The in silico prediction of promoters in bacterial genomes.
In silico approaches to the identification of bacterial promoters are hampered by poor conservation of their characteristic binding sites. This suggests that the usual position weight matrix models of bacterial promoters are incomplete. A number of methods have been used to overcome this inadequacy, one of which is to incorporate structural properties of DNA. In this paper we describe an extension of the promoter description to include SIDD (stress induced duplex destabilization), DNA curvature and stacking energy. Although we report the best result to date for a realistic promoter prediction task, surprisingly, DNA structural properties did not contribute significantly to this result. We also demonstrate for the first time, that sigma-54 promoters have a stronger association with SIDD than do other promoter types.
Towsey
Michael
M
Institute for Health and Biomedical Innovation, Queensland University of Technology, Queensland, Australia. m.towsey@qut.edu.au
Hogan
James M
JM
Mathews
Sarah
S
Timms
Peter
P
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D029968:Escherichia coli Proteins / Q000235:genetics; D016680:Genome, Bacterial; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D051877:RNA Polymerase Sigma 54 / Q000235:genetics; D015203:Reproducibility of Results; D012984:Software
D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; C497751:rpoN protein, E coli; D004247:DNA; D051877:RNA Polymerase Sigma 54