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CARNA--alignment of RNA structure ensembles
Dragos Alexandru Sorescu1, Mathias Möhl, Martin Mann
1Bioinformatics Group, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany.
Nucleic Acids Research
|June 13, 2012
Summary
CARNA is a new web server for RNA structure alignment. It uniquely handles multiple conserved structures and pseudoknots, overcoming limitations of standard methods for analyzing complex RNA molecules.
Area of Science:
- Computational Biology
- Bioinformatics
- Structural Biology
Background:
- Simultaneous RNA alignment and folding (Sankoff-style) is the gold standard but predicts a single consensus structure.
- This limitation is critical for RNAs with multiple conserved structures, such as riboswitches or those with conserved folding pathways.
Purpose of the Study:
- Introduce a web server for the CARNA tool, offering a flexible interface for RNA structure alignment.
- Enable multiple RNA alignment for RNAs with multiple conserved structures and intrinsic pseudoknot alignment.
Main Methods:
- CARNA utilizes advanced, constraint-based algorithmic techniques to optimize structural similarities across entire RNA structure ensembles.
- Input and output are represented as base pair probability dot plots for flexible input and visual analysis.
- The tool intrinsically aligns pseudoknots, a feature not standard in Sankoff-style approaches.
Main Results:
- CARNA supports RNAs with multiple conserved structures per RNA and aligns pseudoknots intrinsically.
- The web server provides a complete and convenient interface for the CARNA tool.
- CARNA's performance is on par with state-of-the-art general-purpose RNA alignment tools, as validated by a Bralibase 2.1 benchmark.
Conclusions:
- CARNA offers a unique solution for aligning RNAs with multiple conserved structures and pseudoknots.
- The CARNA web server enhances accessibility to advanced RNA alignment capabilities.
- This tool advances comparative RNA analysis, particularly for complex RNA molecules.
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