Ribostral

Ribostral integrates atomic-resolution RNA structural information with sequence alignments to map permissible and impermissible nucleotide substitutions at basepair positions using isostericity matrices.

Key Features:

• Isostericity matrix superposition: Superposes isostericity matrices derived from basepair interactions observed in RNA structures onto sequence alignments to identify allowed and unallowed nucleotide substitutions at each BP position.
• Integration with atomic-resolution structures: Overlays atomic-resolution RNA structural data onto sequence alignments to inform assessment of basepairing compatibility.
• Basepair interaction families and sub-families: Utilizes isostericity matrices that represent different families and sub-families of basepair interactions.
• Alignment error detection: Highlights substitutions that are inconsistent with structural isostericity to identify potential misalignments for correction.
• Visual representation of substitution permissibility: Provides a representation of permissible and impermissible nucleotide changes at each alignment position when matrices are overlaid.

Scientific Applications:

• Structural Biology: Supports analysis of RNA structure–function relationships by relating sequence variation to basepair interaction types observed in atomic-resolution structures.
• RNA Sequence Analysis: Refines sequence alignments by incorporating structural constraints from isostericity matrices to improve accuracy for comparative and functional studies.
• Error Detection in Alignments: Detects alignment regions with substitutions incompatible with known basepair isostericity, aiding downstream analyses such as molecular modeling and comparative genomics.

Methodology:

Ribostral integrates RNA atomic-resolution structures with sequence alignments, applies isostericity matrices that encode families and sub-families of basepair interactions, and overlays those matrices onto alignments to indicate permissible and impermissible nucleotide substitutions at each basepair position.