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Setting up JBrowse 2 for Visualizing Genome Synteny
Colin Diesh1, Garrett Stevens1, Scott Cain2
1Department of Bioengineering, University of California, Berkeley, California.
Current Protocols
|December 5, 2025
Summary
This protocol details using JBrowse 2, an open-source genome browser, to visualize genomic synteny. It guides users through data preparation and setup for exploring conserved sequences across multiple genomes.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Genome browsers are essential tools for visualizing genomic data.
- Understanding syntenic relationships aids in comparative genomics and evolutionary studies.
- JBrowse 2 offers advanced features for multi-genome visualization.
Purpose of the Study:
- To provide a protocol for setting up synteny views in JBrowse 2.
- To demonstrate the visualization of whole-genome alignments for synteny analysis.
- To facilitate the exploration of conserved sequences across multiple genomes.
Main Methods:
- Data preparation for whole-genome alignment (WGA) data.
- Formatting WGA data into JBrowse 2 compatible formats.
- Utilizing JBrowse 2's graphical user interface (GUI) for interactive synteny view setup.
Main Results:
- Successful generation of synteny views in JBrowse 2.
- Creation of publication-quality figures from synteny visualizations.
- Demonstration of JBrowse 2's capability for comparative genomics.
Conclusions:
- JBrowse 2 provides an effective platform for visualizing genomic synteny.
- The described protocol simplifies the process of comparative genome analysis.
- This method enhances the exploration of conserved genomic regions across species.
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