The Rat GBrowse Genome Browser

RGD's GBrowse genome browsers are rat-, mouse- and human-specific versions of the Generic Model Organism Database's (GMOD) genome browser.

For more information about GMOD, click here.

To access the rat GBrowse, click here.  For the human GBrowse, click here.

Jump to more information on...

The GBrowse search box
Navigation Functions
Selecting/Deselecting Tracks
The Details Section
Upload, Downloads, & Preferences

To view the "Getting Started with GBrowse" video click here.
 

The GBrowse Search Box

                                                                                                                         

   To select a region of the genome to view:

  1. Enter its name in the text field labeled "Landmark or Region". Recognized types of names/symbols are genes, QTLs, markers, strains, database accession numbers, disease terms, or chromosome number with coordinates. 
  2. Click the "Search" button.                                                                                                                                                                                                                  

Navigation Functions


       Once a region is displayed, you can navigate through it in a number of ways:

  1. Click and drag on a ruler in the "Overview", "Region" and "Details" panels. Click once to recenter the view at the desired position, or click and drag to select a region.

  2. Scroll left or right with the <<, <, > and >> buttons which appear in the "Scroll/Zoom" section of the screen, and at the top right and left corners of the "Details" panel.  The << and >> buttons scroll an entire screen's worth, while < and >> scroll a half screen.

3.  Zoom in or out using the sizing selection drop-down menu ("Show # bp").  The menu item name indicates the number of base pairs to show in the full width of the "Details" panel. For example, selecting the item "100 Kbp" will zoom the "Details" panel so as to show a region 100 Kbp wide.

4.  Make fine adjustments (10-20%) of the zoom level by clicking the "-" and "+" buttons adjacent to the sizing selection drop-down menu.

5.  To flip the browser display so that the sequence coordinates increase from right to left in the "Details" panel, select the "flip" checkbox.

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Selecting/Deselecting Tracks


             To expand/restrict the scope of the displayed information, click on the “Select Tracks” link from the menu bar on the upper left side of the page (1), or either of the two “Select Tracks” buttons found near the bottom of the page (2) to return the "Select Tracks" tab.   


The "Select Tracks" tab features a track search text box and an expandable list of data tracks which can be selected/deselected by the use of checkboxes. To view selected tracks click on the "Back to Browser" link at the upper left of the "Select Tracks" tab (1) or on the "Back to Browser" button at the bottom center of the page (2).

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Details


   Each track displays the group of objects located in the selected stretch of  chromosome.  To the left of the track's title are the following icons, which provide information and added functionality:

/  Show or hide this track  These icons toggle the track between visible and hidden.  Click to see the objects in the track and click to hide the objects.

  Turn off this track  Click this icon to remove the track from the Details display.

  Share this track  Clicking this icon returns a pop-up window that gives the options of sharing or exporting the track via URL.

  Configure this track  Clicking this icon returns a pop-up box that has drop-down menus that can be used to change the visual characteristics of the objects displayed in the track.

  Download this track    Clicking this icon returns a pop-up box that gives multiple options for downloading data from this track.

  About this track   Clicking this icon returns a pop-up box that gives general information about the objects in this track.

 

Information and links relevant to each object in a track appear in pop-up boxes that are accessed by mousing over or clicking an object or symbol.

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Upload, Downloads, & Preferences

Additional functionality of GBrowse is found in the tabs/menu bar at the upper left part of the page and in the drop-down menu above the zoom drop-down menu.

  

  1. Upload and Share Tracks:  Clicking on this link/tab reveals options to upload custom tracks from text, URL, or file.  Detailed help describing the upload process is available here and from that tab.
  2. Preferences:   The preferences tab allows the user to customize the GBrowse interface to personalize the look of the display.  Display width, gridlines, and highlighting are among the changeable properties.
  3. Downloads, etc:  The drop-down menu above the zoom drop-down menu has options of sequence downloads, track data downloads, and data filtering. Clicking the "Configure..." button to the right of the drop-down displays the selectable parameters for the particular choice made in the menu.                                                                                            

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