ModDotPlot-rapid and interactive visualization of tandem repeats.

ABSTRACT:

Motivation

A common method for analyzing genomic repeats is to produce a sequence similarity matrix visualized via a dot plot. Innovative approaches such as StainedGlass have improved upon this classic visualization by rendering dot plots as a heatmap of sequence identity, enabling researchers to better visualize multi-megabase tandem repeat arrays within centromeres and other heterochromatic regions of the genome. However, computing the similarity estimates for heatmaps requires high computational overhead and can suffer from decreasing accuracy.

Results

In this work, we introduce ModDotPlot, an interactive and alignment-free dot plot viewer. By approximating average nucleotide identity via a k-mer-based containment index, ModDotPlot produces accurate plots orders of magnit

SUBMITTER: Sweeten AP 

PROVIDER: S-EPMC11321072 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature