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The UCSC Genome Browser database: 2016 update.
Matthew L Speir1, Ann S Zweig2, Kate R Rosenbloom2
1Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA mspeir@soe.ucsc.edu.
Nucleic Acids Research
|November 22, 2015
Summary
The UCSC Genome Browser provides an integrated platform for analyzing genome data, with recent updates including new assemblies, enhanced gene annotations, and improved tools for data integration and analysis.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- The UCSC Genome Browser has been a vital resource for 15 years, offering a unified platform for genome assembly and annotation analysis.
- Continuous development ensures the platform remains current with new datasets and software features.
Purpose of the Study:
- To report on the latest release highlights and enhancements of the UCSC Genome Browser.
- To showcase improvements in data accessibility, visualization, and analytical tools for genomic research.
Main Methods:
- Development and integration of new genome browsers for various assemblies (e.g., bonobo, zebrafish).
- Expansion of gene annotation sets and genomic regulatory data.
- Enhancements to track and assembly hub support.
- Introduction of the 'Data Integrator' tool for multi-track data intersection.
Main Results:
- New and updated genome browsers are available for multiple species.
- Expanded datasets for the human assembly (hg38/GRCh38) include updated GENCODE gene predictions, ClinVar/ClinGen variants, and regulatory data.
- Improved support for assembly hubs and a new multiple genome alignment feature.
Conclusions:
- The UCSC Genome Browser continues to evolve, offering a comprehensive and enhanced platform for genomic research.
- Recent updates facilitate more sophisticated analysis of complex genomic datasets, including human variation and regulatory elements.
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