Exploring Sequence Alignment Algorithms on FPGA-based Heterogeneous Architectures

Xin Chang; Fernando A. Escobar; Carlos Valderrama; Vincent Robert

Exploring Sequence Alignment Algorithms on FPGA-based Heterogeneous Architectures

Xin Chang, Fernando A. Escobar, Carlos Valderrama, Vincent Robert

Research output: Chapter in book/volume › Contribution to conference proceedings › Scientific › peer-review

Abstract

With the rapid development of DNA sequencer, the rate of data generation is rapidly outpacing the rate at which it can be computationally processed. Traditional sequence alignment based on PC cannot fulfill the increasing demand. Accelerating the algorithm using FPGA provides the better performance compared to the other platforms. This paper will explain and classify the current sequence alignment algorithms. In addition, we analyze the different types of sequence alignment algorithms and present the taxonomy of FPGA-based sequence alignment implementations. This work will conclude the current solutions and provide a reference to further accelerating sequence alignment on a FPGA-based heterogeneous architecture.

Original language	Undefined
Title of host publication	Proceedings IWBBIO 2014
Subtitle of host publication	International Work-Conference on Bioinformatics and Biomedical Engineering
Editors	F. Ortuno, I. Rojas
Place of Publication	Granada
Pages	330-341
Number of pages	12
Volume	1&2
Publication status	Published - 2014

Keywords

Sequence Alignment Algorithm
FPGA
Heterogeneous Architectures
Systolic Array
Parallel Computation
Hardware Acceleration

Cite this

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title = "Exploring Sequence Alignment Algorithms on FPGA-based Heterogeneous Architectures",

abstract = "With the rapid development of DNA sequencer, the rate of data generation is rapidly outpacing the rate at which it can be computationally processed. Traditional sequence alignment based on PC cannot fulfill the increasing demand. Accelerating the algorithm using FPGA provides the better performance compared to the other platforms. This paper will explain and classify the current sequence alignment algorithms. In addition, we analyze the different types of sequence alignment algorithms and present the taxonomy of FPGA-based sequence alignment implementations. This work will conclude the current solutions and provide a reference to further accelerating sequence alignment on a FPGA-based heterogeneous architecture.",

keywords = "Sequence Alignment Algorithm, FPGA, Heterogeneous Architectures, Systolic Array, Parallel Computation, Hardware Acceleration",

author = "Xin Chang and Escobar, {Fernando A.} and Carlos Valderrama and Vincent Robert",

note = "2nd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO), Granada, SPAIN, APR 07-09, 2014",

year = "2014",

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isbn = "978-84-15814-84-9",

volume = "1&2",

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Exploring Sequence Alignment Algorithms on FPGA-based Heterogeneous Architectures. / Chang, Xin; Escobar, Fernando A.; Valderrama, Carlos; Robert, Vincent.

Proceedings IWBBIO 2014: International Work-Conference on Bioinformatics and Biomedical Engineering. ed. / F. Ortuno; I. Rojas. Vol. 1&2 Granada, 2014. p. 330-341.

Research output: Chapter in book/volume › Contribution to conference proceedings › Scientific › peer-review

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T1 - Exploring Sequence Alignment Algorithms on FPGA-based Heterogeneous Architectures

AU - Chang, Xin

AU - Escobar, Fernando A.

AU - Valderrama, Carlos

AU - Robert, Vincent

N1 - 2nd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO), Granada, SPAIN, APR 07-09, 2014

PY - 2014

Y1 - 2014

N2 - With the rapid development of DNA sequencer, the rate of data generation is rapidly outpacing the rate at which it can be computationally processed. Traditional sequence alignment based on PC cannot fulfill the increasing demand. Accelerating the algorithm using FPGA provides the better performance compared to the other platforms. This paper will explain and classify the current sequence alignment algorithms. In addition, we analyze the different types of sequence alignment algorithms and present the taxonomy of FPGA-based sequence alignment implementations. This work will conclude the current solutions and provide a reference to further accelerating sequence alignment on a FPGA-based heterogeneous architecture.

AB - With the rapid development of DNA sequencer, the rate of data generation is rapidly outpacing the rate at which it can be computationally processed. Traditional sequence alignment based on PC cannot fulfill the increasing demand. Accelerating the algorithm using FPGA provides the better performance compared to the other platforms. This paper will explain and classify the current sequence alignment algorithms. In addition, we analyze the different types of sequence alignment algorithms and present the taxonomy of FPGA-based sequence alignment implementations. This work will conclude the current solutions and provide a reference to further accelerating sequence alignment on a FPGA-based heterogeneous architecture.

KW - Sequence Alignment Algorithm

KW - FPGA

KW - Heterogeneous Architectures

KW - Systolic Array

KW - Parallel Computation

KW - Hardware Acceleration

M3 - Bijdrage aan conferentie proceedings

SN - 978-84-15814-84-9

VL - 1&2

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BT - Proceedings IWBBIO 2014

A2 - Ortuno, F.

A2 - Rojas, I.

CY - Granada

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