domains, including architectures, algorithms, and applications. However, due to the tremendous computing and engineering efforts, it is reasonable and acceptable to reduce the sensitivity of the methodology, in order to maintain a satisfying speed. In this paper, we propose a PC-FPGA hybrid system to evaluate and analyze the trade-offs between the sensitivity and the speed of the FPGA-based sequence aligner. With respect to the reconfiguration and adaptation abilities, the FPGA board is able to provide fast prototyping system with different configurations. Experimental results on the FPGA prototype depicts the quantitative analysis of the trade-offs between the sensitivity and the speed.

KW - Genome Alignment

KW - Sensitivity

KW - Trade-off

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U2 - 10.1109/ISICIR.2014.7029587

DO - 10.1109/ISICIR.2014.7029587

M3 - RGC 32 - Refereed conference paper (with host publication)

SN - 9781479948338

SP - 280

EP - 283

BT - Proceedings of the 14th International Symposium on Integrated Circuits, ISIC 2014

PB - IEEE

T2 - 14th International Symposium on Integrated Circuits, ISIC 2014

Y2 - 10 December 2014 through 12 December 2014

ER -

Trade-offs between the sensitivity and the speed of the FPGA-based sequence aligner

Abstract

Conference

UN SDGs

Research Keywords

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