title: Using the fast fourier transform to accelerate the computational search for RNA conformational switches.
abstract: Using complex roots of unity and the Fast Fourier Transform, we design a new thermodynamics-based algorithm, FFTbor, that computes the Boltzmann probability that secondary structures differ by [Formula: see text] base pairs from an arbitrary initial structure of a given RNA sequence. The algorithm, which runs in quartic time O(n(4)) and quadratic space O(n(2)), is used to determine the correlation between kinetic folding speed and the ruggedness of the energy landscape, and to predict the location of riboswitch expression platform candidates. A web server is available at http://bioinformatics.bc.edu/clotelab/FFTbor/.
authors.affiliation: Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America.
authors.forename: Evan
authors.initials: E
authors.lastname: Senter
authors.forename: Saad
authors.initials: S
authors.lastname: Sheikh
authors.forename: Ivan
authors.initials: I
authors.lastname: Dotu
authors.forename: Yann
authors.initials: Y
authors.lastname: Ponty
authors.forename: Peter
authors.initials: P
authors.lastname: Clote
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D048168:Escherichia coli K12 / Q000201:enzymology; D005583:Fourier Analysis; D009690:Nucleic Acid Conformation; D009876:Operon / Q000235:genetics; D010652:Phenylalanine-tRNA Ligase / Q000235:genetics; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D013997:Time Factors
chemical_list: D012313:RNA; D010652:Phenylalanine-tRNA Ligase