RNAmutants

RNAmutants computes ensembles of low-energy RNA secondary structures generated by all possible k-mutations of an input sequence and evaluates their structural and energetic effects.

Key Features:

• k-Mutation Ensemble Analysis: Enumerates all possible k-mutations (user-defined k) and computes corresponding low-energy secondary structure ensembles to assess mutation-induced structural variation.
• Deleterious Mutation Prediction: Identifies mutations that significantly alter minimum free energy (MFE) secondary structures, enabling analysis of regulatory regions such as those in hepatitis C virus and human immunodeficiency virus (HIV).

Scientific Applications:

• Molecular Evolution and Functional Genomics: Quantifies structural impacts of mutations on noncoding RNAs to support studies of RNA evolution, regulatory function, and pathogenic variation.

Methodology:

RNAmutants uses dynamic programming algorithms to compute minimum free energy (MFE) secondary structures for all k-mutant sequences and evaluates structural ensembles to quantify mutation-induced changes in RNA stability and conformation.