MutualFold

MutualFold integrates NGS-derived enzymatic and chemical probing data to simultaneously predict multiple RNA secondary structures and resolve coexisting alternative conformations.

Key Features:

• Integration with NGS technology: Utilizes NGS-based RNA structure probing to incorporate enzymatic and chemical probing signals into folding analyses.
• Combinatorial approach for alternative structures: Employs a combinatorial solution to simultaneously fold two alternative RNA structures from mixed probing data, accounting for signal contamination between conformations.
• Algorithmic innovation: Implements an algorithm that discerns and reconstructs multiple RNA conformations despite overlapping probing signals that can mislead minimum free energy (MFE) folding algorithms.

Scientific Applications:

• RNA Riboswitch Analysis: Recovers distinct ON and OFF structures of riboswitches such as the adenine riboswitch and the thiamine pyrophosphate (TPP) riboswitch.
• Enhanced Structural Predictions: Improves reliability of RNA secondary structure predictions in scenarios with coexisting alternative structures, aiding interpretation of experimental probing data.

Methodology:

MutualFold applies a combinatorial algorithm to process NGS-derived enzymatic and chemical probing information and simultaneously predict multiple RNA secondary structures by modeling mixed probing signals.