Multipla: Multiscale Pangenomic Locus Analysis
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Date
2025
Journal Title
Journal ISSN
Volume Title
Publisher
The Eurographics Association and John Wiley & Sons Ltd.
Abstract
Comparing gene organization across genomic sequences reveals insights into evolutionary and functional diversity among different organisms and varieties. Performing this task across many sequences, such as from a pangenome, is challenging because of the scale, the density of information, and the inherent variation. Often, analyses are centered on a genomic region of interest-a locus that might be associated with a trait or contain genes within the same family or biological pathway. Within these regions, researchers examine the conservation of gene order and orientation across organisms and assess sequence similarity, along with other gene content features such as gene size, to find biological variations or potential errors in the data. Automated methods in comparative genomics struggle to identify meaningful patterns due to varying and often unknown features of interest, leaving manual, time-intensive, and scalability-challenged visualization as the primary alternative. To address these challenges, we present a multiscale design for studying gene organization within pangenomes, developed in close collaboration with domain experts. Our tool, MULTIPLA, enables users to explore organization at multiple levels of detail in a decluttered manner through layout abstractions, semantic zooming, and layouts with flexible distance definitions and feature selections, combining the advantages of manual and automated methods used in practice. We evaluate the design of MULTIPLA through two pangenomic use cases and conclude with lessons learned from designing multiscale views for pangenomic locus analysis.
Description
CCS Concepts: Human-centered computing → Visual analytics; Visualization design and evaluation methods; Applied computing → Genomics
@article{10.1111:cgf.70147,
journal = {Computer Graphics Forum},
title = {{Multipla: Multiscale Pangenomic Locus Analysis}},
author = {Brandt, Astrid van den and Ståhlbom, Emilia and Workum, Fredericus Johannes Maria van and Wetering, Huub van de and Lundström, Claes and Smit, Sandra and Vilanova, Anna},
year = {2025},
publisher = {The Eurographics Association and John Wiley & Sons Ltd.},
ISSN = {1467-8659},
DOI = {10.1111/cgf.70147}
}