IPANEMAP

IPANEMAP predicts RNA secondary structures by integrating multiple chemical probing reactivity profiles to identify stable, experimentally supported conformations.

Key Features:

• Integration of multiple probing protocols: Processes reactivity profiles from chemical probing techniques including SHAPE (Selective 2'-Hydroxyl Acylation analyzed by Primer Extension), DMS (Dimethyl Sulfate), and enzymatic methods.
• Automated interpretation: Automates the interpretation of multiple probing profiles to produce reproducible structure modeling outcomes.
• Sampling, clustering, and multi-optimization: Employs sampling, clustering, and multi-optimization techniques to obtain predicted secondary structures supported by experimental data.
• Versatile data handling: Accepts both publicly available and study-specific reactivity profiles and has been validated on single-probing datasets.

Scientific Applications:

• Probing assay design: Informs the design of more informative chemical probing assays by highlighting experimentally supported structural features.
• Conformational analysis: Identifies dominant RNA conformations inferred from combined reactivity data.
• RNA function and interaction studies: Supports investigations of RNA function, interactions, and dynamics by providing experimentally grounded secondary-structure models.

Methodology:

Processes input sequences with multiple chemical probing reactivity profiles (SHAPE, DMS, enzymatic) and applies sampling, clustering, and multi-optimization techniques to derive stable, experimentally supported secondary-structure predictions.