RNAMotifScan

RNAMotifScan identifies and aligns RNA structural motifs using a structure-based alignment algorithm that incorporates canonical and non-canonical base pairing interactions.

Key Features:

• Isosteric Base Pair Consideration: Integrates Watson-Crick canonical base pairs and non-canonical isosteric interactions derived from uncommon hydrogen-bonding patterns to capture RNA structural diversity.
• Multi-Pairing Analysis: Detects complex RNA motifs involving multi-pairing interactions beyond nested canonical base pairs.
• RNA Structural Alignment: Applies a motif-specific structural alignment method to compare RNA motifs with substantial three-dimensional structural variation.

Scientific Applications:

• Motif Identification: Identifies RNA structural motifs including kink-turns, C-loops, sarcin-ricin loops, reverse kink-turns, and E-loops.
• Large-Scale Database Analysis: Searches RNA structures across the Protein Data Bank (PDB) to estimate motif abundance in diverse RNA molecules.

Methodology:

Performs structural alignment incorporating canonical Watson-Crick and non-canonical isosteric base pairs.