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Identification of potential quadruplex forming sequences

Bioconductor version: Release (3.19)

Pqsfinder detects DNA and RNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, pqsfinder is able to detect G4s folded from imperfect G-runs containing bulges or mismatches or G4s having long loops. Pqsfinder also assigns an integer score to each hit that was fitted on G4 sequencing data and corresponds to expected stability of the folded G4.

Author: Jiri Hon, Dominika Labudova, Matej Lexa and Tomas Martinek

Maintainer: Jiri Hon <jiri.hon at>

Citation (from within R, enter citation("pqsfinder")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

pqsfinder: User Guide HTML R Script
Reference Manual PDF


biocViews GeneRegulation, MotifDiscovery, SequenceMatching, Software
Version 2.20.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License BSD_2_clause + file LICENSE
Depends R (>= 3.5.0), Biostrings
Imports Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods
System Requirements GNU make, C++11
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Suggests BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi
Linking To Rcpp, BH (>= 1.78.0)
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Follow Installation instructions to use this package in your R session.

Source Package pqsfinder_2.20.0.tar.gz
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macOS Binary (x86_64) pqsfinder_2.20.0.tgz
macOS Binary (arm64) pqsfinder_2.20.0.tgz
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