pqsfinder specifications


Unique identifier OMICS_20573
Name pqsfinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Nucleotide sequence
Input format FASTA, XString
Output data Annotation table
Output format GFF3, GRanges, XViews
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 1.4.9
First release date 2016
Stability Stable
Maintained Yes




No version available



Publication for pqsfinder

pqsfinder citation


Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast

BMC Genomics
PMCID: 5838962
PMID: 29510672
DOI: 10.1186/s12864-018-4563-7

[…] We searched for maize LTR retrotransposons having potential quadruplex-forming sequences (PQS) using pqsfinder (Fig. ; Additional files  and ). We found that about 37% of all families contained at least one PQS (Fig. ) with a tendency to have a higher number of PQS in the same element - on average mo […]

pqsfinder institution(s)
IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic; Department of Information Technology, Faculty of Informatics, Masaryk University, Brno, Czech Republic
pqsfinder funding source(s)
Supported by the Czech Science Foundation [15-02891S], IT4Innovations excellence in science project of the Ministry of Education, Youth and Sports of the Czech Republic [IT4I XS – LQ1602] and ICT tools, methods and technologies for smart cities project of the Brno University of Technology [FIT-S-17-3964].

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