"Foxford" Online School, Moscow, 115127, Russia.
Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
Sci Rep. 2024 Nov 19;14(1):28587. 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 .
近年来，RNA 二级结构检测的实验和计算方法的进展揭示了 RNA 结构元件在活细胞内各种分子过程中的关键作用。已经证明，整个病毒基因组的二级结构通常负责在病毒生命周期中执行关键功能，并且还影响病毒进化。为了研究病毒 RNA 二级结构的作用，除了实验技术外，使用生物信息学工具对于分析各种二级结构模式也很重要，包括发夹环、内部环、多分叉、外部环、凸起、茎和假结。在这里，我们引入了一个用于分析病毒基因组中 RNA 二级结构元件的 Python 包，其中包括常见二级结构模式的识别、这些结构元件的描述性统计信息的生成以及它们基本属性的提供。我们应用开发的软件包来分析从文献中收集的完整病毒基因组的二级结构，旨在深入了解病毒的功能和进化。该软件包和病毒基因组的二级结构集合都可以在 http://github.com/KazanovLab/RNAsselem 上获得。
