BEAGLE 2.0

BEAGLE 2.0 detects structural similarities between user-provided RNA molecules and expanded datasets of experimentally supported RNA secondary structures.

Key Features:

• Pairwise alignment: Aligns RNA secondary structures through dynamic programming using the BEAR encoding for RNA secondary structure representation.
• Multiple input formats: Accepts RNA sequences or combinations of sequences and secondary structures in dot-bracket or BEAR format.
• Expanded structure datasets: Includes SHAPE-derived structures from Homo sapiens, Mus musculus, Danio rerio, Escherichia coli, Bacillus subtilis, and viruses including SARS-CoV-2; predicted structures from the NONCODE database for animals and plants; and structures based on constraints from conserved positions within Rfam families.
• Output metrics: Provides pairwise alignments with measures of structural similarity and statistical significance.
• Visual representation: Displays secondary structures with structural elements highlighted in different colors.

Scientific Applications:

• Homology detection: Identifies structural homologies undetectable by sequence analysis alone through detection of structural conservation.
• RNA structure comparison: Enables comparison of RNA secondary structures against experimentally supported structure datasets.
• Cross-species analysis: Supports searches across structures from multiple organisms and viral genomes.

Methodology:

BEAGLE 2.0 uses the BEAGLE algorithm with dynamic programming for pairwise alignments of RNA secondary structures, leveraging the BEAR encoding for RNA secondary structure representation.