RNALOSS

RNALOSS computes and analyzes locally optimal secondary structures of RNA sequences to characterize their distribution, potential kinetic traps, and implications for folding pathways, kinetics, comparative analysis, functional roles, and regulatory mechanisms.

Key Features:

• Locally optimal secondary structure computation: Computes and analyzes locally optimal RNA secondary structures for individual sequences.
• Distribution and kinetic-trap identification: Analyzes the distribution of locally optimal structures to identify potential kinetic traps during RNA folding.
• Folding dynamics and pathway characterization: Addresses structural dynamics, folding pathways, and folding kinetics.
• Comparative RNAomics analysis: Supports comparative analysis across the RNA complement of an organism within an RNAomics framework.
• Non-coding RNA focus: Applies to microRNA, small interfering RNA, riboswitches, and ribozymes.
• Sequence design guidance: Informs design of RNA sequences with desirable properties such as low folding energy and efficient, robust folding kinetics.

Scientific Applications:

• RNA folding pathway studies: Characterizes folding pathways and identifies kinetic traps that affect folding kinetics.
• RNA design and engineering: Guides design of sequences optimized for low folding energy and robust folding behavior.
• Non-coding RNA functional studies: Supports investigation of functional roles and regulatory mechanisms of microRNA, small interfering RNA, riboswitches, and ribozymes.
• Comparative RNAomics: Enables comparative analysis of structural features across an organism's RNAs.
• Folding energy distribution analysis: Analyzes distributions of folding energies among locally optimal structures.

Methodology:

Computation and analysis of locally optimal RNA secondary structures and their distribution to identify potential kinetic traps and inform sequence design.