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The UCSC Genome Browser database: 2014 update
Donna Karolchik1, Galt P Barber, Jonathan Casper
1Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA.
The UCSC Genome Browser provides public access to genomic data for many species, with enhanced tools for analysis and visualization. New features include improved annotation tracks and variant analysis tools for researchers.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- The UCSC Genome Browser offers a comprehensive platform for accessing and analyzing genomic data.
- It serves as a crucial resource for researchers studying the genomes of various organisms, particularly humans and mice.
Purpose of the Study:
- To detail recent updates and new features of the UCSC Genome Browser.
- To highlight improvements in data accessibility, analysis tools, and user-generated data integration.
Main Methods:
- Web-based platform development and data integration.
- Inclusion of new annotation tracks (e.g., conservation, variation, ENCODE data).
- Development of new software tools for variant annotation and data visualization.
Main Results:
- Expanded database with genomic sequences and annotations for approximately 90 organisms as of September 2013.
- Introduction of a 60-species multiple alignment conservation track and updated UCSC Genes tracks.
- New tools like Variant Annotation Integrator and enhanced data hub capabilities for user-provided data.
Conclusions:
- The UCSC Genome Browser continues to evolve as a powerful, integrated resource for genomic research.
- Recent updates enhance data analysis capabilities, particularly for genetic variation and comparative genomics.
- Improved European accessibility through a new mirror site facilitates broader global research collaboration.
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