ArticleBioinformatics (Oxford, England)2024
ModDotPlot-rapid and interactive visualization of tandem repeats.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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61 citing papers in PubMed.
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- Haplotype-resolved DiMeLo-seq maps centromeric chromatin in a complete diploid human genome.Cell genomics · 2026Article
- Telomere-to-telomere genome assembly and a pangenome for the rat.Cell genomics · 2026Article
- Automatic generation of model sequences for complex regions in assembly graphs with TTT.Cell genomics · 2026Article
- Phased T2T horse and donkey assemblies from a mule reveal peculiar equid centromere evolution.Cell genomics · 2026Article
- A complete genome for the common marmoset.Cell · 2026Article
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- AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates.Bioinformatics (Oxford, England) · 2026Article
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- Unconventional centromere architectures in Tapirus indicus reveal hotspots for satellite-free centromere formation in Perissodactyla.Communications biology · 2026Article
- A de novo genome assembly of an Angelman syndrome pig (Sus scrofa domesticus) model to resolve SNHG14.The Journal of heredity · 2026Article
- EasyCen: A Lightweight Framework for Centromere Localisation and Repeat-Organisation Profiling in Telomere-to-Telomere Genomes.Molecular ecology resources · 2026Article
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1 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
motivationA 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.
resultsIn 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 magnitude faster than StainedGlass. We accomplish this through the use of a hierarchical modimizer scheme that can visualize the full 128 Mb genome of Arabidopsis thaliana in under 5 min on a laptop. ModDotPlot is bundled with a graphical user interface supporting real-time interactive navigation of entire chromosomes. AVAILABILITY AND IMPLEMENTATION: ModDotPlot is available at https://github.com/marbl/ModDotPlot.
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