RSCanner: rapid assessment and visualization of RNA structure content.
Ontology highlight
ABSTRACT: Motivation
The increasing availability of RNA structural information that spans many kilobases of transcript sequence imposes a need for tools that can rapidly screen, identify, and prioritize structural modules of interest.Results
We describe RNA Structural Content Scanner (RSCanner), an automated tool that scans RNA transcripts for regions that contain high levels of secondary structure and then classifies each region for its relative propensity to adopt stable or dynamic structures. RSCanner then generates an intuitive heatmap enabling users to rapidly pinpoint regions likely to contain a high or low density of discrete RNA structures, thereby informing downstream functional or structural investigation.Availability and implementation
RSCanner is freely available as both R script and R Markdown files, along with full documentation and test data (https://github.com/pylelab/RSCanner).
SUBMITTER: Mahadeshwar G
PROVIDER: S-EPMC10017096 | biostudies-literature | 2023 Mar
REPOSITORIES: biostudies-literature
Publications
RSCanner: rapid assessment and visualization of RNA structure content.
Mahadeshwar Gandhar G Tavares Rafael de Cesaris Araujo RCA Wan Han H Perry Zion R ZR Pyle Anna Marie AM
Bioinformatics (Oxford, England) 20230301 3
<h4>Motivation</h4>The increasing availability of RNA structural information that spans many kilobases of transcript sequence imposes a need for tools that can rapidly screen, identify, and prioritize structural modules of interest.<h4>Results</h4>We describe RNA Structural Content Scanner (RSCanner), an automated tool that scans RNA transcripts for regions that contain high levels of secondary structure and then classifies each region for its relative propensity to adopt stable or dynamic struc ...[more]
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