Analysis of the abundance and diversity of RNA secondary structure elements in RNA viruses using the RNAsselem Python package

• Published in: Scientific reports Vol. 14; no. 1; pp. 28587 - 8
• Main Authors: Kazanov, Fedor M., Matveev, Evgenii V., Ponomarev, Gennady V., Ivankov, Dmitry N., Kazanov, Marat D.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 19-11-2024; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114/794; 631/326/596/2148; 631/45/500; Bioinformatics; Connectivity table; Genomes; Genomic analysis; Humanities and Social Sciences; multidisciplinary; Protein structure; RNA secondary structure; RNA viruses; Science; Science (multidisciplinary); Secondary structure; Statistical analysis; WUSS; RNA viruses; Connectivity table; RNA secondary structure; WUSS
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-80240-5

Recent advancements in experimental and computational methods for RNA secondary structure detection have revealed the crucial role of RNA structural elements in diverse molecular processes within living cells. It has been demonstrated that the secondary structure of the entire viral genome is often responsible for performing crucial functions in the viral life cycle and also influences virus evolution. To investigate the role of viral RNA secondary structure, alongside experimental techniques, the use of bioinformatics tools is important for analyzing various secondary structure patterns, including hairpin loops, internal loops, multifurcations, external loops, bulges, stems, and pseudoknots. Here, we have introduced a Python package for analyzing RNA secondary structure elements in viral genomes, which includes the recognition of common secondary structure patterns, the generation of descriptive statistics for these structural elements, and the provision of their basic properties. We applied the developed package to analyze the secondary structures of complete viral genomes collected from the literature, aiming to gain insights into viral function and evolution. Both the package and the collection of secondary structures of viral genomes are available at
http://github.com/KazanovLab/RNAsselem
.