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Nucleic Acids Res. 2008 Oct;36(18):6013-20. doi: 10.1093/nar/gkn578. Epub 2008 Sep 27.

KnotInFrame: prediction of -1 ribosomal frameshift events.

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  • 1Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany.

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.

PMID:
18820303
[PubMed - indexed for MEDLINE]
PMCID:
PMC2566878
Free PMC Article

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