R3D-2-MSA

R3D-2-MSA: Ribosomal RNA Structure–Alignment Mapping and Variant Analysis

R3D-2-MSA maps user-specified ribosomal RNA nucleotide ranges to corresponding columns in curated multiple sequence alignments (MSAs) and links them to representative atomic-resolution 3D structures for integrated sequence and structural analysis.

Key Features:

• Flexible Nucleotide Range Query: Accepts up to five nucleotide ranges with up to 50 positions per range for targeted analysis.
• MSA Column Mapping: Maps specified nucleotide positions to corresponding MSA columns and retrieves aligned sequence data.
• Structured Data Output: Returns MSA column contents in JSON format for computational analysis.
• 3D Structural Visualization: Provides interactive 3D visualization of RNA structures aligned with sequence data.
• Variant and Taxonomic Profiling: Reports sequence variants within specified ranges, including taxonomic annotations and statistical summaries of distinct variants.

Scientific Applications:

• Ribosomal RNA Evolution and Comparative Analysis: Supports molecular evolution, phylogenetics, and comparative genomics by correlating ribosomal RNA sequence variation with 3D structural features across domains of life.

Methodology:

Curated high-quality ribosomal RNA MSAs from diverse biological sources are mapped to nucleotide positions in representative atomic-resolution 3D structures. User-defined nucleotide ranges are projected onto aligned columns, enabling integrated analysis of sequence variation, taxonomic distribution, and structural context.