UCSC Genome Browser Tutorials: Back to Basics and Exploring SARS-CoV-2

Go to UCSC Genome BrowserFor 20 years, the University of California-Santa Cruz Genome Browser (UCSC Genome Browser) has provided free public access to the human genome assembly and the information it contains via a comprehensive and well-utilized graphical viewing tool. Developed and maintained by the Genome Bioinformatics Group within the UCSC Genomics Institute, it has grown over the years to include a large collection of tools for viewing, analyzing, and downloading data from a broad array of vertebrate and model organism assemblies and annotations.

The UCSC Genome Browser group recently created a three-part video series designed to explain the Browser to new users. Previous videos primarily focused on answering specific task-related questions for experienced users and introducing new features. This new series fills in the background with more basic information.

  • Part One: Getting around in the Browser (15:55)
    • Focuses on using accession numbers and genomic annotation identifiers in various formats to navigate the Browser.
    • Examples include gene names, genomic coordinates, codon numbers, SNP rsIDs, and RefSeq NM identifiers.
  • Part Two: Configuring the Browser (11:57)
    • Presents configuration options geared toward making the Browser look the way you want and for making the graphic image suitable for export.
    • Examples include changing font size and screen width, removing blue guidelines, and navigating quickly to nearby annotations.
  • Part Three: Configuration + DNA Navigation (14:08)
    • Explores ways to configure the graphical viewer and looks at ways to use DNA sequences to find a location on a reference genomic assembly.
    • Examples include BLAT, Short Match, Drag-N-Highlight, removing highlights, Drag-N-Zoom, configuring the scale bar/base position track, and adding a title to an image.

All three tutorials are available on the UCSC Genome Browser YouTube channel and include a transcript and time-stamped content outline.

The UCSC Genome Browser group also recently added a video and transcript using the context of SARS-CoV-2 genome assembly to describe Browser features for the benefit of virologists and molecular biologists developing Coronavirus assays and vaccines. The tour highlights RT-PCR data, UniProt, crowd-sourced data, T-cell Reactive epitopes, and comparative genomics data for global viral isolates and those infecting non-human vertebrates. More information on the UCSC SARS-CoV-2 Genome Browser is available in a manuscript posted on the preprint server, bioRxiv.

~Carrie Iwema