KnotInFrame: prediction of −1 ribosomal frameshift events

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...

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Detalles Bibliográficos
Autores principales: Theis, Corinna, Reeder, Jens, Giegerich, Robert
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Computational Biology
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2566878/
https://www.ncbi.nlm.nih.gov/pubmed/18820303
http://dx.doi.org/10.1093/nar/gkn578
Descripción
Sumario: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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