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The UCSC Genome Browser

Background

The UCSC Genome Browser is a well-curated site that provides users with a view of gene or sequence information in genomic context for a specific species, and to control the data viewed in the browser by selecting specfic types of data from available menus.

The browser was created by the Genome Bioinformatics Group of the University of California at Santa Cruz .  It incorporates data from many reference sequences such as NCBI RefSeq, Ensembl, data from the ENCODE project, and many more sources.

This guide is an introduction to the UCSC Genome browser: how to locate it, manage tracks and annotations and how to get to sequence data from the browser view.  It also includes a brief introduction to the table browser, where users can obtain more detailed genomic information in table format that cannot be obtained from the browser view.

 

Accessing the UCSC Genome Browser

Screenshot of the UCSC Genome Browser Homepage.

 

 

Access to the genome browser is through the Genomes links in the top menu bar, or through the Genome Browserlink at the top of Our tools.  This will take you directly to the Human Genome Browser Gateway, which is the default gateway, since the human genome is the most popularly searched at the UCSC Genome Browser.

 

Screenshot of the Gateway Start page.

 

 

To change the species, select from the icons on the left, or search using the search box.  You can also change the assembly.  By default, the current assembly for any given genome is selected.  If a new build has just been created for a particular species, not all annotations may be viewable, but they are added over time.

You can search by known genomic position, or search a whole chromosome, or use the search term box to enter a gene symbol, accession number, or any text word to search.  The browser gateway has some examples of types of search terms to use on the entry page.

Note:  The UCSC Genome Browser saves your session settings as cookies in your web browser's settings.  This is a nice feature, because you can move seamlessly between the genome browser and the table browser without having to re-enter your search terms.  However, this can be confusing if you want to start a new search for a new region.  To do that, click the text link: Reset All User Settings under the Genome Browser menu item on the top menu in the page.  This will remove your earlier search terms and let you start a new search.

This search will use the example gene ACE - agiotensin converting enzyme.

Type your search term into the search term box.  As you do, you will get suggested results that pop up as you are typing, much like in a Google search. You can select from these suggestions, or ignore them and keep typing your search terms.  Click the GO button.