KnotInFrame: prediction of -1 ribosomal frameshift events |
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Authors: | Theis Corinna Reeder Jens Giegerich Robert |
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Affiliation: | Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany. |
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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. |
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