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
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author Theis, Corinna
Reeder, Jens
Giegerich, Robert
author_facet Theis, Corinna
Reeder, Jens
Giegerich, Robert
author_sort Theis, Corinna
collection PubMed
description 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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spelling pubmed-25668782008-10-17 KnotInFrame: prediction of −1 ribosomal frameshift events Theis, Corinna Reeder, Jens Giegerich, Robert Nucleic Acids Res Computational Biology 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. Oxford University Press 2008-10 2008-09-27 /pmc/articles/PMC2566878/ /pubmed/18820303 http://dx.doi.org/10.1093/nar/gkn578 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ 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.
spellingShingle Computational Biology
Theis, Corinna
Reeder, Jens
Giegerich, Robert
KnotInFrame: prediction of −1 ribosomal frameshift events
title KnotInFrame: prediction of −1 ribosomal frameshift events
title_full KnotInFrame: prediction of −1 ribosomal frameshift events
title_fullStr KnotInFrame: prediction of −1 ribosomal frameshift events
title_full_unstemmed KnotInFrame: prediction of −1 ribosomal frameshift events
title_short KnotInFrame: prediction of −1 ribosomal frameshift events
title_sort knotinframe: prediction of −1 ribosomal frameshift events
topic Computational Biology
url 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
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AT giegerichrobert knotinframepredictionof1ribosomalframeshiftevents

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