{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T08:07:02Z","timestamp":1776326822273,"version":"3.50.1"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"8","funder":[{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"US National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>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 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\u2009min on a laptop. ModDotPlot is bundled with a graphical user interface supporting real-time interactive navigation of entire chromosomes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>ModDotPlot is available at https:\/\/github.com\/marbl\/ModDotPlot.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae493","type":"journal-article","created":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T23:57:32Z","timestamp":1723075052000},"source":"Crossref","is-referenced-by-count":44,"title":["ModDotPlot\u2014rapid and interactive visualization of tandem repeats"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5316-2973","authenticated-orcid":false,"given":"Alexander P","family":"Sweeten","sequence":"first","affiliation":[{"name":"Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health , Bethesda, MD 20892,","place":["United States"]},{"name":"Department of Computer Science, Johns Hopkins University , Baltimore, MD 21211,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4118-4446","authenticated-orcid":false,"given":"Michael C","family":"Schatz","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University , Baltimore, MD 21211,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2983-8934","authenticated-orcid":false,"given":"Adam M","family":"Phillippy","sequence":"additional","affiliation":[{"name":"Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health , Bethesda, MD 20892,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2024,8,7]]},"reference":[{"key":"2025012912411242000_btae493-B1","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1093\/bioinformatics\/btz540","article-title":"Cooler: scalable storage for Hi-C data and other genomically labeled arrays","volume":"36","author":"Abdennur","year":"2020","journal-title":"Bioinformatics"},{"key":"2025012912411242000_btae493-B2","doi-asserted-by":"crossref","first-page":"eabl4178","DOI":"10.1126\/science.abl4178","article-title":"Complete genomic and epigenetic maps of human centromeres","volume":"376","author":"Altemose","year":"2022","journal-title":"Science"},{"key":"2025012912411242000_btae493-B3","author":"Appleby","year":"2016"},{"key":"2025012912411242000_btae493-B4","first-page":"21","volume-title":"Proceedings: Compression and Complexity of SEQUENCES 1997 (Cat. 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