CARNA web server

CARNA aligns RNA structure ensembles, including pseudoknots, by performing Sankoff-style simultaneous alignment and folding to enable comparative analysis of multiple conserved RNA conformations.

Key Features:

• Simultaneous alignment and folding: Implements Sankoff-style simultaneous alignment and folding and accommodates multiple conserved structures per RNA.
• Intrinsic pseudoknot alignment: Aligns pseudoknots intrinsically, allowing analysis of complex RNAs such as riboswitches and RNAs with conserved folding pathways.
• Structural input/output representation: Uses base pair probability dot plots to represent structural input and output, supporting fixed structures and structure ensembles.
• Constraint-based algorithmics: Employs advanced, constraint-based algorithmic techniques to optimize all structural similarities across inputs simultaneously.
• Benchmark performance: Demonstrates competitive performance with state-of-the-art general-purpose RNA alignment tools on the Bralibase 2.1 benchmark.

Scientific Applications:

• Riboswitch analysis: Enables comparative alignment of riboswitches that adopt multiple conserved structures and may contain pseudoknots.
• Conserved folding pathway studies: Supports analysis of RNAs with conserved folding pathways by aligning multiple structural conformations per sequence.
• Comparative RNA structure analysis: Facilitates comparative studies requiring simultaneous consideration of entire RNA structure ensembles to elucidate structure–function relationships.

Methodology:

Performs Sankoff-style simultaneous alignment and folding using constraint-based algorithmic techniques to optimize structural similarities across RNA structure ensembles represented as base pair probability dot plots.