RNAentropy

RNAentropy computes conformational entropy of RNA secondary structures using cubic time thermodynamic algorithms based on the Turner energy model.

Key Features:

• Thermodynamic Entropy Calculation: Implements two cubic time algorithms to calculate structural entropy from RNA secondary structure ensembles using Turner'99 and Turner'04 free energy parameters derived from UV absorption experiments.
• Temperature-Dependent Analysis: Computes and plots structural entropy as a function of temperature and supports analysis of specific genomic regions, including thermoswitches and viral genomes.

Scientific Applications:

• RNA Thermodynamics and Functional Studies: Enables analysis of structural entropy in thermoswitches such as the ROSE element, hammerhead ribozyme cleavage activity, and genomic regions including HIV-1.

Methodology:

RNAentropy applies thermodynamic ensemble-based calculations under the Turner energy model to derive structural entropy, providing consistent and efficient alternatives to stochastic context-free grammar (SCFG)-based entropy computations.