IndelsRNAmute

IndelsRNAmute predicts the effects of insertion, deletion, and substitution mutations on RNA secondary structure to identify deleterious mutations affecting structural RNAs.

Key Features:

• Extension of RNAmute and MultiRNAmute: Extends RNAmute and MultiRNAmute by adding prediction of insertion and deletion (indel) mutations alongside substitutions.
• Suboptimal folding–based algorithm: Uses suboptimal folding solutions to efficiently predict multiple deleterious mutations, including combinations of deletions, insertions, and substitutions.
• User-defined mutation sets: Supports specification of the number and types of mutations to investigate, enabling modeling of combinatorial mutation scenarios.
• Computational complexity handling: Addresses the computational challenges of finding the most deleterious mutation sets in structural RNAs and provides a more practical alternative to brute-force enumeration for long sequences.

Scientific Applications:

• Site-directed mutagenesis: Identifies indel and substitution targets that are likely to disrupt critical RNA secondary-structure motifs for experimental validation.
• Viral research: Evaluates how specific indels and substitutions may disrupt essential structural elements in RNA viruses and affect viral functionality.
• Functional genomics: Predicts impacts of diverse mutation types on RNA stability and structure to support studies of genetic regulation and RNA function.

Methodology:

Builds on the MultiRNAmute method and incorporates strategies for predicting insertion and deletion mutations by stabilizing suboptimal folding solutions or destabilizing the wild-type optimal fold to predict deleterious effects, providing greater efficiency than brute-force approaches.