CUDA performance in DNA analysis: Analysis of CUDA architecture performance in DNA analysis

Daniel Cadete; António Dos Anjos; Hamid Reza Shahbazkia; Richard Christen

CUDA performance in DNA analysis: Analysis of CUDA architecture performance in DNA analysis

Daniel Cadete^*, António Dos Anjos, Hamid Reza Shahbazkia, Richard Christen

^*Corresponding author for this work

Department of Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference Proceeding (Non-Journal item)

Abstract

It is shown how Nvidia Cuda can contribute to the analysis of DNA data. Three approaches are described, one using CPU threads and the other two using Cuda. For both Cuda approaches, advantages and disadvantages related to the Cuda Architecture, are presented. It is shown that, in some cases, one of these two approaches is competitive with the approach using CPU threads, and the other approach may produce good results in a near future.

Original language	English
Title of host publication	Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms
Publisher	SciTePress
Pages	253-257
Number of pages	5
ISBN (Print)	9789898425362, 9898425369
Publication status	Published - 2011
Event	International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2011 - Rome, Italy Duration: 26 Jan 2011 → 29 Jan 2011

Conference

Conference	International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2011
Country/Territory	Italy
City	Rome
Period	26 Jan 2011 → 29 Jan 2011

Keywords

CUDA
DNA analysis
Parallel computing

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@inproceedings{0abfbe1c34b24d238770614713ec7fc1,

title = "CUDA performance in DNA analysis: Analysis of CUDA architecture performance in DNA analysis",

abstract = "It is shown how Nvidia Cuda can contribute to the analysis of DNA data. Three approaches are described, one using CPU threads and the other two using Cuda. For both Cuda approaches, advantages and disadvantages related to the Cuda Architecture, are presented. It is shown that, in some cases, one of these two approaches is competitive with the approach using CPU threads, and the other approach may produce good results in a near future.",

keywords = "CUDA, DNA analysis, Parallel computing",

author = "Daniel Cadete and {Dos Anjos}, Ant{\'o}nio and Shahbazkia, {Hamid Reza} and Richard Christen",

year = "2011",

language = "English",

isbn = "9789898425362",

pages = "253--257",

booktitle = "Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms",

publisher = "SciTePress",

address = "Portugal",

note = "International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2011 ; Conference date: 26-01-2011 Through 29-01-2011",

}

Cadete, D, Dos Anjos, A, Shahbazkia, HR & Christen, R 2011, CUDA performance in DNA analysis: Analysis of CUDA architecture performance in DNA analysis. in Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. SciTePress, pp. 253-257, International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2011, Rome, Italy, 26 Jan 2011.

CUDA performance in DNA analysis: Analysis of CUDA architecture performance in DNA analysis. / Cadete, Daniel; Dos Anjos, António; Shahbazkia, Hamid Reza et al.
Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. SciTePress, 2011. p. 253-257.

Research output: Chapter in Book/Report/Conference proceeding › Conference Proceeding (Non-Journal item)

TY - GEN

T1 - CUDA performance in DNA analysis

T2 - International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2011

AU - Cadete, Daniel

AU - Dos Anjos, António

AU - Shahbazkia, Hamid Reza

AU - Christen, Richard

PY - 2011

Y1 - 2011

N2 - It is shown how Nvidia Cuda can contribute to the analysis of DNA data. Three approaches are described, one using CPU threads and the other two using Cuda. For both Cuda approaches, advantages and disadvantages related to the Cuda Architecture, are presented. It is shown that, in some cases, one of these two approaches is competitive with the approach using CPU threads, and the other approach may produce good results in a near future.

AB - It is shown how Nvidia Cuda can contribute to the analysis of DNA data. Three approaches are described, one using CPU threads and the other two using Cuda. For both Cuda approaches, advantages and disadvantages related to the Cuda Architecture, are presented. It is shown that, in some cases, one of these two approaches is competitive with the approach using CPU threads, and the other approach may produce good results in a near future.

KW - CUDA

KW - DNA analysis

KW - Parallel computing

UR - http://www.scopus.com/inward/record.url?scp=79960158669&partnerID=8YFLogxK

M3 - Conference Proceeding (Non-Journal item)

AN - SCOPUS:79960158669

SN - 9789898425362

SN - 9898425369

SP - 253

EP - 257

BT - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms

PB - SciTePress

Y2 - 26 January 2011 through 29 January 2011

ER -

CUDA performance in DNA analysis: Analysis of CUDA architecture performance in DNA analysis

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Keywords

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