QGRS-H Predictor: a web server for predicting homologous quadruplex forming G-rich sequence motifs in nucleotide sequences.

Nucleic Acids Research
Camille MenendezParamjeet S Bagga

Abstract

Naturally occurring G-quadruplex structural motifs, formed by guanine-rich nucleic acids, have been reported in telomeric, promoter and transcribed regions of mammalian genomes. G-quadruplex structures have received significant attention because of growing evidence for their role in important biological processes, human disease and as therapeutic targets. Lately, there has been much interest in the potential roles of RNA G-quadruplexes as cis-regulatory elements of post-transcriptional gene expression. Large-scale computational genomics studies on G-quadruplexes have difficulty validating their predictions without laborious testing in 'wet' labs. We have developed a bioinformatics tool, QGRS-H Predictor that can map and analyze conserved putative Quadruplex forming 'G'-Rich Sequences (QGRS) in mRNAs, ncRNAs and other nucleotide sequences, e.g. promoter, telomeric and gene flanking regions. Identifying conserved regulatory motifs helps validate computations and enhances accuracy of predictions. The QGRS-H Predictor is particularly useful for mapping homologous G-quadruplex forming sequences as cis-regulatory elements in the context of 5'- and 3'-untranslated regions, and CDS sections of aligned mRNA sequences. QGRS-H Predictor f...Continue Reading

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Citations

Jul 23, 2014·Archives of Biochemistry and Biophysics·Hansraj DhayanAndreas Kukol
Apr 29, 2014·Nucleic Acids Research·Annekathrin von HachtJens Kurreck
Dec 4, 2014·Cell Reports·Phillip J KennyStephanie Ceman
Aug 19, 2015·Genome Biology·Tomáš HronDaniel Elleder
May 18, 2016·Nucleic Acids Research·Parashar Dhapola, Shantanu Chowdhury
Dec 1, 2015·PloS One·Ezekiel CrenshawAleister J Saunders
Sep 26, 2016·Journal of Inorganic Biochemistry·Taiga FujiiNaoki Sugimoto
Oct 17, 2017·Bioinformatics·Jean-Michel GarantMichelle S Scott
May 5, 2017·Bioinformatics and Biology Insights·Rogelio Alcántara-SilvaSilvia Carolina Galván
Aug 1, 2018·ELife·Helen Louise LightfootJonathan Hall
Jul 2, 2019·Human Molecular Genetics·Mansur M NaeemNeal Sondheimer
Nov 19, 2017·Current Medicinal Chemistry·Katrina N EstepRobert M Brosh
Jan 2, 2019·BMC Genomics·Chao Zeng, Michiaki Hamada

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Software Mentioned

Linux
BioJava
Apache Tomcat instance
J2EE
Mozilla Firefox
Internet Explorer
JUnit
QGRS
- Homology Predictor
H Predictor

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