pqsfinder specifications

Information


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

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Publication for pqsfinder

pqsfinder citation

library_books

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

2018
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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