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Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2
Mutational profiling (MaP) enables detection of sites of chemical modification in RNA as sequence changes during reverse transcription (RT), subsequently read out by massively parallel sequencing. We introduce ShapeMapper 2, which integrates careful handling of all classes of adduct-induced sequence...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769742/ https://www.ncbi.nlm.nih.gov/pubmed/29114018 http://dx.doi.org/10.1261/rna.061945.117 |
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author | Busan, Steven Weeks, Kevin M. |
author_facet | Busan, Steven Weeks, Kevin M. |
author_sort | Busan, Steven |
collection | PubMed |
description | Mutational profiling (MaP) enables detection of sites of chemical modification in RNA as sequence changes during reverse transcription (RT), subsequently read out by massively parallel sequencing. We introduce ShapeMapper 2, which integrates careful handling of all classes of adduct-induced sequence changes, sequence variant correction, basecall quality filters, and quality-control warnings to now identify RNA adduct sites as accurately as achieved by careful manual analysis of electrophoresis data, the prior highest-accuracy standard. MaP and ShapeMapper 2 provide a robust, experimentally concise, and accurate approach for reading out nucleic acid chemical probing experiments. |
format | Online Article Text |
id | pubmed-5769742 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-57697422019-02-01 Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2 Busan, Steven Weeks, Kevin M. RNA Bioinformatics Mutational profiling (MaP) enables detection of sites of chemical modification in RNA as sequence changes during reverse transcription (RT), subsequently read out by massively parallel sequencing. We introduce ShapeMapper 2, which integrates careful handling of all classes of adduct-induced sequence changes, sequence variant correction, basecall quality filters, and quality-control warnings to now identify RNA adduct sites as accurately as achieved by careful manual analysis of electrophoresis data, the prior highest-accuracy standard. MaP and ShapeMapper 2 provide a robust, experimentally concise, and accurate approach for reading out nucleic acid chemical probing experiments. Cold Spring Harbor Laboratory Press 2018-02 /pmc/articles/PMC5769742/ /pubmed/29114018 http://dx.doi.org/10.1261/rna.061945.117 Text en © 2018 Busan and Weeks; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. |
spellingShingle | Bioinformatics Busan, Steven Weeks, Kevin M. Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2 |
title | Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2 |
title_full | Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2 |
title_fullStr | Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2 |
title_full_unstemmed | Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2 |
title_short | Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2 |
title_sort | accurate detection of chemical modifications in rna by mutational profiling (map) with shapemapper 2 |
topic | Bioinformatics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769742/ https://www.ncbi.nlm.nih.gov/pubmed/29114018 http://dx.doi.org/10.1261/rna.061945.117 |
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