title: KnotInFrame: prediction of -1 ribosomal frameshift events.
abstract: Programmed -1 ribosomal frameshift (-1 PRF) allows for alternative reading frames within one mRNA. First found in several viruses, it is now believed to exist in all kingdoms of life. Strong stimulators for -1 PRF are a heptameric slippery site and an RNA pseudoknot. Here, we present a new algorithm KnotInFrame, for the automatic detection of -1 PRF signals from genomic sequences. It finds the frameshifting stimulators by means of a specialized RNA-pseudoknot folding program, fast enough for genome-wide analyses. Evaluations on known -1 PRF signals demonstrate a high sensitivity.
authors.affiliation: Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany.
authors.forename: Corinna
authors.initials: C
authors.lastname: Theis
authors.forename: Jens
authors.initials: J
authors.lastname: Reeder
authors.forename: Robert
authors.initials: R
authors.lastname: Giegerich
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology; D016384:Consensus Sequence; D030561:Databases, Nucleic Acid; D018965:Frameshifting, Ribosomal; D023281:Genomics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012984:Software