Development of MapReduce and MPI programs for motif search

Mejdl Safran; Saad Al-Qahtani; Michelle Zhu; Dunren Che

doi:10.1109/CLUSTER.2015.82

Development of MapReduce and MPI programs for motif search

Mejdl Safran
, Saad Al-Qahtani
, Michelle Zhu
, Dunren Che

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

As one of the important problems in molecular biology, motif search is computationally expensive, especially when the size of DNA sequences is large. Extended from a graduate course project in parallel and distributed computing (PDC), this paper investigates two different programming frameworks, namely MapReduce and MPI on motif finding. We implemented a serial algorithm, a MapReduce based algorithm, and a MPI program to calculate the best motif in given DNA sequences. The experimental results demonstrate that our MPI program outperformed both the MapReduce-based algorithm and the serial program with superior efficiency.

Original language	English
Title of host publication	Proceedings - 2015 IEEE International Conference on Cluster Computing, CLUSTER 2015
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	500-501
Number of pages	2
ISBN (Electronic)	9781467365987
DOIs	https://doi.org/10.1109/CLUSTER.2015.82
State	Published - 26 Oct 2015
Externally published	Yes

Publication series

Name	Proceedings - IEEE International Conference on Cluster Computing, ICCC
Volume	2015-October
ISSN (Print)	1552-5244

Bibliographical note

Publisher Copyright:
© 2015 IEEE.

Keywords

Algorithm
MPI
MapReduce
Motif
Parallel processing

ASJC Scopus subject areas

Software
Hardware and Architecture
Signal Processing

Access to Document

10.1109/CLUSTER.2015.82

Cite this

Safran, M., Al-Qahtani, S., Zhu, M., & Che, D. (2015). Development of MapReduce and MPI programs for motif search. In Proceedings - 2015 IEEE International Conference on Cluster Computing, CLUSTER 2015 (pp. 500-501). Article 7307629 (Proceedings - IEEE International Conference on Cluster Computing, ICCC; Vol. 2015-October). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CLUSTER.2015.82

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title = "Development of MapReduce and MPI programs for motif search",

abstract = "As one of the important problems in molecular biology, motif search is computationally expensive, especially when the size of DNA sequences is large. Extended from a graduate course project in parallel and distributed computing (PDC), this paper investigates two different programming frameworks, namely MapReduce and MPI on motif finding. We implemented a serial algorithm, a MapReduce based algorithm, and a MPI program to calculate the best motif in given DNA sequences. The experimental results demonstrate that our MPI program outperformed both the MapReduce-based algorithm and the serial program with superior efficiency.",

keywords = "Algorithm, MPI, MapReduce, Motif, Parallel processing",

author = "Mejdl Safran and Saad Al-Qahtani and Michelle Zhu and Dunren Che",

note = "Publisher Copyright: {\textcopyright} 2015 IEEE.",

year = "2015",

month = oct,

day = "26",

doi = "10.1109/CLUSTER.2015.82",

language = "English",

series = "Proceedings - IEEE International Conference on Cluster Computing, ICCC",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

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booktitle = "Proceedings - 2015 IEEE International Conference on Cluster Computing, CLUSTER 2015",

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}

Safran, M, Al-Qahtani, S, Zhu, M & Che, D 2015, Development of MapReduce and MPI programs for motif search. in Proceedings - 2015 IEEE International Conference on Cluster Computing, CLUSTER 2015., 7307629, Proceedings - IEEE International Conference on Cluster Computing, ICCC, vol. 2015-October, Institute of Electrical and Electronics Engineers Inc., pp. 500-501. https://doi.org/10.1109/CLUSTER.2015.82

Development of MapReduce and MPI programs for motif search. / Safran, Mejdl; Al-Qahtani, Saad; Zhu, Michelle et al.
Proceedings - 2015 IEEE International Conference on Cluster Computing, CLUSTER 2015. Institute of Electrical and Electronics Engineers Inc., 2015. p. 500-501 7307629 (Proceedings - IEEE International Conference on Cluster Computing, ICCC; Vol. 2015-October).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Development of MapReduce and MPI programs for motif search

AU - Safran, Mejdl

AU - Al-Qahtani, Saad

AU - Zhu, Michelle

AU - Che, Dunren

PY - 2015/10/26

Y1 - 2015/10/26

N2 - As one of the important problems in molecular biology, motif search is computationally expensive, especially when the size of DNA sequences is large. Extended from a graduate course project in parallel and distributed computing (PDC), this paper investigates two different programming frameworks, namely MapReduce and MPI on motif finding. We implemented a serial algorithm, a MapReduce based algorithm, and a MPI program to calculate the best motif in given DNA sequences. The experimental results demonstrate that our MPI program outperformed both the MapReduce-based algorithm and the serial program with superior efficiency.

AB - As one of the important problems in molecular biology, motif search is computationally expensive, especially when the size of DNA sequences is large. Extended from a graduate course project in parallel and distributed computing (PDC), this paper investigates two different programming frameworks, namely MapReduce and MPI on motif finding. We implemented a serial algorithm, a MapReduce based algorithm, and a MPI program to calculate the best motif in given DNA sequences. The experimental results demonstrate that our MPI program outperformed both the MapReduce-based algorithm and the serial program with superior efficiency.

KW - Algorithm

KW - MPI

KW - MapReduce

KW - Motif

KW - Parallel processing

UR - https://www.scopus.com/pages/publications/84959295447

U2 - 10.1109/CLUSTER.2015.82

DO - 10.1109/CLUSTER.2015.82

M3 - Conference contribution

AN - SCOPUS:84959295447

T3 - Proceedings - IEEE International Conference on Cluster Computing, ICCC

SP - 500

EP - 501

BT - Proceedings - 2015 IEEE International Conference on Cluster Computing, CLUSTER 2015

PB - Institute of Electrical and Electronics Engineers Inc.

ER -

Safran M, Al-Qahtani S, Zhu M, Che D. Development of MapReduce and MPI programs for motif search. In Proceedings - 2015 IEEE International Conference on Cluster Computing, CLUSTER 2015. Institute of Electrical and Electronics Engineers Inc. 2015. p. 500-501. 7307629. (Proceedings - IEEE International Conference on Cluster Computing, ICCC). doi: 10.1109/CLUSTER.2015.82

Development of MapReduce and MPI programs for motif search

Abstract

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Bibliographical note

Keywords

ASJC Scopus subject areas

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