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RNAProbe: a web server for normalization and analysis of RNA structure probing data
RNA molecules play key roles in all living cells. Knowledge of the structural characteristics of RNA molecules allows for a better understanding of the mechanisms of their action. RNA chemical probing allows us to study the susceptibility of nucleotides to chemical modification, and the information...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319577/ https://www.ncbi.nlm.nih.gov/pubmed/32504492 http://dx.doi.org/10.1093/nar/gkaa396 |
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author | Wirecki, Tomasz K Merdas, Katarzyna Bernat, Agata Boniecki, Michał J Bujnicki, Janusz M Stefaniak, Filip |
author_facet | Wirecki, Tomasz K Merdas, Katarzyna Bernat, Agata Boniecki, Michał J Bujnicki, Janusz M Stefaniak, Filip |
author_sort | Wirecki, Tomasz K |
collection | PubMed |
description | RNA molecules play key roles in all living cells. Knowledge of the structural characteristics of RNA molecules allows for a better understanding of the mechanisms of their action. RNA chemical probing allows us to study the susceptibility of nucleotides to chemical modification, and the information obtained can be used to guide secondary structure prediction. These experimental results can be analyzed using various computational tools, which, however, requires additional, tedious steps (e.g., further normalization of the reactivities and visualization of the results), for which there are no fully automated methods. Here, we introduce RNAProbe, a web server that facilitates normalization, analysis, and visualization of the low-pass SHAPE, DMS and CMCT probing results with the modification sites detected by capillary electrophoresis. RNAProbe automatically analyzes chemical probing output data and turns tedious manual work into a one-minute assignment. RNAProbe performs normalization based on a well-established protocol, utilizes recognized secondary structure prediction methods, and generates high-quality images with structure representations and reactivity heatmaps. It summarizes the results in the form of a spreadsheet, which can be used for comparative analyses between experiments. Results of predictions with normalized reactivities are also collected in text files, providing interoperability with bioinformatics workflows. RNAProbe is available at https://rnaprobe.genesilico.pl. |
format | Online Article Text |
id | pubmed-7319577 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-73195772020-07-01 RNAProbe: a web server for normalization and analysis of RNA structure probing data Wirecki, Tomasz K Merdas, Katarzyna Bernat, Agata Boniecki, Michał J Bujnicki, Janusz M Stefaniak, Filip Nucleic Acids Res Web Server Issue RNA molecules play key roles in all living cells. Knowledge of the structural characteristics of RNA molecules allows for a better understanding of the mechanisms of their action. RNA chemical probing allows us to study the susceptibility of nucleotides to chemical modification, and the information obtained can be used to guide secondary structure prediction. These experimental results can be analyzed using various computational tools, which, however, requires additional, tedious steps (e.g., further normalization of the reactivities and visualization of the results), for which there are no fully automated methods. Here, we introduce RNAProbe, a web server that facilitates normalization, analysis, and visualization of the low-pass SHAPE, DMS and CMCT probing results with the modification sites detected by capillary electrophoresis. RNAProbe automatically analyzes chemical probing output data and turns tedious manual work into a one-minute assignment. RNAProbe performs normalization based on a well-established protocol, utilizes recognized secondary structure prediction methods, and generates high-quality images with structure representations and reactivity heatmaps. It summarizes the results in the form of a spreadsheet, which can be used for comparative analyses between experiments. Results of predictions with normalized reactivities are also collected in text files, providing interoperability with bioinformatics workflows. RNAProbe is available at https://rnaprobe.genesilico.pl. Oxford University Press 2020-07-02 2020-06-06 /pmc/articles/PMC7319577/ /pubmed/32504492 http://dx.doi.org/10.1093/nar/gkaa396 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Web Server Issue Wirecki, Tomasz K Merdas, Katarzyna Bernat, Agata Boniecki, Michał J Bujnicki, Janusz M Stefaniak, Filip RNAProbe: a web server for normalization and analysis of RNA structure probing data |
title | RNAProbe: a web server for normalization and analysis of RNA structure probing data |
title_full | RNAProbe: a web server for normalization and analysis of RNA structure probing data |
title_fullStr | RNAProbe: a web server for normalization and analysis of RNA structure probing data |
title_full_unstemmed | RNAProbe: a web server for normalization and analysis of RNA structure probing data |
title_short | RNAProbe: a web server for normalization and analysis of RNA structure probing data |
title_sort | rnaprobe: a web server for normalization and analysis of rna structure probing data |
topic | Web Server Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319577/ https://www.ncbi.nlm.nih.gov/pubmed/32504492 http://dx.doi.org/10.1093/nar/gkaa396 |
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