RNAexpNumNbors

RNAexpNumNbors computes the expected degree of an RNA secondary structure network, defined as the average number of neighboring structures under uniform or Boltzmann probability distributions.

Key Features:

• Expected Degree Computation: Calculates the average number of neighboring secondary structures for a given RNA sequence using uniform or Boltzmann-weighted ensembles.
• Cubic-Time Algorithm: Implements a C-based algorithm with O(n^3) time and O(n^2) space complexity for efficient analysis of RNA structural networks.

Scientific Applications:

• RNA Structural Diversity Analysis: Quantifies network-based structural complexity and deviations from minimum free energy (MFE) structures, enabling comparison of structural RNAs such as purine riboswitches with random RNA sequences.

Methodology:

Constructs the full secondary structure network for an RNA sequence, defines edges by base pair distance between structures, and computes the expected node degree by averaging over all structures under uniform or Boltzmann ensemble probabilities.