MutaRNA

MutaRNA predicts and visualizes mutation-induced structural changes in RNA molecules to assess how single-nucleotide polymorphisms (SNPs) and single-nucleotide variants (SNVs) alter RNA folding, base-pairing probabilities, and accessibility relevant to post-transcriptional regulation.

Key Features:

• Mutation-focused structural analysis: Analyzes the structural impact of single-nucleotide polymorphisms (SNPs) and single-nucleotide variants (SNVs) on RNA folding.
• Base-pairing probability computation: Computes probabilities of base pairing (base-pairing probability matrices) for both wildtype and mutated RNA sequences.
• Position-wise unpaired probabilities: Computes position-wise unpaired (accessibility) probabilities for wildtype and mutated sequences.
• Comparative profiling: Performs direct comparisons between wildtype and mutated probability profiles to identify mutation-induced changes.
• Visualizations: Generates differential heatmap-like dot plots, circular plots, and arc diagrams to display structural differences.
• Local aberration detection: Highlights local structural aberrations that may be obscured in standard outputs.
• Targeted RNA classes: Supports analysis of non-coding RNAs and cis-regulatory elements of messenger RNAs.

Scientific Applications:

• Structure-function interpretation: Interpreting how SNVs and SNPs alter RNA secondary structure and base-pairing potentials.
• Post-transcriptional regulation assessment: Evaluating consequences of mutation-induced structural changes for post-transcriptional regulation and RNA function.
• Non-coding RNA and cis-regulatory studies: Investigating structural perturbations in non-coding RNAs and cis-regulatory elements within mRNAs.
• Comparative accessibility analysis: Providing comparative overviews of mutation-induced changes in base-pairing potentials and accessibility.

Methodology:

Computes base-pairing probabilities and position-wise unpaired probabilities for wildtype and mutated RNA sequences, compares these probability profiles, and visualizes differences using differential heatmap-like dot plots, circular plots, and arc diagrams to reveal local structural aberrations.