Evolutionary Conservation of RNA Secondary Structure

Maria Beatriz Walter Costa

doi:10.1007/978-1-0716-2768-6_8

Evolutionary Conservation of RNA Secondary Structure

Methods Mol Biol. 2023:2586:121-146. doi: 10.1007/978-1-0716-2768-6_8.

Author

Maria Beatriz Walter Costa^{1

2}

Affiliations

¹ Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.
² Institute of Laboratory Medicine, Clinical Chemistry und Molecular Diagnostics, University of Leipzig Medical Center, Leipzig, Germany.

PMID: 36705902
DOI: 10.1007/978-1-0716-2768-6_8

Abstract

Noncoding RNAs, ncRNAs, naturally fold into structures, which allow them to perform their functions in the cell. Evolutionarily close species share structures and functions. This occurs because of shared selective pressures, resulting in conserved groups. Previous efforts in finding functional RNAs have been made in detecting conserved structures in genomes or alignments. It may occur that, within a conserved group, species-specific structures arise after species split due to positive selection. Detecting positive selection in ncRNAs is a hard problem in biology as well as bioinformatics. To detect positive selection, one should find species-specific structures within a conserved set. This chapter provides protocols to detect and analyze positive selection in ncRNA structures with the SSS-test and other free software.

Keywords: Conservation; Evolution; Noncoding RNA; Positive selection; Secondary structure.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biological Evolution
Nucleic Acid Conformation
RNA* / genetics
RNA, Untranslated* / chemistry
RNA, Untranslated* / genetics
Software

Substances

RNA
RNA, Untranslated