Telomeres and Cancer Laboratory, Institut Curie, PSL Research University, Sorbonne Universités, CNRS UMR3244, 75005 Paris, France.
Nucleic Acids Res. 2020 Jan 10;48(1):1-15. doi: 10.1093/nar/gkz1097.
Guanine-rich nucleic acids can fold into the non-B DNA or RNA structures called G-quadruplexes (G4). Recent methodological developments have allowed the characterization of specific G-quadruplex structures in vitro as well as in vivo, and at a much higher throughput, in silico, which has greatly expanded our understanding of G4-associated functions. Typically, the consensus motif G3+N1-7G3+N1-7G3+N1-7G3+ has been used to identify potential G-quadruplexes from primary sequence. Since, various algorithms have been developed to predict the potential formation of quadruplexes directly from DNA or RNA sequences and the number of studies reporting genome-wide G4 exploration across species has rapidly increased. More recently, new methodologies have also appeared, proposing other estimates which consider non-canonical sequences and/or structure propensity and stability. The present review aims at providing an updated overview of the current open-source G-quadruplex prediction algorithms and straightforward examples of their implementation.
富含鸟嘌呤的核酸可以折叠成非 B 型 DNA 或 RNA 结构，称为 G-四链体（G4）。最近的方法学发展使得能够在体外以及在体内，以及在更高的通量下，在计算机上对特定的 G-四链体结构进行特征描述，这极大地扩展了我们对 G4 相关功能的理解。通常，使用共识基序 G3+N1-7G3+N1-7G3+N1-7G3+ 从原始序列中识别潜在的 G-四链体。自那时以来，已经开发了各种算法来直接从 DNA 或 RNA 序列预测四链体的潜在形成，并且报告跨物种进行全基因组 G4 探索的研究数量迅速增加。最近，新的方法也出现了，提出了其他考虑非规范序列和/或结构倾向和稳定性的估计值。本综述旨在提供当前开源 G-四链体预测算法的最新概述，并提供其实现的简单示例。
