Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, Poznan, 60-965, Poland.
Poznan Supercomputing and Networking Center, Jana Pawla II 10, Poznan, 61-139, Poland.
BMC Bioinformatics. 2020 Jan 31;21(1):40. doi: 10.1186/s12859-020-3385-1.
Quadruplexes are specific structure motifs occurring, e.g., in telomeres and transcriptional regulatory regions. Recent discoveries confirmed their importance in biomedicine and led to an intensified examination of their properties. So far, the study of these motifs has focused mainly on the sequence and the tertiary structure, and concerned canonical structures only. Whereas, more and more non-canonical quadruplex motifs are being discovered.
Here, we present ElTetrado, a software that identifies quadruplexes (composed of guanine- and other nucleobase-containing tetrads) in nucleic acid structures and classifies them according to the recently introduced ONZ taxonomy. The categorization is based on the secondary structure topology of quadruplexes and their component tetrads. It supports the analysis of canonical and non-canonical motifs. Besides the class recognition, ElTetrado prepares a dot-bracket and graphical representations of the secondary structure, which reflect the specificity of the quadruplex's structure topology. It is implemented as a freely available, standalone application, available at https://github.com/tzok/eltetrado.
The proposed software tool allows to identify and classify tetrads and quadruplexes based on the topology of their secondary structures. It complements existing approaches focusing on the sequence and 3D structure.
四联体是特定的结构基序，例如在端粒和转录调控区域中出现。最近的发现证实了它们在生物医学中的重要性，并促使人们对它们的性质进行了深入研究。到目前为止，这些基序的研究主要集中在序列和三级结构上，并且只关注规范结构。然而，越来越多的非规范四联体基序被发现。
在这里，我们介绍了 ElTetrado，这是一款软件，可以识别核酸结构中的四联体（由鸟嘌呤和其他含核碱基的四联体组成），并根据最近引入的 ONZ 分类法对它们进行分类。分类是基于四联体及其组成四联体的二级结构拓扑结构。它支持规范和非规范基序的分析。除了类别的识别，ElTetrado 还准备了二级结构的点线和图形表示，反映了四联体结构拓扑的特异性。它作为一个免费的独立应用程序实现，可在 https://github.com/tzok/eltetrado 上获得。
所提出的软件工具允许根据二级结构的拓扑结构识别和分类四联体及其组成的四联体。它补充了专注于序列和 3D 结构的现有方法。
