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Genome Browser

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On June 22, 2000, UCSC and the other members of the International Human Genome Project consortium completed the first working draft of the human genome assembly, forever ensuring free public access to the genome and the information it contains. A few weeks later, on July 7, 2000, the newly assembled genome was released on the web at http://genome.ucsc.edu, along with the initial prototype of a graphical viewing tool, the UCSC Genome Browser. In the ensuing years, the website has grown to include a broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analyzing and downloading data. 

Tools provided on Genome Browser:
  • Genome Browser
    interactively visualize genomic data
  • BLAT
    rapidly align sequences to the genome
  • Table Browser
    download data from the Genome Browser database
  • Variant Annotation Integrator
    get functional effect predictions for variant calls
  • Data Integrator
    combine data sources from the Genome Browser database
  • Gene Sorter
    find genes that are similar by expression and other metrics
  • Genome Browser in a Box (GBiB)
    run the Genome Browser on your laptop or server
  • In-Silico PCR
    rapidly align PCR primer pairs to the genome
  • LiftOver
    convert genome coordinates between assemblies
  • VisiGene
    interactively view in situ images of mouse and frog 
     
    The following tools and utilities created by the UCSC Genome Browser Group are available for public use:
    • Batch Coordinate Conversion (liftOver) - converts genome coordinates and genome annotation files between assemblies. The current version supports both forward and reverse conversions, as well as conversions between selected species.
    • DNA Duster - removes formatting characters and other non-sequence-related characters from an input sequence. Offers several configuration options for the output format, including translated protein.
    • Protein Duster - removes formatting characters and other non-sequence-related characters from an input sequence. Offers several configuration options for the output format.
    • Phylogenetic Tree PNG Maker - creates a PNG image from the phylogenetic tree specification given. Offers several configuration options for branch lengths, normalized lengths, branch labels, legend etc.
    • Executable and Source Code Downloads - executable and source code downloads of the Genome Browser, Blat and liftOver.
     

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