{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T20:30:06Z","timestamp":1776025806309,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2025,9,15]],"date-time":"2025-09-15T00:00:00Z","timestamp":1757894400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Revealing structural variations within and across populations is crucial for understanding their diversification mechanisms and roles. Existing tools for visualization of structural variations often require labor-intensive figure preparation and are limited in their ability to integrate annotations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed PatchWorkPlot, a tool for automated visualization of pairwise alignments of multiple annotated sequences as dot plots combined into a single matrix. PatchWorkPlot enables exploration of positions, breakpoints, and architectures of structural variations across two or more sequences. The tool supports customization of visualization parameters and produces high-resolution, publication-ready figures. PatchWorkPlot significantly reduces manual work and simplifies the generation of complex plots for various cases, from individual loci to large-scale comparative projects.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PatchWorkPlot is implemented using Python 3 and is publicly available at GitHub: github.com\/yana-safonova\/PatchWorkPlot.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf504","type":"journal-article","created":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T20:46:23Z","timestamp":1758314783000},"source":"Crossref","is-referenced-by-count":2,"title":["PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences"],"prefix":"10.1093","volume":"41","author":[{"given":"Mariia","family":"Pospelova","sequence":"first","affiliation":[{"name":"Computer Science and Engineering Department, Pennsylvania State University , State College, PA 16802,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9634-4216","authenticated-orcid":false,"given":"Yana","family":"Safonova","sequence":"additional","affiliation":[{"name":"Computer Science and Engineering Department, Pennsylvania State University , State College, PA 16802,","place":["United States"]},{"name":"Huck Institutes of Life Science, Pennsylvania State University , State College, PA 16802,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,9,15]]},"reference":[{"key":"2025101607385014700_btaf504-B1","doi-asserted-by":"crossref","first-page":"2555","DOI":"10.1093\/hmg\/ddp187","article-title":"Characterization of six human disease-associated inversion polymorphisms","volume":"18","author":"Antonacci","year":"2009","journal-title":"Hum Mol 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