BEAM

BEAM identifies RNA secondary structure motifs in large high-throughput datasets such as eCLIP and PAR-CLIP by encoding secondary structures with the BEAR method to enable scalable motif discovery.

Key Features:

• Scalability: Processes tens of thousands of RNA sequences from high-throughput datasets such as eCLIP and PAR-CLIP.
• Fast processing: BEAR encoding simplifies representation of RNA secondary structures into character strings, significantly reducing computational demands for motif discovery.
• BEAR encoding: Transforms each RNA secondary structure into a string of characters for downstream sequence-like analysis.
• Evolutionary insight: Incorporates a substitution matrix derived from the RFAM database to account for evolutionary conservation among homologous RNAs.
• Automated folding and encoding: Performs folding and encoding of RNA sequences with a selectable folding program.
• Results reporting: Produces identified secondary structure motifs with visual logos, measures of statistical significance, graphical representations, and positional information within RNA molecules.

Scientific Applications:

• Gene regulation: Identification of RNA secondary structure motifs that may influence gene expression.
• RNA–protein interactions: Detection of structural motifs relevant for binding by RNA-binding proteins.
• Evolutionary studies: Analysis of conserved RNA secondary structure motifs across homologous RNAs.

Methodology:

Folding of RNA sequences (with selectable folding program), conversion of secondary structures to BEAR encoding strings, use of an RFAM-derived substitution matrix to incorporate evolutionary information, and computation of statistical significance for identified motifs.