The Genome Browser's Tool Bar allows you to customize the Genome Viewer
and change the appearance of tracks. To reveal or hide the Tool Bar,
click Open/Close Tool Bar in the "General" Panel at the top right of the Genome Browser window.
The Tool Bar offers the following groups of controls:
- Click on the icon at the top right of the Browser Toolbar to apply all of your selections to the Genome Viewer.
Track Viewing Options
- Load Default Track Settings. Show all the
tracks that appear by default in their default viewing modes.
- Load Default Settings. Set track and Browser formatting to default settings.
- Clear Track Highlighting. Remove yellow highlight
tracks, such as gene models previously viewed on the Protein page.
- Clear Blast Tracks. Remove tracks added by
viewing a BLAST result on the Genome Browser.
- Reorder Tracks. Open the Track Reordering Tool to change the order of tracks in the Genome Browser.
- View browser image. Capture the entire state of the Genome Viewer in a .png image. This image will open in a page in your web browser. You can now use your web browser to save the image to a file (For instance on Firefox or Internet Explorer, right click on the image and select "Save image." or "Save picture.")
Advanced Track Controls
Advanced Track Controls allow you to easily set the display mode of multiple tracks simultaneously based on track type.
At the top of Advanced Track controls, you can set the display mode globally for either All tracks or All visible tracks (all tracks not hidden) by clicking on the icon representing hide, dense, full, or pack modes.
Each track type (e.g. BLAT, Blastx, Fcurve...) is represented by a collapsible panel within the Advanced Track Controls. These panels are used as follows to set track display modes:
- Click on to the left of the track type name to expand (show) the panel
- Click on to the left of the track type name to collapse (hide) the panel
- Click on to the right of the track type to update the Genome Viewer with the selected display mode settings.
- When the panel is expanded click on to set all tracks listed in the panel to the given display mode.
- Track display modes can be set individually using the grid of radio buttons shown in the panel.
Clicking on the Scaffold Track in the Genome Viewer, recenters the currently viewed position on the scaffold. The Recenter Options setting determines the Genome Viewer behavior after a recenter:
3x (default) the Genome Viewer will re-center and zoom in three
times closer to show more detail.
Zoom only the re-centering will occur.
- Zoom AA the Genome Viewer will zoom in to show the 3-frame
amino acid translation (AA) on the scaffold, centered on the current view.
- Zoom NA the Genome Viewer will zoom in the show the nucleotide
with 3-frame amino acid translation (NA) on the scaffold, centered on the
Browser Formatting allows the user to control the appearance of the Genome Viewer:
- Browser Width. The width in pixels of the tracks
and controls in the Genome Viewer (when opened far enough to require
no scroll bar).
- Font Size. The relative size of fonts in the
- Background Color. RGB values for the background
color of the Genome Viewer.
- Track Height. The height in pixels of each
track in the Genome Viewer.
- Track Height in %. Track height as a percentage of the default track height.
- Base Position. The location of the scale that
shows base positions along the scaffold.
- Guidelines. Turns on or off display of vertical
lines to aid determination of base positions in the tracks. (The line
spacings are not related to the scale.)
- Track Labels. Sets the locations of track labels in the Genome Viewer. (Labels on the right are not currently available.)
- Show full tooltips. Enable or disable the preview of protein pages when you hover your mouse over a gene model.
To enable or disable tooltips when you hover over gene models in the browser, use the Show full tooltips
checkbox at the bottom of the Browser Toolbar.
Use the Saved Views tool to temporarily save one or more configurations of the Genome Viewer, including scaffold position, zoom, and track settings. Your saved views are only available during the current session. If you close your Web browser, links to any saved views will disappear.
- To save the current settings, click Save the Current View>>.
- To open a saved view, click the numbered view link (labeled
as the range of base locations on the scaffold).
- To delete a saved view, click the word delete after
the numbered view link.