pknotsRG

pknotsRG predicts RNA secondary structures including pseudoknots to identify energetically favorable folding conformations.

Key Features:

• Incorporation of Pseudoknots: Handles pseudoknot structures including canonical simple recursive pseudoknots in the predicted secondary structures.
• Energy Minimization: Uses the Turner energy rules to predict minimum free energy RNA secondary structures.
• Algorithmic Efficiency: Implemented in C with a reported 60-fold increase in speed compared to earlier implementations.
• Suboptimal Foldings Enumeration: Enumerates suboptimal foldings up to a user-specified energy threshold to explore alternative conformations.
• Sliding Window Mode: Provides a sliding window mode for fast analysis of long sequences or large datasets.
• Visualization Output: Produces outputs compatible with PseudoViewer Web Service and RNAmovies for visualizing structures and suboptimal foldings.

Scientific Applications:

• Pseudoknot RNA analysis: Enables prediction and analysis of RNAs that contain pseudoknot structures.
• Structural genomics and RNA folding studies: Supports investigation of energetically optimal and alternative RNA conformations for structural genomics research.
• Virology: Facilitates structural analysis of viral genomes where pseudoknots contribute to function.

Methodology:

Performs energy minimization using the Turner energy rules, explicitly includes pseudoknots (canonical simple recursive pseudoknots), enumerates suboptimal foldings up to a user-specified threshold, supports a sliding-window mode for long sequences, and is implemented in C with a reported 60-fold speed increase.