G4Hunter web application: a web server for G-quadruplex prediction
Jazyk angličtina Země Velká Británie, Anglie Médium print
Typ dokumentu časopisecké články, práce podpořená grantem
PubMed
30721922
PubMed Central
PMC6748775
DOI
10.1093/bioinformatics/btz087
PII: 5306941
Knihovny.cz E-zdroje
- MeSH
- DNA MeSH
- G-kvadruplexy * MeSH
- guanin MeSH
- internet MeSH
- počítače MeSH
- sekvenční analýza DNA MeSH
- software MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- DNA MeSH
- guanin MeSH
MOTIVATION: Expanding research highlights the importance of guanine quadruplex structures. Therefore, easy-accessible tools for quadruplex analyses in DNA and RNA molecules are important for the scientific community. RESULTS: We developed a web version of the G4Hunter application. This new web-based server is a platform-independent and user-friendly application for quadruplex analyses. It allows retrieval of gene/nucleotide sequence entries from NCBI databases and provides complete characterization of localization and quadruplex propensity of quadruplex-forming sequences. The G4Hunter web application includes an interactive graphical data representation with many useful options including visualization, sorting, data storage and export. AVAILABILITY AND IMPLEMENTATION: G4Hunter web application can be accessed at: http://bioinformatics.ibp.cz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
ARNA Laboratory Inserm U1212 CNRS UMR5320 IECB Université de Bordeaux Pessac France
Brno University of Technology Technicka 2896 2 61969 Brno Czech Republic
Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czech Republic
Department of Informatics Mendel University in Brno Brno Czech Republic
Zobrazit více v PubMed
Bedrat A. et al. (2016) Re-evaluation of G-quadruplex propensity with G4Hunter. Nucleic Acids Res., 44, 1746–1759. PubMed PMC
Brázda V. et al. (2011) Cruciform structures are a common DNA feature important for regulating biological processes. BMC Mol. Biol., 12, 33.. PubMed PMC
Brázda V. et al. (2014) DNA and RNA quadruplex-binding proteins. Int. J. Mol. Sci., 15, 17493–17517. PubMed PMC
Brázda V. et al. (2016) Palindrome analyser—a new web-based server for predicting and evaluating inverted repeats in nucleotide sequences. Biochem. Biophys. Res. Commun., 478, 1739–1745. PubMed
Brázda V. et al. (2018) The amino acid composition of quadruplex binding proteins reveals a shared motif and predicts new potential quadruplex interactors. Molecules, 23, 2341. PubMed PMC
Brázda V., Coufal J. (2017) Recognition of local DNA structures by p53 protein. Int. J. Mol. Sci., 18, 375. PubMed PMC
Cheung I. et al. (2002) Disruption of dog-1 in Caenorhabditis elegans triggers deletions upstream of guanine-rich DNA. Nat. Genet., 31, 405–409. PubMed
Comoglio F. et al. (2015) High-resolution profiling of Drosophila replication start sites reveals a DNA shape and chromatin signature of metazoan origins. Cell Rep., 11, 821–834. PubMed PMC
De Cian A. et al. (2008) Targeting telomeres and telomerase. Biochimie, 90, 131–155. PubMed
Garant J.-M. et al. (2018) G4RNA screener web server: user focused interface for RNA G-quadruplex prediction. Biochimie, 151, 115–118. PubMed
Hon J. et al. (2017) pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. Bioinformatics, 33, 3373–3379. PubMed
Huppert J.L., Balasubramanian S. (2005) Prevalence of quadruplexes in the human genome. Nucleic Acids Res., 33, 2908–2916. PubMed PMC
Kikin O. et al. (2006) QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res., 34, W676–W682. PubMed PMC
Murat P., Balasubramanian S. (2014) Existence and consequences of G-quadruplex structures in DNA. Curr. Opin. Genet. Dev., 25, 22–29. PubMed
Paeschke K. et al. (2011) DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase. Cell, 145, 678–691. PubMed PMC
Siddiqui-Jain A. et al. (2002) Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc. Natl Acad. Sci. USA, 99, 11593–11598. PubMed PMC
Todd A.K. et al. (2005) Highly prevalent putative quadruplex sequence motifs in human DNA. Nucleic Acids Res., 33, 2901–2907. PubMed PMC
Todolli S. et al. (2017) Contributions of sequence to the higher-order structures of DNA. Biophys. J., 112, 416–426. PubMed PMC
Valton A.-L. et al. (2014) G4 motifs affect origin positioning and efficiency in two vertebrate replicators. EMBO J., 33, 732–746. PubMed PMC
Vasilyev N. et al. (2015) Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP. Proc. Natl Acad. Sci. USA, 112, E5391–E5400. PubMed PMC
Wieland M., Hartig J.S. (2007) RNA quadruplex-based modulation of gene expression. Chem. Biol., 14, 757–763. PubMed
Wong H.M. et al. (2010) A toolbox for predicting G-quadruplex formation and stability. J. Nucleic Acids, 2010, 1. PubMed PMC
Zimmermann M. et al. (2014) TRF1 negotiates TTAGGG repeat-associated replication problems by recruiting the BLM helicase and the TPP1/POT1 repressor of ATR signaling. Genes Dev., 28, 2477–2491. PubMed PMC
Asymmetric distribution of G-quadruplex forming sequences in genomes of retroviruses
Special Issue "Bioinformatics of Unusual DNA and RNA Structures"
Abundance of G-Quadruplex Forming Sequences in the Hepatitis Delta Virus Genomes
G-quadruplex ligands as potent regulators of lysosomes
Inverted repeats in the monkeypox virus genome are hot spots for mutation
G-quadruplexes in helminth parasites
A new lineage of non-photosynthetic green algae with extreme organellar genomes
R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences
G-Quadruplex in Gene Encoding Large Subunit of Plant RNA Polymerase II: A Billion-Year-Old Story
Analysis of putative quadruplex-forming sequences in fungal genomes: novel antifungal targets?
Tracing dsDNA Virus-Host Coevolution through Correlation of Their G-Quadruplex-Forming Sequences
G-quadruplexes in H1N1 influenza genomes
G-Quadruplexes in the Archaea Domain