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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Structural Alignment and Covariation Analysis of RNA Sequences.

Nicolas J Tourasse1, Fabien Darfeuille1

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Bio-Protocol
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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.

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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.