title: A new approach for detecting riboswitches in DNA sequences.
abstract: BACKGROUND
  Riboswitches are short sequences of messenger RNA that can change their structural conformation to regulate the expression of adjacent genes. Computational prediction of putative riboswitches can provide direction to molecular biologists studying riboswitch-mediated gene expression.
  
  
  RESULTS
  The Denison Riboswitch Detector (DRD) is a new computational tool with a Web interface that can quickly identify putative riboswitches in DNA sequences on the scale of bacterial genomes. Riboswitch descriptions are easily modifiable and new ones are easily created. The underlying algorithm converts the problem to a 'heaviest path' problem on a multipartite graph, which is then solved using efficient dynamic programming. We show that DRD can achieve ∼ 88-99% sensitivity and >99.99% specificity on 13 riboswitch families.
  
  
  METHODS
  DRD is available at http://drd.denison.edu.
authors.affiliation: Department of Mathematics and Computer Science, Department of Biology, Denison University, Granville, OH 43023, Capco, New York, NY, 10005, Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA.
authors.forename: Jessen T
authors.initials: JT
authors.lastname: Havill
authors.affiliation: Department of Mathematics and Computer Science, Department of Biology, Denison University, Granville, OH 43023, Capco, New York, NY, 10005, Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA.
authors.forename: Chinmoy
authors.initials: C
authors.lastname: Bhatiya
authors.affiliation: Department of Mathematics and Computer Science, Department of Biology, Denison University, Granville, OH 43023, Capco, New York, NY, 10005, Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA.
authors.forename: Steven M
authors.initials: SM
authors.lastname: Johnson
authors.affiliation: Department of Mathematics and Computer Science, Department of Biology, Denison University, Granville, OH 43023, Capco, New York, NY, 10005, Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA.
authors.forename: Joseph D
authors.initials: JD
authors.lastname: Sheets
authors.affiliation: Department of Mathematics and Computer Science, Department of Biology, Denison University, Granville, OH 43023, Capco, New York, NY, 10005, Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA.
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Thompson
mesh_terms: D000465:Algorithms; D058928:Riboswitch; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D058928:Riboswitch