The UCSC Genome Browser database: 2025 update

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• The UCSC Genome Browser is a vital web-based platform for genomic data visualization and analysis.
• It hosts over 4000 assemblies and diverse annotation data from internal and community sources.
• Established in 2001, it remains a cornerstone resource for the scientific community.

Purpose of the Study:

• To detail recent updates and improvements to the UCSC Genome Browser.
• To highlight new features enhancing data accessibility and user experience.
• To showcase the platform's continued evolution as a leading genomics resource.

Main Methods:

• Integration of new annotation tracks, including gnomAD 4.1 on GRCh38/hg38.
• Expansion of the Genome Archive (GenArk) system for assembly management.
• Interface enhancements: popup dialogs, improved track navigation, and grouping features.

Main Results:

• Addition of over 25 new annotation tracks and three public hubs.
• Significant improvements in user interface for data exploration and navigation.
• Enhanced functionality for GenePred tracks and track hub management.

Conclusions:

• The UCSC Genome Browser continues to expand its capabilities with new data and features.
• Recent updates enhance usability and data accessibility for genomic research.
• The platform remains a critical resource for the global genomics and bioinformatics community.