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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:

Chicago
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.
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.
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.
MLA
De Witte, Dieter, Michiel Van Bel, Pieter Audenaert, 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.
@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},
  keyword      = {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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