pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R.
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TLDR
A newly developed Bioconductor package for identifying potential quadruplex‐forming sequences (PQS), which allows for sequence searches that accommodate possible divergences from the optimal G4 base composition and demonstrates that the algorithm behind the searches has a 96% accuracy.Abstract:
Motivation: G-quadruplexes (G4s) are one of the non-B DNA structures easily observed in vitro and assumed to form in vivo. The latest experiments with G4-specific antibodies and G4-unwinding helicase mutants confirm this conjecture. These four-stranded structures have also been shown to influence a range of molecular processes in cells. As G4s are intensively studied, it is often desirable to screen DNA sequences and pinpoint the precise locations where they might form. Results: We describe and have tested a newly-developed Bioconductor package for identifying potential quadruplex-forming sequences (PQS). The package is easy-to-use, flexible and customizable. It allows for sequence searches that accommodate possible divergences from the optimal G4 base composition. A novel aspect of our research was the creation and training (parametrization) of an advanced scoring model which resulted in increased precision compared to similar tools. We demonstrate that the algorithm behind the searches has a 96% accuracy on 392 currently known and experimentally observed G4 structures. We also carried out searches against the recent G4-seq data to verify how well we can identify the structures detected by that technology. The correlation with pqsfinder predictionswas 0.622, higher than the correlation 0.491 obtained with the second best G4Hunter. Availability:http://bioconductor.org/packages/pqsfinder/ This paper is based on pqsfinder-1.4.1.read more
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Whole genome experimental maps of DNA G-quadruplexes in multiple species.
Giovanni Marsico,Vicki S Chambers,Vicki S Chambers,Aleksandr B. Sahakyan,Patrick Mccauley,Jonathan Mark Boutell,Marco Di Antonio,Shankar Balasubramanian +7 more
TL;DR: An improved version of a G-quadruplex sequencing method is employed to generate whole genome G4 maps for 12 species that include widely studied model organisms and also pathogens of clinical relevance, and reveals that the enrichment of OQs in gene promoters is particular to mammals such as mouse and human, among the species studied.
Journal ArticleDOI
A guide to computational methods for G-quadruplex prediction
TL;DR: The present review aims at providing an updated overview of the current open-source G-quadruplex prediction algorithms and straightforward examples of their implementation, and proposing other estimates which consider non-canonical sequences and/or structure propensity and stability.
Journal ArticleDOI
G4Hunter web application: a web server for G-quadruplex prediction.
Václav Brázda,Jan Kolomazník,Jiří Lýsek,Martin Bartas,Martin Bartas,Miroslav Fojta,Jiří Šťastný,Jiří Šťastný,Jean-Louis Mergny,Jean-Louis Mergny +9 more
TL;DR: A web version of the G4Hunter application is developed that allows retrieval of gene/nucleotide sequence entries from NCBI databases and provides complete characterization of localization and quadruplex propensity of quadruplex-forming sequences.
Journal ArticleDOI
Detecting RNA G-Quadruplexes (rG4s) in the Transcriptome.
TL;DR: Methodologies including predictive algorithms and structure-based sequencing have enabled the detection and mapping of rG4 structures on a transcriptome-wide scale at high sensitivity and resolution and the associated findings in relation to rG 4-related biological mechanisms are discussed.
Journal ArticleDOI
Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome.
Wilfried Guiblet,Marzia A. Cremona,Marzia A. Cremona,Robert S. Harris,Di Chen,Kristin A. Eckert,Francesca Chiaromonte,Francesca Chiaromonte,Yi-Fei Huang,Kateryna D. Makova +9 more
TL;DR: In this article, the authors conducted a comprehensive analysis of nucleotide substitution frequencies at non-B DNA loci within non-coding, non-repetitive genome regions, their ±2 kb flanking regions, and 1-Megabase windows, using human-orangutan divergence and human single-nucleotide polymorphisms.
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