Department of Molecular Medicine, University of Padova, Padova I-35131, Italy.
CRIBI Biotech Centre, University of Padova, Padova I-35131, Italy.
Bioinformatics. 2020 Jan 15;36(2):393-399. doi: 10.1093/bioinformatics/btz569.
G-quadruplexes (G4s) are non-canonical nucleic acid conformations that are widespread in all kingdoms of life and are emerging as important regulators both in RNA and DNA. Recently, two new higher-order architectures have been reported: adjacent interacting G4s and G4s with stable long loops forming stem-loop structures. As there are no specialized tools to identify these conformations, we developed QPARSE.
QPARSE can exhaustively search for degenerate potential quadruplex-forming sequences (PQSs) containing bulges and/or mismatches at genomic level, as well as either multimeric or long-looped PQS (MPQS and LLPQS, respectively). While its assessment versus known reference datasets is comparable with the state-of-the-art, what is more interesting is its performance in the identification of MPQS and LLPQS that present algorithms are not designed to search for. We report a comprehensive analysis of MPQS in human gene promoters and the analysis of LLPQS on three experimentally validated case studies from HIV-1, BCL2 and hTERT.
QPARSE is freely accessible on the web at http://www.medcomp.medicina.unipd.it/qparse/index or downloadable from github as a python 2.7 program https://github.com/B3rse/qparse.
Supplementary data are available at Bioinformatics online.
G-四链体（G4s）是非经典的核酸构象，广泛存在于所有生命领域，并且作为 RNA 和 DNA 中的重要调节剂而出现。最近，已经报道了两种新的高级结构：相邻相互作用的 G4 和具有稳定长环形成茎环结构的 G4。由于没有专门的工具来识别这些构象，我们开发了 QPARSE。
QPARSE 可以在基因组水平上穷举搜索包含凸起和/或错配的退化潜在四链体形成序列（PQS），以及多聚体或长环 PQS（分别为 MPQS 和 LLPQS）。虽然它与最新技术的评估相当，但更有趣的是它在识别 MPQS 和 LLPQS 方面的性能，而目前的算法并不是专门为搜索这些结构而设计的。我们报告了人类基因启动子中 MPQS 的综合分析，以及 HIV-1、BCL2 和 hTERT 三个实验验证案例研究中 LLPQS 的分析。
QPARSE 可在 http://www.medcomp.medicina.unipd.it/qparse/index 上在线免费访问，也可从 github 下载作为 python 2.7 程序 https://github.com/B3rse/qparse。
补充数据可在 Bioinformatics 在线获得。
