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Genome-specific higher-order background models to improve motif detection

(2003) TRENDS IN MICROBIOLOGY. 11(2). p.61-66
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Abstract
Motif detection based on Gibbs sampling is a common procedure used to retrieve regulatory motifs in silico. Using a species-specific background model was previously shown to increase the robustness of the algorithm. Here, we demonstrate that selecting a non-species-adapted background model can have an adverse effect on the results of motif detection. The large differences in the average nucleotide composition of prokaryotic sequences exacerbate the problem of exchanging background models. Therefore, we have developed complex background models for all prokaryotic species with available genome sequences.
Keywords
FACTOR-BINDING SITES, Species specificity, UPSTREAM, GENES

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Citation

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

MLA
Marchal, Kathleen, Gert Thijs, Sigrid De Keersmaecker, et al. “Genome-specific Higher-order Background Models to Improve Motif Detection.” TRENDS IN MICROBIOLOGY 11.2 (2003): 61–66. Print.
APA
Marchal, K., Thijs, G., De Keersmaecker, S., Monsieurs, P., De Moor, B., & Vanderleyden, J. (2003). Genome-specific higher-order background models to improve motif detection. TRENDS IN MICROBIOLOGY, 11(2), 61–66.
Chicago author-date
Marchal, Kathleen, Gert Thijs, Sigrid De Keersmaecker, Pieter Monsieurs, Bart De Moor, and Jos Vanderleyden. 2003. “Genome-specific Higher-order Background Models to Improve Motif Detection.” Trends in Microbiology 11 (2): 61–66.
Chicago author-date (all authors)
Marchal, Kathleen, Gert Thijs, Sigrid De Keersmaecker, Pieter Monsieurs, Bart De Moor, and Jos Vanderleyden. 2003. “Genome-specific Higher-order Background Models to Improve Motif Detection.” Trends in Microbiology 11 (2): 61–66.
Vancouver
1.
Marchal K, Thijs G, De Keersmaecker S, Monsieurs P, De Moor B, Vanderleyden J. Genome-specific higher-order background models to improve motif detection. TRENDS IN MICROBIOLOGY. 2003;11(2):61–6.
IEEE
[1]
K. Marchal, G. Thijs, S. De Keersmaecker, P. Monsieurs, B. De Moor, and J. Vanderleyden, “Genome-specific higher-order background models to improve motif detection,” TRENDS IN MICROBIOLOGY, vol. 11, no. 2, pp. 61–66, 2003.
@article{3186996,
  abstract     = {Motif detection based on Gibbs sampling is a common procedure used to retrieve regulatory motifs in silico. Using a species-specific background model was previously shown to increase the robustness of the algorithm. Here, we demonstrate that selecting a non-species-adapted background model can have an adverse effect on the results of motif detection. The large differences in the average nucleotide composition of prokaryotic sequences exacerbate the problem of exchanging background models. Therefore, we have developed complex background models for all prokaryotic species with available genome sequences.},
  author       = {Marchal, Kathleen and Thijs, Gert and De Keersmaecker, Sigrid and Monsieurs, Pieter and De Moor, Bart and Vanderleyden, Jos},
  issn         = {0966-842X},
  journal      = {TRENDS IN MICROBIOLOGY},
  keywords     = {FACTOR-BINDING SITES,Species specificity,UPSTREAM,GENES},
  language     = {eng},
  number       = {2},
  pages        = {61--66},
  title        = {Genome-specific higher-order background models to improve motif detection},
  url          = {http://dx.doi.org/10.1016/S0966-842X(02)00030-6},
  volume       = {11},
  year         = {2003},
}

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