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Structural Alignment and Covariation Analysis of RNA Sequences.

ABSTRACT: RNA molecules adopt defined structural conformations that are essential to exert their function. During the course of evolution, the structure of a given RNA can be maintained via compensatory base-pair changes that occur among covarying nucleotides in paired regions. Therefore, for comparative, structural, and evolutionary studies of RNA molecules, numerous computational tools have been developed to incorporate structural information into sequence alignments and a number of tools have been developed to study covariation. The bioinformatic protocol presented here explains how to use some of these tools to generate a secondary-structure-aware multiple alignment of RNA sequences and to annotate the alignment to examine the conservation and covariation of structural elements among the sequences.

SUBMITTER: Tourasse NJ

PROVIDER: S-EPMC7842705 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Structural Alignment and Covariation Analysis of RNA Sequences.

Tourasse Nicolas J NJ Darfeuille Fabien F

Bio-protocol 20200205 3

RNA molecules adopt defined structural conformations that are essential to exert their function. During the course of evolution, the structure of a given RNA can be maintained via compensatory base-pair changes that occur among covarying nucleotides in paired regions. Therefore, for comparative, structural, and evolutionary studies of RNA molecules, numerous computational tools have been developed to incorporate structural information into sequence alignments and a number of tools have been deve ...[more]

PMID: 33654736

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