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

Maintainer


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Publication for Quadfinder

Quadfinder in publications

 (8)
PMCID: 4482433
PMID: 26110785
DOI: 10.1371/journal.pone.0131240

[…] (selex), we demonstrated the first aptamer (s15) that can bind to denv-2 envelop protein domain iii (ed3) with a high binding affinity. s15 was found to form a parallel quadruplex based on quadfinder prediction, gel mobility assay and circular dichroism studies. both the quadruplex structure and the sequence on 5’-end were necessary for the binding activity of s15. nmr titration […]

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

[…] (). the resulting amplicons were purified and sequenced as above., 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 […]

PMCID: 3985701
PMID: 24564458
DOI: 10.1021/bi401523b

[…] the c-myc gene., 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), […]

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

[…] 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 […]

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 […]


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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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