SCFG Structural Entropy

SCFG Structural Entropy computes Shannon entropy of RNA secondary-structure ensembles using stochastic context-free grammars to quantify ensemble diversity and the probability distributions of alternative equilibrium structures.

Key Features:

• Entropy Calculation: Implements Shannon entropy to quantify the diversity within RNA structural ensembles.
• Polynomial Time Implementation: Derives and computes SCFG-ensemble entropy in polynomial time for both ambiguous and unambiguous grammars.
• Application to microRNA and ncRNA: Applied to microRNA sequences, which typically show low folding entropy, and to non-coding RNA (ncRNA) families that can exhibit high folding entropy.
• Enhanced Modeling and Analysis: Integrates improved SCFG models and conducts targeted randomization tests to probe folding characteristics of RNA families.

Scientific Applications:

• RNA Structure Prediction: Quantifies ensemble diversity to aid prediction and analysis of potential RNA secondary structures.
• Comparative Genomics: Assesses structural diversity across RNA families or species using entropy-based metrics.
• Functional Annotation: Identifies ncRNAs with high folding entropy that may correlate with regulatory or catalytic functions.

Methodology:

Models RNA secondary-structure ensembles with stochastic context-free grammars and derives Shannon entropy that is computed in polynomial time for ambiguous and unambiguous grammars, with integration of improved SCFG models and application of targeted randomization tests.