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Set of tools to identify periodic occurrences of k-mers in DNA sequences

Bioconductor version: Release (3.19)

This R package helps the user identify k-mers (e.g. di- or tri-nucleotides) present periodically in a set of genomic loci (typically regulatory elements). The functions of this package provide a straightforward approach to find periodic occurrences of k-mers in DNA sequences, such as regulatory elements. It is not aimed at identifying motifs separated by a conserved distance; for this type of analysis, please visit MEME website.

Author: Jacques Serizay [aut, cre]

Maintainer: Jacques Serizay <jacquesserizay at>

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


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:

Introduction to periodicDNA HTML R Script
Reference Manual PDF


biocViews Alignment, Coverage, DataImport, MotifAnnotation, MotifDiscovery, SequenceMatching, Sequencing, Software
Version 1.14.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3 + file LICENSE
Depends R (>= 4.0), Biostrings, GenomicRanges, IRanges, BSgenome, BiocParallel
Imports S4Vectors, rtracklayer, stats, GenomeInfoDb, magrittr, zoo, ggplot2, methods, parallel, cowplot
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Suggests BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, reticulate, testthat, covr, knitr, rmarkdown, pkgdown
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Follow Installation instructions to use this package in your R session.

Source Package periodicDNA_1.14.0.tar.gz
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macOS Binary (x86_64) periodicDNA_1.14.0.tgz
macOS Binary (arm64) periodicDNA_1.14.0.tgz
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