PortEco logo

Help:Gbrowse

From EcoliWiki
Jump to: navigation, search

Contents

Selecting a genome to view

Gene pages in EcoliWiki have links that will take you to the appropriate view in Gbrowse. To change the genome being viewed while you are in Gbrowse, use the Data source menu.

Gbrowse data source menu.png

Contact us if there is a genome that you would like to see in the browser.

Finding a particular gene or region

Using search

To direct Gbrowse to a particular region of the chromosome, type a gene name, a short sequence (minimum of 15 bp), or a nucleotide range in the Landmark or Region box located near the top left of the page and click on the Search button. Gbrowse will recognize a standard gene name as well as its synonyms. For example, in the MG1655 browser you can search for b numbers by typing bxxxx.

To find a nucleotide range, type: <accession>:xx..yy, where

  • <accession> is the accession of the genome you are looking at. This will usually already be in the search box from the last thing you navigated to.
  • xx and yy indicate the nucleotide positions of the start and end of the range you want

"Rubber band" selection

A convenient way to move along the genome is to click and drag in either the overview or region panels. Gbrowse will reload the image to encompass selected area when you release the mouse buttong

Sliding handles

The area shown in the Details panel is highlighted by a box in the Overview and Region panels. You can grab the box and slide it left or right within limits (it can't slide over the whole genome).

Scroll/Zoom

Once you get to a particular location, you can fine-tune the view the Scroll/Zoom buttons to move along the chromosome or change magnification.


Gbrowse navigation.png

Information displayed in Gbrowse

The information in Gbrowse is displayed in tracks, as shown in the image below.

  • Overview is a linear display of the entire genome with two dotted lines marking the location of the region being viewed.
  • Region displays 400 kb on either side of the position being viewed. This can change w/ scale.
  • The Details section displays more detailed information on genes in the region and contains multiple tracks. The user can set which of the tracks are shown. The image below has the tracks that show gene names (Genes), gene names and a brief description of gene product function (GenesDetail), Noncoding RNAs, and the known or predicted operons (operon_RegulonDB).
Gbrowse for ecoliwiki.jpeg
  • The Genes track contains link to other databases. To see the links, move the cursor over the bar representing the gene.
GBrowse update2.jpg
  • To set which tracks are shown, scroll to the Tracks display near the bottom of the page. Click the tracks you want displayed and click on the Update Image button. Each of the tracks has display options that can be set by clicking the Configure tracks button.
Gbrowse possible tracks.jpg

See also

Genome-specific information

Additional functionalities