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Published on: May 24, 2017
Structural Alignment and Covariation Analysis of RNA Sequences
Nicolas J Tourasse1, Fabien Darfeuille1
1ARNA Laboratory, INSERM U1212, CNRS UMR5320, University of Bordeaux, Bordeaux, France.
This study presents a bioinformatic protocol for RNA sequence analysis. It enables the generation of structure-aware multiple alignments and annotation to study conserved and covarying structural elements.
Area of Science:
- Bioinformatics
- Molecular Biology
- Computational Biology
Background:
- RNA molecules possess crucial structural conformations for their function.
- Compensatory base-pair changes maintain RNA structure evolutionarily through covarying nucleotides.
- Existing computational tools aid in incorporating structural information and studying covariation in RNA sequences.
Purpose of the Study:
- To present a bioinformatic protocol for RNA sequence analysis.
- To generate secondary-structure-aware multiple alignments of RNA sequences.
- To annotate alignments for examining conservation and covariation of structural elements.
Main Methods:
- Utilizing computational tools for RNA sequence alignment.
- Incorporating structural information into sequence alignments.
- Applying tools to study nucleotide covariation within RNA structures.
Main Results:
- A protocol for generating structure-aware multiple RNA sequence alignments.
- Annotation methods to analyze conservation of structural elements.
- Analysis of covarying nucleotides within paired RNA regions.
Conclusions:
- The presented protocol facilitates comparative, structural, and evolutionary studies of RNA.
- It enables detailed examination of RNA structural element conservation and covariation.
- This approach enhances understanding of RNA structure-function relationships.
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