Abstract
Periodic occurrences of oligonucleotide sequences can impact the physical properties of DNA. For example, DNA bendability is modulated by 10-bp periodic occurrences of WW (W = A/T) dinucleotides. We present periodicDNA, an R package to identify k-mer periodicity and generate continuous tracks of k-mer periodicity over genomic loci of interest, such as regulatory elements. periodicDNA will facilitate investigation and improve understanding of how periodic DNA sequence features impact function.
Highlights
Short DNA sequence motifs provide key information for interpreting the instructions in DNA, for example by providing binding sites for proteins or altering the structure of the double-helix
We present periodicDNA, an R package to investigate k-mer periodicity. periodicDNA provides a framework to quantify the periodicity of any k-mer of interest in DNA sequences
> remotes::install_github("js2264/periodicDNA") > library("periodicDNA") Quantifying k-mer periodicity over a set of sequences Using a provided k-mer (e.g. WW, motif argument) and a set of sequences of interest, getPeriodicity() computes several different metrics: 1. The k-mer power spectral density (PSD) values at different periods obtained by Fourier Transform
Summary
2. Sabarinathan Radhakrishnan , National Centre for Biological Sciences, Bangalore, India. This article is included in the RPackage gateway. Imperial College London, This article is included in the Bioconductor gateway. Any reports and responses or comments on the article can be found at the end of the article
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