RNApdbee

RNApdbee analyzes RNA secondary structures with emphasis on pseudoknot identification, classification, and hierarchical representation from BPSEQ input.

Key Features:

• Pseudoknot Identification and Classification: Detects pseudoknots using novel algorithms, determines their order based on genus and hierarchical folding complexity, and ranks alternative dot-bracket representations using scoring functions.
• Hybrid Dynamic Programming Framework: Combines dynamic programming with exhaustive search and random walk methods, derived from RNA FRABASE 1.0 algorithms, and encodes structures using dot-bracket-letter notation.

Scientific Applications:

• Pseudoknot and RNA Folding Analysis: Supports structural bioinformatics studies by improving accuracy of pseudoknot detection and hierarchical RNA architecture characterization.

Methodology:

RNApdbee processes RNA structures in BPSEQ format, applies hybrid dynamic programming integrating exhaustive search and random walk strategies to detect and classify pseudoknots by genus, and generates scored dot-bracket-letter encodings to represent RNA folding hierarchy.