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The Ensembl Genome Browser

Background

The Ensembl Genome Browser is a highly integrated platform for genetic, genomic and protein data from many eukaryotic species. It is a joint project between EMBL-EBI  and the Wellcome Trust Sanger Institute . Data in the browser are automatically annotated on selected eukaryotic genomes, and some data are also collected from "curated" sources, such as UniProt. The site also has integrated data download features directly from the browser or from its related data platform BioMart.

This guide provides a brief overview on most popular features of the browser. Much more data is available at Ensembl than can be collected on a single guide, so users are encouraged to visit the information and training tuturials from Ensembl that are listed at the end of this guide.

Accessing the Ensembl Genome Browser

Screen shot of the Ensemble home screen.

The home page features quick links to browse popular genomes, access tools or help, search the site (from two different search boxes) and featured panels that will take you directly to instructions on searching for commonly-asked questions about Ensembl data, such as gene expression in different tissues, retrieving sequencescomparing genesphenotypes and much more.

The easiest way to begin a search in Ensembl is to use the main search box in the light blue area at the top of the page. Use the pull-down Species menu and type in your term of interest. You can search by gene or protein name, genomic location or simply by using key words such as the name of a disease.

This guide will demonstrate using the human protein APP, amyloid beta (A4) precursor protein.

Use the species pull-down to select Human and type APP in the search box.

  • As you type, results may be suggested to you (like in a Google search). 
  • You can use the suggested "Direct link" for APP human gene ENS00000142192, or just hit the Go button.
  • If you use a suggested direct link to a gene record, you will be taking directly to that gene record in Ensembl.
  • If you use the Go button, you will need to find your target in a list of results.

Note: during times of heavy use or during site updates, the browser may retrieve results very slowly. Be patient and wait for the search results page to populate.

If you used the Go button, you will see a list of results from which you can select your desired target. Usually gene results are featured at the top of the list. However, there are other filtered links that might be of interest that are arranged in the left-hand menu, such as transcript links, phenotypes, alignments, proteins and variants.

In this case, click on the link that reads "APP (Human Gene) " in the center portion of the page under the search box.