ViennaRNA

ViennaRNA predicts and analyzes RNA secondary structures and RNA–RNA interactions using dynamic programming and thermodynamic parameters, including the Turner 2004 energy model, to study RNA folding, base pairing probabilities, and structure-function relationships.

Key Features:

• C library and programs: Provides a C code library and multiple standalone programs to perform RNA folding and analysis calculations.
• Dynamic programming algorithms: Implements dynamic programming algorithms to compute RNA ground states, base pairing probabilities, and thermodynamic properties.
• Thermodynamic model: Uses the Turner 2004 energy model for thermodynamic parameterization of folding calculations.
• ViennaRNA Package 2.0 enhancements: Includes expanded tools for RNA–RNA interaction prediction, restricted-ensemble analyses, centroid and maximum expected accuracy (MEA) structures derived from base pairing probabilities, z-score calculations for local stability, and OpenMP support for concurrent computation.
• Parallelization: Supports OpenMP-based concurrent computations to utilize multi-core CPUs.
• Input format: Accepts fasta format input for sequence-based analyses.
• Backward compatibility: Maintains compatibility with previous ViennaRNA versions.

Scientific Applications:

• Secondary structure prediction: Predicts RNA secondary structures and ground states for single sequences.
• Probabilistic structure analysis: Computes base pairing probabilities and derives centroid and MEA structures for probabilistic structure inference.
• Local stability assessment: Evaluates locally stable secondary structures using z-scores.
• RNA–RNA interaction analysis: Predicts and analyzes RNA–RNA interactions between nucleic acid sequences.
• Restricted ensemble analysis: Analyzes restricted ensembles of structures for constrained folding studies.
• Structure-function and evolutionary studies: Investigates RNA structure–function relationships and evolutionary conservation of nucleic acid structures.

Methodology:

Computations use a C code library and standalone programs implementing dynamic programming algorithms with the Turner 2004 energy model to compute ground states, base pairing probabilities, thermodynamic properties, centroid and MEA structures, z-scores, RNA–RNA interactions and restricted-ensemble analyses, with optional OpenMP parallelization and fasta input support.