RNAgraphdist

RNAgraphdist computes the equilibrium distribution of graph-distances between nucleotide pairs in RNA secondary structures to approximate spatial proximity and domain organization.

Key Features:

• Graph-Distance Distribution Calculation: Calculates equilibrium distributions of secondary structure graph-distances between arbitrary nucleotide pairs to approximate spatial relationships.
• Dynamic Programming and Sampling: Uses a dynamic programming algorithm reducing complexity from O(n^6 D^5) to O(n^4) and incorporates sampling approaches for long-range interactions in large RNAs.

Scientific Applications:

• RNA Structural and Functional Analysis: Supports investigation of functional domain organization, long-range interactions in RNA virus genomes, and comparison with single-molecule Förster resonance energy transfer (smFRET) data.

Methodology:

RNAgraphdist processes RNA secondary structures generated by RNAsubopt and computes equilibrium graph-distance distributions using dynamic programming and sampling methods to model nucleotide pair distances.