BEAR Brand nEw Alphabet for RNA

BEAR Brand nEw Alphabet for RNA encodes RNA secondary structures as a context-aware string representation to enable precise analysis, comparison, classification, motif discovery, and phylogenetic assessment.

Key Features:

• Context-Aware Structural Encoding: Replaces dot-bracket notation with a string-based encoding in which each character uniquely represents specific secondary structure elements (loops, stems, bulges, internal loops) and their lengths.
• Enhanced Structural Representation: Incorporates element-length information to reduce ambiguity and provide more informative descriptions of RNA secondary structures.
• Structural Variation Quantification: Analyzes multiple alignments of related RNAs to quantify structural variation tolerated within RNA families and converts this variation into transition rates among secondary structure elements.
• MBR Substitution Matrix: Implements the MBR matrix derived from encoded structural information to align and compare RNA secondary structures while accounting for evolutionary relationships.

Scientific Applications:

• RNA Secondary Structure Analysis: Enables detailed characterization of secondary structure elements and their distribution within RNA molecules.
• Comparison and Classification: Facilitates comparison and classification of RNA molecules based on encoded structural features and alignment scores using the MBR matrix.
• Motif Finding: Supports discovery of recurring structural motifs by providing precise, length-aware structural representations.
• Phylogenetic Studies: Allows exploration of evolutionary relationships among RNAs by aligning secondary structures using transition rates and the MBR substitution matrix.

Methodology:

Encode secondary structures as a string where each character denotes a specific element type and length; analyze multiple sequence/structure alignments of related RNAs to quantify structural variation and derive transition rates among structural elements; construct and apply the MBR substitution matrix to align and compare encoded secondary structures.