RASS

RASS aligns RNA molecules in a joint sequence-structure space to compare and analyze sequence and three-dimensional structural variation.

Key Features:

• Integration of Sequence and Structure: Combines RNA sequence information with three-dimensional structural data by treating RNA molecules as 3D curves with encoded sequences on additional dimensions to enable joint alignment.
• Elastic Shape Analysis (ESA): Applies Elastic Shape Analysis (ESA) to treat RNAs as elastic shapes and quantify similarity using geodesic distance.
• Mathematical Rigor: Defines and computes means and covariances of full RNA structures to support construction of probability distributions over RNA structure spaces.
• Function Prediction and Classification: Predicts RNA functions and performs classification by leveraging combined sequence and structural information, with reported performance superior to existing methods.
• Evolutionary Insights: Enables detailed sequence-structure comparisons to investigate evolutionary relationships among RNA families.

Scientific Applications:

• Functional Genomics: Predicts functions of novel or uncharacterized RNAs by comparing joint sequence-structure representations to annotated RNAs.
• Structural Biology: Provides structural comparisons that inform analyses of RNA stability, dynamics, and molecular interactions.
• Evolutionary Studies: Investigates evolutionary trajectories and relationships among RNA families through sequence-structure alignments.

Methodology:

Encodes RNA sequences onto their three-dimensional structures, representing RNAs as 3D curves with sequences on additional dimensions, and aligns them in a multidimensional sequence-structure space; applies Elastic Shape Analysis to compute geodesic distances and derives means, covariances, and probability distributions over RNA structure space.