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Nucleic Acids Research Advance Access originally published online on September 27, 2008
Nucleic Acids Research 2008 36(18):6013-6020; doi:10.1093/nar/gkn578
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Nucleic Acids Research, 2008, Vol. 36, No. 18 6013-6020
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

KnotInFrame: prediction of –1 ribosomal frameshift events

Corinna Theis, Jens Reeder and Robert Giegerich*

Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany

*To whom correspondence should be addressed. Tel: +49 521 106 2903; Fax: +49 521 106 6411; Email: robert{at}techfak.uni-bielefeld.de

Received June 12, 2008. Revised August 28, 2008. Accepted August 28, 2008.

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.


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