ShapeSorter

ShapeSorter predicts RNA structure features by integrating evolutionary conservation and SHAPE (Selective 2'-Hydroxyl Acylation analyzed by Primer Extension) probing evidence within a probabilistic framework.

Key Features:

• Probabilistic Framework: Employs a fully probabilistic approach to integrate SHAPE (Selective 2'-Hydroxyl Acylation analyzed by Primer Extension) probing data and evolutionary conservation without assuming thermodynamic minimum-free-energy folding.
• Detection of Diverse Structural Features: Detects RNA structural heterogeneity, pseudoknots, transient structures, and mutually exclusive conformations.
• Performance Benchmarking: Benchmarked against state-of-the-art methods and demonstrated superior performance in predicting base pairs.
• Statistical Validation: Estimates P-values for predicted RNA structural features to enable filtering and ranking of predictions.

Scientific Applications:

• RNA Structure Determination: Integrates high-throughput SHAPE probing data to aid in in vivo RNA secondary-structure determination.
• Evolutionary Studies: Incorporates evolutionary evidence to identify conserved structural features across species or gene families.
• Functional Genomics: Provides structure predictions that can inform studies of RNA-mediated gene regulation and disease mechanisms.

Methodology:

Uses a fully probabilistic model that integrates SHAPE (Selective 2'-Hydroxyl Acylation analyzed by Primer Extension) probing data and evolutionary conservation, and computes P-values for predicted structural features.