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RNApredator: fast accessibility-based prediction of sRNA targets

Bacterial genomes encode a plethora of small RNAs (sRNAs), which are heterogeneous in size, structure and function. Most sRNAs act as post-transcriptional regulators by means of specific base pairing interactions with the 5′-untranslated region of mRNA transcripts, thereby modifying the stability of...

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Detalles Bibliográficos
Autores principales: Eggenhofer, Florian, Tafer, Hakim, Stadler, Peter F., Hofacker, Ivo L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125805/
https://www.ncbi.nlm.nih.gov/pubmed/21672960
http://dx.doi.org/10.1093/nar/gkr467
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author Eggenhofer, Florian
Tafer, Hakim
Stadler, Peter F.
Hofacker, Ivo L.
author_facet Eggenhofer, Florian
Tafer, Hakim
Stadler, Peter F.
Hofacker, Ivo L.
author_sort Eggenhofer, Florian
collection PubMed
description Bacterial genomes encode a plethora of small RNAs (sRNAs), which are heterogeneous in size, structure and function. Most sRNAs act as post-transcriptional regulators by means of specific base pairing interactions with the 5′-untranslated region of mRNA transcripts, thereby modifying the stability of the target transcript and/or its ability to be translated. Here, we present RNApredator, a web server for the prediction of sRNA targets. The user can choose from a set of over 2155 genomes and plasmids from 1183 bacterial species. RNApredator then uses a dynamic programming approach, RNAplex, to compute putative targets. Compared to web servers with a similar task, RNApredator takes the accessibility of the target during the target search into account, improving the specificity of the predictions. Furthermore, enrichment in Gene Ontology terms, cellular pathways as well as changes in accessibilities along the target sequence can be done in fully automated post-processing steps. The predictive performance of the underlying dynamic programming approach RNAplex is similar to that of more complex methods, but needs at least three orders of magnitude less time to complete. RNApredator is available at http://rna.tbi.univie.ac.at/RNApredator.
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spelling pubmed-31258052011-07-05 RNApredator: fast accessibility-based prediction of sRNA targets Eggenhofer, Florian Tafer, Hakim Stadler, Peter F. Hofacker, Ivo L. Nucleic Acids Res Articles Bacterial genomes encode a plethora of small RNAs (sRNAs), which are heterogeneous in size, structure and function. Most sRNAs act as post-transcriptional regulators by means of specific base pairing interactions with the 5′-untranslated region of mRNA transcripts, thereby modifying the stability of the target transcript and/or its ability to be translated. Here, we present RNApredator, a web server for the prediction of sRNA targets. The user can choose from a set of over 2155 genomes and plasmids from 1183 bacterial species. RNApredator then uses a dynamic programming approach, RNAplex, to compute putative targets. Compared to web servers with a similar task, RNApredator takes the accessibility of the target during the target search into account, improving the specificity of the predictions. Furthermore, enrichment in Gene Ontology terms, cellular pathways as well as changes in accessibilities along the target sequence can be done in fully automated post-processing steps. The predictive performance of the underlying dynamic programming approach RNAplex is similar to that of more complex methods, but needs at least three orders of magnitude less time to complete. RNApredator is available at http://rna.tbi.univie.ac.at/RNApredator. Oxford University Press 2011-07-01 2011-06-14 /pmc/articles/PMC3125805/ /pubmed/21672960 http://dx.doi.org/10.1093/nar/gkr467 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Eggenhofer, Florian
Tafer, Hakim
Stadler, Peter F.
Hofacker, Ivo L.
RNApredator: fast accessibility-based prediction of sRNA targets
title RNApredator: fast accessibility-based prediction of sRNA targets
title_full RNApredator: fast accessibility-based prediction of sRNA targets
title_fullStr RNApredator: fast accessibility-based prediction of sRNA targets
title_full_unstemmed RNApredator: fast accessibility-based prediction of sRNA targets
title_short RNApredator: fast accessibility-based prediction of sRNA targets
title_sort rnapredator: fast accessibility-based prediction of srna targets
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125805/
https://www.ncbi.nlm.nih.gov/pubmed/21672960
http://dx.doi.org/10.1093/nar/gkr467
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