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

K Marchal, G Thijs, S De Keersmaecker, P Monsieurs, B De Moor, J Vanderleyden

Research output: Contribution to journalA1: Web of Science-article

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.

Original languageEnglish
JournalTrends in Microbiology
Volume11
Issue number2
Pages (from-to)61-66
Number of pages6
ISSN0966-842X
DOIs
Publication statusPublished - Feb-2003
Externally publishedYes

Keywords

  • FACTOR-BINDING SITES
  • UPSTREAM

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