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The UCSC Genome Browser Database: 2008 update.

D Karolchik1, R M Kuhn, R Baertsch

  • 1Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA. donnak@soe.ucsc.edu

Nucleic Acids Research
|December 19, 2007
PubMed
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This summary is machine-generated.

The University of California, Santa Cruz, Genome Browser Database (GBD) now includes 19 vertebrate and 21 invertebrate genomes. This updated database offers enhanced genome annotation data and new web tools for efficient data exploration and analysis.

Area of Science:

  • Genomics
  • Bioinformatics
  • Comparative Genomics

Background:

  • The University of California, Santa Cruz, Genome Browser Database (GBD) is a comprehensive resource for genomic sequence and annotation data.
  • It covers a wide range of vertebrate and model organisms.

Purpose of the Study:

  • To update the GBD with new genome assemblies and annotation data.
  • To introduce enhanced web-based tools for improved data visualization and analysis.

Main Methods:

  • Integration of 17 new genome assemblies, expanding coverage to 19 vertebrate and 21 invertebrate species.
  • Inclusion of diverse annotation datasets, including vertebrate conservation, UCSC Genes, human variation, MGC, and ENCODE data.
  • Development and enhancement of web-based tools for data viewing, manipulation, filtering, and downloading.

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Main Results:

  • The GBD now provides integrated data for 40 species.
  • New features include a 28-species human-based vertebrate conservation track and enhanced UCSC Genes.
  • Advanced tools like Genome Graphs, session management, and custom track management are now available.

Conclusions:

  • The updated GBD and its associated toolset offer a powerful and efficient platform for genomic research.
  • Enhanced data integration and user-friendly tools facilitate deeper insights into genome structure and function.