Journal ArticleDOI
G4Catchall: A G-quadruplex prediction approach considering atypical features
Reads0
Chats0
TLDR
It is shown that the allowance of a single atypical G-tract which includes a mismatched or a bulging non-guanine nucleotide, and a single loop of extreme size benefits the overall prediction, an improvement over other computational approaches.About:
This article is published in Journal of Theoretical Biology.The article was published on 2019-02-21. It has received 15 citations till now.read more
Citations
More filters
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
Whole Genome Identification of Potential G-Quadruplexes and Analysis of the G-Quadruplex Binding Domain for SARS-CoV-2
TL;DR: In this article, the potential G-quadruplexes of SARS-CoV-2 were characterized in both positive and negative-sense viral strands, showing that the G-tracts rather than the loops were under heightened selective constraints.
Journal ArticleDOI
Potential G-quadruplexes and i-Motifs in the SARS-CoV-2.
Efres Belmonte-Reche,Israel Serrano-Chacón,Carlos González,Juan E Gallo,Manuel Bañobre-López +4 more
TL;DR: In this paper, the authors report the extensive bioinformatic analysis of the SARS-CoV-2 genome and related viruses using an upgraded version of the open-source algorithm G4-iM Grinder.
Journal ArticleDOI
The Fragile X Mental Retardation Protein Regulates RIPK1 and Colorectal Cancer Resistance to Necroptosis
Antonio Di Grazia,Irene Marafini,Giorgia Pedini,Davide Di Fusco,Federica Laudisi,Vincenzo Dinallo,Eleonora Rosina,Carmine Stolfi,Eleonora Franzè,Pierpaolo Sileri,Giuseppe S. Sica,Giovanni Monteleone,Claudia Bagni,Claudia Bagni,Ivan Monteleone +14 more
TL;DR: A role for FMRP in controlling RIPK1 expression and necroptotic activation in CRC is supported and specific immunoprecipitation experiments indicated that FMRp binds receptor-interacting protein kinase 1 (RIPK1) mRNA, suggesting that F MRP acts as a regulator of necroPTosis pathway through the surveillance of RIPK 1 mRNA metabolism.
Journal ArticleDOI
How bioinformatics resources work with G4 RNAs.
TL;DR: All available bioinformatics resources dedicated to quadruplexes are reviewed and their usefulness in G4 RNA analysis is examined and the results obtained from processing specially created RNA datasets with these tools are shared.
References
More filters
Journal ArticleDOI
Prevalence of quadruplexes in the human genome
TL;DR: There is a significant repression of quadruplexes in the coding strand of exonic regions, which suggests that quadruplex-forming patterns are disfavoured in sequences that will form RNA.
Journal ArticleDOI
Highly prevalent putative quadruplex sequence motifs in human DNA
TL;DR: Using arithmetic ratio and probability techniques, frequent and systematic occurrence of certain sequence types are discovered, the most prominent being a potential quadruplex containing CCTGT in the first ‘loop’ position.
Journal ArticleDOI
High-throughput sequencing of DNA G-quadruplex structures in the human genome
Vicki S Chambers,Giovanni Marsico,Jonathan Mark Boutell,Marco Di Antonio,Geoffrey Paul Smith,Shankar Balasubramanian +5 more
TL;DR: A high-resolution sequencing–based method is presented to detect G4s in the human genome and observed a high G4 density in functional regions, as well as in genes previously not predicted to contain these structures (such as BRCA2).
Journal ArticleDOI
QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences
TL;DR: A web-based server that predicts quadruplex forming G-rich sequences (QGRS) in nucleotide sequences and features interactive graphic representation of the data is developed, very useful for investigating the functional relevance of G-quadruplex structure, in particular its role in regulating the gene expression by alternative processing.