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The human genome browser at UCSC.

W James Kent1, Charles W Sugnet, Terrence S Furey

  • 1Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA. kent@biology.ucsc.edu

Genome Research
|June 5, 2002
PubMed
Summary
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The UCSC Genome Browser offers a powerful web tool for visualizing and analyzing vertebrate genome sequences. It displays diverse annotation tracks, enabling detailed genomic research and data exploration.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Vertebrate genome sequencing is nearing completion, necessitating effective analysis and visualization tools.
  • Displaying complex genomic data, including numerous annotation tracks, presents a significant challenge for researchers.

Purpose of the Study:

  • To introduce and describe a mature web-based tool for the display and analysis of vertebrate genome sequences.
  • To provide a platform for rapid, reliable visualization of any genomic region at any scale with aligned annotation tracks.

Main Methods:

  • Development of a web browser accessible at http://genome.ucsc.edu.
  • Integration of a MySQL database to manage diverse genomic data.
  • Implementation of text and sequence-based search functionalities for precise region access.

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  • Inclusion of numerous annotation tracks, including mRNA alignments, gene predictions, and cross-species homologies.

    • Main Results:

    • The browser displays assembly contigs, gaps, various alignment data, gene predictions, homologies, SNPs, and more.
    • Users can perform text/sequence searches for specific genomic regions.
    • Custom tracks can be added by users for personalized research and educational use.
    • The tool serves over 3000 users daily, handling over 50,000 page views.

    Conclusions:

    • The UCSC Genome Browser provides a robust and versatile platform for exploring and annotating vertebrate genomes.
    • Its comprehensive features and user-friendly interface facilitate genomic research and data sharing worldwide.