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.

SUBMITTER: Theis C 

PROVIDER: S-EPMC2566878 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature