Web-Beagle

Web-Beagle performs pairwise global and local alignment of RNA secondary structures to identify structurally homologous regions and support comparative analyses of RNA structure-function relationships.

Key Features:

• BEAR encoding and MBR substitution matrix: Uses the BEAR (BEar Alignment Global and Local) encoding scheme together with the MBR substitution matrix to represent and score RNA structural elements.
• Alignment modes: Performs pairwise global and local alignment of RNA secondary structures.
• Input handling and structure prediction: Accepts RNA sequences and structures or primary sequences alone, and predicts secondary structures for sequence-only inputs with RNAfold using free energy minimization.
• High-throughput alignments: Computes up to 10,000 alignments per execution.
• Dataset comparison: Enables comparison against five pre-compiled datasets, including long non-coding RNAs (lncRNAs) and 3' untranslated regions (3' UTRs).
• Outputs and statistics: Produces pairwise alignments with measures of structural similarity and statistical significance for each alignment.
• Performance: Benchmarking indicates lower computational complexity and reduced running time compared to other available methods.

Scientific Applications:

• Structural region identification: Identifies structurally related regions across RNAs to detect structural homology.
• Functional annotation support: Aids functional annotation by locating conserved structural elements that may underlie function.
• Comparative and evolutionary analysis: Enables comparative analysis of lncRNAs and 3' UTRs across datasets to study structural conservation.
• Structure-function relationship studies: Supports investigations into RNA structure-function relationships by providing structural similarity metrics.

Methodology:

Web-Beagle applies the BEAR encoding scheme with the MBR substitution matrix to perform pairwise global or local alignments of RNA secondary structures, and uses RNAfold free-energy minimization to predict secondary structures when only primary sequences are provided.