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A parallel, distributed-memory framework for comparative motif discovery

Dieter De Witte (UGent) , Michiel Van Bel (UGent) , Pieter Audenaert (UGent) , Piet Demeester (UGent) , Bart Dhoedt (UGent) , Klaas Vandepoele (UGent) and Jan Fostier (UGent)
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
The increasing number of sequenced organisms has opened new possibilities for the computational discovery of cis-regulatory elements ('motifs') based on phylogenetic footprinting. Word-based, exhaustive approaches are among the best performing algorithms, however, they pose significant computational challenges as the number of candidate motifs to evaluate is very high. In this contribution, we describe a parallel, distributed-memory framework for de novo comparative motif discovery. Within this framework, two approaches for phylogenetic footprinting are implemented: an alignment-based and an alignment-free method. The framework is able to statistically evaluate the conservation of motifs in a search space containing over 160 million candidate motifs using a distributed-memory cluster with 200 CPU cores in a few hours. Software available from http://bioinformatics.intec.ugent.be/blsspeller/
Keywords
IBCN, COMPARATIVE GENOMICS, REGULATORY ELEMENTS, SYSTEMATIC DISCOVERY, ALGORITHMS, PLAZA, Motif discovery, Phylogenetic footprinting, Parallel computing, Distributed memory

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Citation

Please use this url to cite or link to this publication:

MLA
De Witte, Dieter et al. “A Parallel, Distributed-memory Framework for Comparative Motif Discovery.” Lecture Notes in Computer Science. Ed. R Wyrzykowski et al. Vol. 8385. Springer, 2014. 268–277. Print.
APA
De Witte, D., Van Bel, M., Audenaert, P., Demeester, P., Dhoedt, B., Vandepoele, K., & Fostier, J. (2014). A parallel, distributed-memory framework for comparative motif discovery. In R. Wyrzykowski, J. Dongarra, K. Karczewski , & J. Wasniewski (Eds.), Lecture Notes in Computer Science (Vol. 8385, pp. 268–277). Presented at the 10th International Conference on Parallel Processing and Applied Mathematics (PPAM), Springer.
Chicago author-date
De Witte, Dieter, Michiel Van Bel, Pieter Audenaert, Piet Demeester, Bart Dhoedt, Klaas Vandepoele, and Jan Fostier. 2014. “A Parallel, Distributed-memory Framework for Comparative Motif Discovery.” In Lecture Notes in Computer Science, ed. R Wyrzykowski, J Dongarra, K Karczewski , and J Wasniewski, 8385:268–277. Springer.
Chicago author-date (all authors)
De Witte, Dieter, Michiel Van Bel, Pieter Audenaert, Piet Demeester, Bart Dhoedt, Klaas Vandepoele, and Jan Fostier. 2014. “A Parallel, Distributed-memory Framework for Comparative Motif Discovery.” In Lecture Notes in Computer Science, ed. R Wyrzykowski, J Dongarra, K Karczewski , and J Wasniewski, 8385:268–277. Springer.
Vancouver
1.
De Witte D, Van Bel M, Audenaert P, Demeester P, Dhoedt B, Vandepoele K, et al. A parallel, distributed-memory framework for comparative motif discovery. In: Wyrzykowski R, Dongarra J, Karczewski K, Wasniewski J, editors. Lecture Notes in Computer Science. Springer; 2014. p. 268–77.
IEEE
[1]
D. De Witte et al., “A parallel, distributed-memory framework for comparative motif discovery,” in Lecture Notes in Computer Science, Warsaw, Poland, 2014, vol. 8385, pp. 268–277.
@inproceedings{4193767,
  abstract     = {The increasing number of sequenced organisms has opened new possibilities for the computational discovery of cis-regulatory elements ('motifs') based on phylogenetic footprinting. Word-based, exhaustive approaches are among the best performing algorithms, however, they pose significant computational challenges as the number of candidate motifs to evaluate is very high. In this contribution, we describe a parallel, distributed-memory framework for de novo comparative motif discovery. Within this framework, two approaches for phylogenetic footprinting are implemented: an alignment-based and an alignment-free method. The framework is able to statistically evaluate the conservation of motifs in a search space containing over 160 million candidate motifs using a distributed-memory cluster with 200 CPU cores in a few hours. Software available from http://bioinformatics.intec.ugent.be/blsspeller/},
  author       = {De Witte, Dieter and Van Bel, Michiel and Audenaert, Pieter and Demeester, Piet and Dhoedt, Bart and Vandepoele, Klaas and Fostier, Jan},
  booktitle    = {Lecture Notes in Computer Science},
  editor       = {Wyrzykowski, R and Dongarra, J and Karczewski , K and Wasniewski, J},
  isbn         = {9783642551956},
  issn         = {0302-9743},
  keywords     = {IBCN,COMPARATIVE GENOMICS,REGULATORY ELEMENTS,SYSTEMATIC DISCOVERY,ALGORITHMS,PLAZA,Motif discovery,Phylogenetic footprinting,Parallel computing,Distributed memory},
  language     = {eng},
  location     = {Warsaw, Poland},
  pages        = {268--277},
  publisher    = {Springer},
  title        = {A parallel, distributed-memory framework for comparative motif discovery},
  url          = {http://dx.doi.org/10.1007/978-3-642-55195-6_25},
  volume       = {8385},
  year         = {2014},
}

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