R4RNA

R4RNA provides arc-diagram visualization and quantitative analysis of RNA basepairs to represent secondary structures, assess conservation and covariation across multiple sequence alignments, and compute basepair-level statistics.

Key Features:

• Arc Diagram Visualization: Represents RNA secondary structures using arc diagrams to display pseudoknots and alternative or transient basepairing patterns.
• Comparison and Annotation: Enables direct comparison and annotation of sequence and structure within arc-diagram representations.
• Integration with Multiple Sequence Alignments (MSAs): Projects arc diagrams onto MSAs to assess basepair conservation and covariation across sequences.
• Statistical Analysis: Computes numerical statistics for individual basepairs to quantify stability, variability, and support for predicted interactions.

Scientific Applications:

• RNA structure-function studies: Visualizes and quantifies secondary-structure features relevant to RNA functional roles.
• Structure prediction evaluation: Compares predicted and known structures to assess prediction accuracy at the basepair level.
• Evolutionary analysis: Identifies conserved structural motifs and covarying basepairs across alignments for evolutionary inference.

Methodology:

Generates arc-diagram representations of RNA secondary structures, projects these diagrams onto multiple sequence alignments for conservation and covariation assessment, supports sequence-structure annotation and comparison, and computes numerical statistics for each basepair.