PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences.

IF 5.4

Bioinformatics (Oxford, England) Pub Date : 2025-09-15 DOI:10.1093/bioinformatics/btaf504

Mariia Pospelova, Yana Safonova

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Abstract

Motivation: 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.

Results: 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.

Availability: PatchWorkPlot is implemented using Python 3 and is publicly available at GitHub: github.com/yana-safonova/PatchWorkPlot.

Supplementary information: Supplementary data are available at Bioinformatics online.

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PatchWorkPlot：同时可视化跨多个序列的局部比对。

动机：揭示人口内部和人口之间的结构变化对于理解其多样化机制和作用至关重要。用于结构变化可视化的现有工具通常需要耗费大量人力的图形准备工作，并且集成注释的能力有限。结果：我们开发了PatchWorkPlot，这是一个自动可视化工具，可以将多个注释序列的成对比对作为点图组合成单个矩阵。PatchWorkPlot允许在两个或多个序列中探索结构变化的位置，断点和架构。该工具支持自定义可视化参数，并生成高分辨率、可发布的图形。PatchWorkPlot显著减少了手工工作，简化了从单个位点到大型比较项目的各种情况下复杂地块的生成。可用性：PatchWorkPlot使用Python 3实现，并可在GitHub上公开获取：github.com/yana-safonova/PatchWorkPlot.Supplementary information：补充数据可在Bioinformatics在线获取。

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Bioinformatics (Oxford, England)

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