DOI: 10.18129/B9.bioc.pqsfinder    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see pqsfinder.

Identification of potential quadruplex forming sequences

Bioconductor version: 3.9

Pqsfinder detects DNA 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 gmail.com>

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


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biocViews GeneRegulation, MotifDiscovery, SequenceMatching, Software
Version 2.0.2
In Bioconductor since BioC 3.3 (R-3.3) (3.5 years)
License BSD_2_clause + file LICENSE
Depends Biostrings
Imports Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods
LinkingTo Rcpp, BH (>= 1.69.0)
Suggests BiocStyle, knitr, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi
SystemRequirements GNU make, C++11
Depends On Me
Imports Me
Suggests Me
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Source Package pqsfinder_2.0.2.tar.gz
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