Tourasse Nicolas J, Darfeuille Fabien
ARNA Laboratory, INSERM U1212, CNRS UMR5320, University of Bordeaux, Bordeaux, France.
Bio Protoc. 2020 Feb 5;10(3):e3511. doi: 10.21769/BioProtoc.3511.
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.
RNA分子会采用特定的结构构象，这些构象对于发挥其功能至关重要。在进化过程中，给定RNA的结构可以通过配对区域中共同变化的核苷酸之间发生的补偿性碱基对变化得以维持。因此，为了进行RNA分子的比较、结构和进化研究，已经开发了许多计算工具，将结构信息纳入序列比对，并且还开发了一些工具来研究共变。本文介绍的生物信息学方案解释了如何使用其中一些工具来生成RNA序列的二级结构感知多序列比对，并对标注该比对以检查序列之间结构元件的保守性和共变性。
