FlyBase:GBrowse Help
Choosing a genome
The genome is set to D. melanogaster by default, but other Drosophila genomes are available using the Data Source box in the search panel.
Available genomes are:
- D. pseudoobscura
- D. ananaassae
- D. erecta
- D. grimshawi
- D. mojavensis
- D. persimilis
- D. sechelia
- D. simulans
- D. virilis
- D. wilistoni
- D. yakuba
Displaying a specific region of the genome
To select a specific region of the chosen genome to view, enter any of the following in the text field labeled "Landmark or Region". This box will accept:
- FlyBase symbols, e.g., cnn
- FlyBase IDs e.g., FBgn0000490
- Sequence locations e.g., X:6000..8000, 2L:80,000..100,000
To select a sub region of the region already displayed, click and drag along the coordinate scale in the detail panel. A pop-up box will appear that shows the coordinates of the region selected (rounded to the nearest mark on the coordinate scale at each end) and offers options to center the genome view on the selected region or to zoom in to the selected region; there is also an option to obtain the genomic sequence of the selected region in FASTA format.
To move to a different section of the chromosome, click on the chromosome scale in the Overview panel. The region of the chromosome that is currently displayed in the detail panel is indicated with two dotted lines.
Moving across the genome
Once a region of the genome is displayed there are two ways you can move across the genome from that location.
Using scroll buttons - Scroll defined distances left or right with the <<, <, > and >> buttons in the search panel. A pop up will indicate the distance that each button will scroll. In general, clicking the single arrow will move the view over by half the length displayed in the viewer and the double arrow will move the full distance, e.g. if the scroll/zoom box indicates "Show 10 kbp", a click on the single right arrow will move the view to the right by 5 kbp and a click on the double right arrow will move the view to the right by 10kbp.
Dragging the detail panel - drag the detail panel left or right to move across the genome. Note that the drag option works to move the screen for a limited distance in either direction equal to the extent in kbp displayed on the screen, e.g., if the scroll/zoom box indicates "Show 10 kbp", the view can be dragged for 10kb in either directon of the original view. If you wish to move further, use the scroll buttons to advance laterally and then the drag option will be reset.
Customizing the display
Zooming
Zoom in or out using the "Show XXX bp" menu in the search panel. The available options are:
- 100bp
- 200bp
- 1kbp
- 2kbp
- 5kbp
- 10kbp
- 20kbp
- 40kbp
- 70kbp
- 100kbp
- 200kbp
Press the - and + buttons either side of the menu to change the zoom level by 10%.
Centering
Click on the coordinate scale (at the top of the detail panel) to recenter the detail panel around the location you clicked.
Flipping the genome
To flip the browser display so that the minus strand points to the right, select the "flip" checkbox in the search panel.
Displaying restriction sites
Restriction sites can be displayed by choosing 'Annotate Restriction Sites" from the top right hand drop down box. Click 'Configure' to choose the restriction sites you would like to display.
Changing the order of the tracks
To change the order of the tracks in the display panel click on the track label and drag up or down.
Opening/closing panels
Click on the red add/minus sign at the top of each panel to open and close that panel.
Other display preferences
A number of other display preferences can be found in the Preferences tab including
- Showing/hiding the grid lines on the detail panel. These are displayed by default.
- Enabling/disabling caching of tracks.
- Show/hide tooltips. These are displayed by default.
- Changing the width of the image. The default image width is 800. Other options are 1024 and 2048.
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Choosing tracks
The default GBrowse view comprises a predetermined set of 10 tracks. For details of all of the tracks available see here
Selecting existing tracks
To select tracks go to the 'Select Tracks' tab and choose the tracks you would like to display.
Adding custom Tracks
To add custom tracks go to the 'Custom Tracks' tab.
You have the option of adding tracks from text, from a URL or from a file.
For more information about how to add custom tracks see here
Customizing tracks
Favorites
Show or hide this track
Turn off this track
Share this track
Download this track
Configure this track
About track