KnotInFrame: prediction of –1 ribosomal frameshift events

Theis C, Reeder J, Giegerich R (2008)
Nucleic Acids Research 36(18): 6013-6020.

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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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Theis C, Reeder J, Giegerich R. KnotInFrame: prediction of –1 ribosomal frameshift events. Nucleic Acids Research. 2008;36(18):6013-6020.
Theis, C., Reeder, J., & Giegerich, R. (2008). KnotInFrame: prediction of –1 ribosomal frameshift events. Nucleic Acids Research, 36(18), 6013-6020. doi:10.1093/nar/gkn578
Theis, C., Reeder, J., and Giegerich, R. (2008). KnotInFrame: prediction of –1 ribosomal frameshift events. Nucleic Acids Research 36, 6013-6020.
Theis, C., Reeder, J., & Giegerich, R., 2008. KnotInFrame: prediction of –1 ribosomal frameshift events. Nucleic Acids Research, 36(18), p 6013-6020.
C. Theis, J. Reeder, and R. Giegerich, “KnotInFrame: prediction of –1 ribosomal frameshift events”, Nucleic Acids Research, vol. 36, 2008, pp. 6013-6020.
Theis, C., Reeder, J., Giegerich, R.: KnotInFrame: prediction of –1 ribosomal frameshift events. Nucleic Acids Research. 36, 6013-6020 (2008).
Theis, Corinna, Reeder, Jens, and Giegerich, Robert. “KnotInFrame: prediction of –1 ribosomal frameshift events”. Nucleic Acids Research 36.18 (2008): 6013-6020.
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