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QuadBase specifications

Information


Unique identifier OMICS_11872
Name QuadBase
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Shantanu Chowdhury <>

Publications for QuadBase

QuadBase in publications

 (7)
PMCID: 5804116
PMID: 29464116
DOI: 10.1155/2017/6513720

[…] to the putative sequence, it was also judged to be suitable for inclusion. in principle, we applied criteria similar to those utilized by qgrs mapper and the more comprehensive mining tool quadbase2, a program which predicts g-quadruplex forming g-rich sequences (qgrs) in nucleotide sequences [, ]. the scores of g-quadruplex putative sequences found in hiv genomes were also analyzed […]

PMCID: 5414184
PMID: 28447610
DOI: 10.1038/ncomms15110

[…] secondary dna structures. we examined the recruitment of blm to a crispr-cas9-targeted dsb in the cd4 locus by chip. we selected the cd4 locus because two different in silico algorithms (qgrs and quadbase2) predicted that the cd4 locus contains abundant guanine-rich repeats predicted to form g4 dna (). furthermore, a genome-wide sequencing-based study reported a high concentration of g4 dna […]

PMCID: 5516150
PMID: 27287611
DOI: 10.1002/bip.22891

[…] are analyzed, identified and/or graphically visualized using the ucsc genome browser (http://genome.ucsc.edu/cgi-bin/hggateway). the g‐quadruplex structure consensus sites were identified by quadbase (http://quadbase.igib.res.in) and qgrs mapper (http://bioinformatics.ramapo.edu/qgrs)., for the in vitro analysis we used two oligonucleotides derived from the polymorphic region of hs1.2 […]

PMCID: 4692102
PMID: 26695179
DOI: 10.1371/journal.pone.0144275

[…] []. in addition we studied similar gggga(t/c)t repeats in the cyanobacterium nostoc sp. strain pcc7120 (ana) []., potential g4 forming sequences were initially obtained from proquad database (http://quadbase.igib.res.in/) []. using the following query parameters for xcc: pattern g (or c for minus strand), stem size g3 (or c3) and loop size l1-5, genomic location: all. for further studies […]

PMCID: 2880320
PMID: 20433698
DOI: 10.1186/1471-2199-11-32

[…] region 251-294 has a g4 motif sequence g3-n1-7-g3-n1-7-g3-n1-7-g3, and nucleotide region 22-55 has a similar sequence with a potential g4 structure. moreover, the genome wide g4 dna database quadbase [] predicted an antisense g4 motif at nucleotide region 322-360. g4-structures are formed not only on dna but also on rna [], and a g4 motif on the nras mrna was reported to suppress […]


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QuadBase institution(s)
GNR Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
QuadBase funding source(s)
CSIR Project BSC0123 (GENCODE-A); Wellcome Trust/DBT India Alliance Research Fellowship; CSIR SPM Junior Research Fellowship

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