RNAbor

RNAbor computes RNA secondary structure variations by enumerating delta-neighbors, defined as structures differing by exactly δ base pairs through base pair additions or removals.

Key Features:

• Delta-Neighbor Enumeration: Calculates the number and density of δ-neighbors around a reference structure and identifies the minimum free energy (MFE) structure among them.
• Energy-Based Structural Analysis: Evaluates energies of neighboring structures to identify low-energy alternatives and characterize intermediate conformations.
• Nucleation Site Identification: Detects potential initial base pair formation sites relevant to early folding events.

Scientific Applications:

• RNA Folding Pathway Analysis: Investigates conformational diversity, intermediate states, and energetically favorable alternative structures to study RNA folding dynamics and function.

Methodology:

RNAbor takes an RNA sequence and a reference secondary structure (e.g., MFE structure), enumerates all structures differing by a specified δ base pair distance, and computes statistical and energetic properties to analyze structural neighborhoods and folding pathways.