kmerPyramid: an interactive visualization tool for nucleobase and k-mer frequencies

Abstract

Summary: Bioinformatics methods often incorporate the frequency distribution of nulecobases or k-mers in DNA or RNA sequences, for example as part of metagenomic or phylogenetic analysis. Because the frequency matrix with sequences in the rows and nucleobases in the columns is multi-dimensional it is hard to visualize. We present the R-package 'kmerPyramid' that allows to display each sequence, based on its nucleobase or k-mer distribution projected to the space of principal components, as a point within a 3-dimensional, interactive pyramid. Using the computer mouse, the user can turn the pyramid's axes, zoom in and out and identify individual points. Additionally, the package provides the k-mer frequency matrices of about 2000 bacteria and 5000 virus reference sequences calculated from the NCBI RefSeq genbank. The 'kmerPyramid' can particularly be used for visualization of intra- and inter species differences. Availability and implementation: The R-package 'kmerPyramid' is available from the GitHub website at https://github.com/jkruppa/kmerPyramid. Contact: klaus.jung@tiho-hannover.de. Supplementary information: Supplementary data are available at Bioinformatics online.