KnotInFrame: prediction of -1 ribosomal frameshift events.
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.
Theis
Corinna
C
Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany.
Reeder
Jens
J
Giegerich
Robert
R
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