RNAwolf

RNAwolf predicts RNA secondary structures and models non-canonical base pairs and extended secondary-structure motifs to improve secondary and tertiary structure prediction.

Key Features:

• Theoretical Model: Uses a model based on 2-diagrams to represent various RNA pair families and extended secondary-structure motifs, including non-canonical base pairs.
• Parameter Optimization and Folding Algorithms: Provides optimization routines and folding algorithms for tuning parameters specific to RNA pair families and extended motifs.
• Program Suite: Includes multiple programs for parameter optimization, structure prediction, and evaluation of secondary-structure models.
• Extended Motif Visualization: Offers visualization capabilities tailored to extended secondary structures with shared nucleotides to explore intricate structural motifs.

Scientific Applications:

• Improved Secondary Structure Prediction: Enhances prediction accuracy by explicitly modeling non-canonical base pairs and extended motifs for downstream tertiary-structure and functional analyses.
• Simultaneous Folding and Alignment: Supports analyses that require handling complex structural features for integrated folding and sequence-alignment tasks.

Methodology:

Represents RNA pair families and extended motifs using a 2-diagram theoretical model and applies parameter optimization routines and folding algorithms via a suite of programs; includes visualization of extended motifs.