FlyBase:GBrowse Help

Navigating around the Genome

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

Finding a specific region of the genome

To select a region of the chosen genome to view, enter its name 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 in the coordinate scale in the detail panel.

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.

Dragging the detail panel - drag the detail panel left or right to move across the genome.

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 racks

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