RNAthor – fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis
RNAs adopt specific structures to perform their functions, which are critical to fundamental cellular processes. For decades, these structures have been determined and modeled with strong support from computational methods. Still, the accuracy of the latter ones depends on the availability of experi...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2020-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7529196/?tool=EBI |
| _version_ | 1828530959929049088 |
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| author | Julita Gumna Tomasz Zok Kacper Figurski Katarzyna Pachulska-Wieczorek Marta Szachniuk Danny Barash |
| author_facet | Julita Gumna Tomasz Zok Kacper Figurski Katarzyna Pachulska-Wieczorek Marta Szachniuk Danny Barash |
| author_sort | Julita Gumna |
| collection | DOAJ |
| description | RNAs adopt specific structures to perform their functions, which are critical to fundamental cellular processes. For decades, these structures have been determined and modeled with strong support from computational methods. Still, the accuracy of the latter ones depends on the availability of experimental data, for example, chemical probing information that can define pseudo-energy constraints for RNA folding algorithms. At the same time, diverse computational tools have been developed to facilitate analysis and visualization of data from RNA structure probing experiments followed by capillary electrophoresis or next-generation sequencing. RNAthor, a new software tool for the fully automated normalization of SHAPE and DMS probing data resolved by capillary electrophoresis, has recently joined this collection. RNAthor automatically identifies unreliable probing data. It normalizes the reactivity information to a uniform scale and uses it in the RNA secondary structure prediction. Our web server also provides tools for fast and easy RNA probing data visualization and statistical analysis that facilitates the comparison of multiple data sets. RNAthor is freely available at http://rnathor.cs.put.poznan.pl/. |
| first_indexed | 2024-12-11T22:30:44Z |
| format | Article |
| id | doaj.art-f816c0c34d2d4e4abedc17262250b938 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-11T22:30:44Z |
| publishDate | 2020-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-f816c0c34d2d4e4abedc17262250b9382022-12-22T00:48:09ZengPublic Library of Science (PLoS)PLoS ONE1932-62032020-01-011510RNAthor – fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresisJulita GumnaTomasz ZokKacper FigurskiKatarzyna Pachulska-WieczorekMarta SzachniukDanny BarashRNAs adopt specific structures to perform their functions, which are critical to fundamental cellular processes. For decades, these structures have been determined and modeled with strong support from computational methods. Still, the accuracy of the latter ones depends on the availability of experimental data, for example, chemical probing information that can define pseudo-energy constraints for RNA folding algorithms. At the same time, diverse computational tools have been developed to facilitate analysis and visualization of data from RNA structure probing experiments followed by capillary electrophoresis or next-generation sequencing. RNAthor, a new software tool for the fully automated normalization of SHAPE and DMS probing data resolved by capillary electrophoresis, has recently joined this collection. RNAthor automatically identifies unreliable probing data. It normalizes the reactivity information to a uniform scale and uses it in the RNA secondary structure prediction. Our web server also provides tools for fast and easy RNA probing data visualization and statistical analysis that facilitates the comparison of multiple data sets. RNAthor is freely available at http://rnathor.cs.put.poznan.pl/.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7529196/?tool=EBI |
| spellingShingle | Julita Gumna Tomasz Zok Kacper Figurski Katarzyna Pachulska-Wieczorek Marta Szachniuk Danny Barash RNAthor – fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis PLoS ONE |
| title | RNAthor – fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis |
| title_full | RNAthor – fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis |
| title_fullStr | RNAthor – fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis |
| title_full_unstemmed | RNAthor – fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis |
| title_short | RNAthor – fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis |
| title_sort | rnathor fast accurate normalization visualization and statistical analysis of rna probing data resolved by capillary electrophoresis |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7529196/?tool=EBI |
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