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Quadfinder specifications

Information


Unique identifier OMICS_14489
Name Quadfinder
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Stability No
Maintained No

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Publication for Quadfinder

Quadfinder citations

 (8)
library_books

Selection and Characterization of DNA Aptamers Targeting All Four Serotypes of Dengue Viruses

2015
PLoS One
PMCID: 4482433
PMID: 26110785
DOI: 10.1371/journal.pone.0131240

[…] ther water or 100 mM KCl buffer, had a faster mobility than other 34-mer oligonucleotide (). Aptamer S15 contained 17 guanines separated into four guanine-rich regions. According to the prediction by QuadFinder (G stretch: 2–5, N stretch: 1–10), aptamer S15 had a G2L1-10 profile between G6 and G33, and was able to fold into a G-quadruplex structure composed of two G·G·G·G tetrads and external loop […]

library_books

G Quadruplex Structures and CpG Methylation Cause Drop Out of the Maternal Allele in Polymerase Chain Reaction Amplification of the Imprinted MEST Gene Promoter

2014
PLoS One
PMCID: 4249981
PMID: 25437198
DOI: 10.1371/journal.pone.0113955

[…] Predictions of putative G4 motifs were made using the software algorithms Quadparser G4P_calculator.exe , QGRS Mapper , Quadfinder , QGRS Predictor . Where necessary, both strands were analysed separately to ensure G4-motifs were detected in both orientations. Primer design, analysis of sequence alignments, and DNA seq […]

library_books

Epigenetic Modification, Dehydration, and Molecular Crowding Effects on the Thermodynamics of i Motif Structure Formation from C Rich DNA

2014
Biochemistry
PMCID: 3985701
PMID: 24564458
DOI: 10.1021/bi401523b

[…] To determine how widespread the phenomenon of 5hmC incorporation into putative iM structures in genomic DNA is, we first identified all of the putative unimolecular iMs using the Quadfinder tool developed by Scaria et al. This tool searches for sequences composed of CxNyCxNyCxNyCx motifs (for iMs on template strands) or GxNyGxNyGxNyGx motifs (for iMs on nontemplate strands), w […]

library_books

Ultrasensitive Norovirus Detection Using DNA Aptasensor Technology

2013
PLoS One
PMCID: 3828344
PMID: 24244426
DOI: 10.1371/journal.pone.0079087

[…] these structures did not account for G-quadruplex formation, which was considered as a possible secondary structure given observations of the sequences’ high G-content, particularly for AG3 (see ). A QuadFinder analysis showed potential for G-quadruplexes mostly in regions shared by the random region and the primer region (data not shown). Indeed, a DNA melt experiment at 295 nm shows an initial […]

library_books

Clostridium difficile TcdC protein binds four stranded G quadruplex structures

2013
Nucleic Acids Res
PMCID: 3575817
PMID: 23303781
DOI: 10.1093/nar/gks1448

[…] (). When QS are present in the 5′ untranslated region of the mRNA, it can interfere with ribosome binding and translation initiation (,).When we analyzed the whole C. difficile (strain 630) genome in Quadfinder, an online server for prediction of quadruplex-forming motifs in nucleotide sequences (), we found five pQS. Unfortunately, none of these were located in the PaLoc, where TcdC is speculated […]

library_books

Epigenetic Instability due to Defective Replication of Structured DNA

2010
Mol Cell
PMCID: 3145961
PMID: 21145480
DOI: 10.1016/j.molcel.2010.11.009

[…] a mean WT probe intensity level of 7. From this list, targets were selected at random and analyzed in the same way as the upregulated set. The sequence data from both sets was then analyzed with the Quadfinder server (http://miracle.igib.res.in/quadfinder/) () to search for potential G4 forming motifs on either strand according to the consensus G(3-5)L(1-7)G(3-5)L(1-7)G(3-5)L(1-7)G(3-5). We used […]

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Quadfinder institution(s)
GN Ramachandran Knowledge Center for Genome Informatics, CSIR, Delhi, India; Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi, India

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