RNAfold

RNAfold is a program within the ViennaRNA Package used to predict the secondary structure of a single RNA sequence. It computes the minimum free-energy (MFE) structure under the Turner energy model, providing a canonical prediction of base pairings that stabilize the molecule.

The primary outputs include the MFE structure in dot-bracket notation and the associated free energy value (in kcal/mol). When run with the partition function option, RNAfold also calculates base-pairing probabilities and prints a probability matrix or dot plot, enabling assessment of structural ensembles and alternative pairings beyond the single MFE structure.

Method and scope: RNAfold uses dynamic programming to evaluate possible secondary structures without pseudoknots, applying the established Turner energy parameters. It is designed for non-pseudoknotted RNA structures and supports sequence constraints, energy parameter files, and various output options for integration into workflows. It can also report the centroid structure, which represents the structure with maximum expected accuracy under the ensemble distribution produced by the partition function.

Input and usage: The program accepts a single RNA sequence or a FASTA file as input. Output typically includes the predicted MFE structure and energy, with optional partition-function related data when requested. RNAfold is widely used to study RNA folding thermodynamics, to annotate functional RNAs, and to inform RNA design and comparative analyses in computational biology.

Availability and context: RNAfold is a core tool in the ViennaRNA Package, frequently cited and integrated into research pipelines for RNA structure prediction and analysis.