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Updated: Aug 8, 2025

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
RSCanner: rapid assessment and visualization of RNA structure content
Gandhar Mahadeshwar1, Rafael de Cesaris Araujo Tavares2, Han Wan3
1Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, United States.
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).
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