FlyBase:GBrowse Help

GBrowse2

GBrowse2 was developed and is maintained by the Generic Model Organism Database (GMOD) consortium. It was first released in 2010, replacing the original 2000 version of GBrowse (Stein 2013). FlyBase has offered GBrowse2 since March 2013, primarily because of its ability more and larger data tracks, particularly next-generation sequencing data.

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

Note that an additional option in the Data Source box is 'D. melanogaster MegaView'. This option has been optimised for viewing larger regions of the D.melanogaster genome. For more information see the Zooming section.

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:

Click & drag the scale to select a region.

• FlyBase symbols, e.g., cnn

• FlyBase IDs e.g., FBgn0000490

• Sequence locations e.g., X:6000..8000, 2L:80,000-100,000

• Select a Region of Interest

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.

Panning - position the mouse over an "empty" region of the GBrowse image, and when the mouse cursor displays a double headed arrow (<->), click and drag left/right to pan across the genome. Note that the panning 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.

Zooming

Zoom in or out using the "Show XXX bp" menu in the search panel. Ranges from 100 bp to 200 kbp are available.

Larger view ranges of 1, 5 and 20 Mbp are available in D.melanogaster MegaView (see Data Source menu). This view has been optimised for viewing larger genome regions and restricted to the following tracks: Gene Span, Estimated Cytological Band, Deleted Segment, Duplicated segment and Tiling BAC (only visible below 300Kb).

In either view you can 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.

Customizing the display

Track Title Tool Bar

Many customization features are accessed via the Track Title Tool Bar found at the top left of each track. Mousing over an icon reveals its function.

Show or hide this track. Toggle it to open and close/minimize the track. When hidden, the track title bar persists.

Turn off this track. To reinstate the track, it must be re-selected (see Selecting existing tracks section).

Share this track. Provides a sharable URL that captures the display configurations.

Download this track. Not enabled. For FlyBase data download options, see FilesOverview.

Configure this track. Options vary by the track data type. For tracks with simple box glyphs, options include changing color, height and packing. Extensive configuration options for RNA-Seq tracks, including sample selection and log2/linear data scales, are described here.

About track. Links out to FlyBase GBrowse Tracks Wiki page. The "Download ALL DATA for this track" has not been enabled.

Changing the order of the tracks

To change the order of the tracks in the display panel click on the Track Title Tool Bar and drag up or down.

Customizing subtrack display

Some GBrowse tracks have multiple data subtracks. The presence of subtracks is indicated in the track title itself (as shown to the left). To select which subtracks to display, and in what order, click on the blue "subtracks" label to pull up a customization menu.

Displaying restriction sites

Annotate restriction sites

Restriction sites can be displayed by choosing 'Annotate Restriction Sites" from the top right hand drop down box. A menu of restriction sites will open up. Select the restriction sites of interest and hit "Configure" again. If the track does not show up, see the "Select Tracks" tab at the top, scroll to the bottom "Analysis" section, and tick the "Restriction Sites" box to make the track visible.

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.

Choosing data tracks

The default GBrowse view comprises a predetermined set of 10 tracks chosen from among the many dozens that are available. For details on the entire set of tracks available see GBrowse Tracks. For a more compact list of track choices, go to the "Select Tracks" tab at the top of the GBrowse genome viewer.

Selecting existing tracks

To select the tracks you would like to have displayed in your GBrowse genome viewer, go to the 'Select Tracks' tab at the top of the GBrowse window and choose your tracks of interest (click on the box to the left of the track). Then hit the "Back to Browser" links at the top and bottom of the page take you back to the GBrowse genome viewer, which will now have all of the selected tracks displayed.

Tracks are organized in various sections:

• Reference Gene Annotations (iso-1)
• General
• Aligned Evidence
• Mapped Mutations
• Gene Predictions
• Similarity (Proteins and Synteny features)
• Noncoding Features
• Microarray Features
• Expression Levels (RNA-Seq and RNA-Seq by Tissue)
• Aberrations
• RNAi Reagents and Data
• Other Reagents
• BLAST Hit
• Analysis

One can turn all of the tracks in a given section on or off simultaneously by selecting the "All on" or "All off" options next to the section heading. Clicking on the star designates the track as a "Favorite" (see below). Detailed information about the each track can be accessed by clicking on the "[?]" icon next to the track name.

Note that newly selected tracks always appear at the top of the GBrowse viewer and can be rearranged by clicking on the track name and dragging to the desired position. Only one track can be moved at a time. With a few exceptions, including resets occurring with new FlyBase releases, track selections are preserved from session to session.

Add track to favorites

Clicking on the star icon (on the 'Select Tracks' page) adds a track to your favorites. This feature enables you to view only a subset of tracks on the 'Select Tracks' tab, making it easier to find the tracks you use more frequently. The star icon is also found next to the track names on the 'Select Tracks' tab itself. A yellow star indicates that the track is in your favorites list.

To view your favorite tracks in the 'Select Tracks' tab, choose the 'Select Favorites Only' option at the top of the page. To return to the full list click 'Show All'. Note that this does not add the tracks to your browser, you still need to tick the adjacent boxes to add them to the display.

To clear your favorites list click 'Clear All Favorites' at the top of the 'Select Tracks' tab'.

Adding custom tracks

To add custom tracks go to the 'Custom Tracks' tab. Though three options are listed (text, URL and file), our curators have only had success using the file option.

Discrete features (regions with discrete starts and stops) like BACs, genomic deletions or transcription factor ChIP-peak calls can be uploaded in "GFF3" format. A sample GFF3 file that will upload correctly is available here. Note that the uploaded file must have a ".gff3" extension to be recognized by GBrowse. It's also important to have no configuration lines within the file itself. Configuration of the glyphs (color, line color, packing, labeling, size, etc.) can be done after upload using the Track Title Tool Bar.

For upload of genomic or transcriptomic profiles, we've had success uploading profiles using "bedGraph" format. A sample bedgraph file is available here (note that coordinates are interbase/0-based). Importantly, bedgraph files must be disguised as "wig" files for proper profile display: i.e., must have a ".wig" extension, and must specify "track_type=wiggle_0" in the first line of the file.

For upload of sparse, single base genomic/transcriptomic data (e.g., mapped 5'-ends of CAGE sequences), the variableStep "wig" format is useful. A sample wig file configured with default span=1 (for single base signals) is available here.

Once uploaded, configuration options are available from the Track Title Tool Bar. Note that the y-axis scaling to local min-max in FlyBase-GBrowse2 is a bit buggy (will not always set minimum at zero, may not set to max values) so preferably change the y-axis to fixed values. It's also recommended to change the track height (which is narrow by default).

For additional uploading options, see the GBrowse developers' documentation here. If you have trouble, contact FlyBase help (link at the bottom of any FlyBase webpage).

Other useful features

Saving as a picture

GBrowse views can be exported as low-resolution PNG images or high-resolution, editable SVG images. Access the "File" pull down menu (top right, under FlyBase "Jump to Gene" box), select "Export as..." and choose between the PNG or SVG options. The image should appear in the folder that you've specified for other internet browser downloads.

Note that the high-resolution SVG option only supports the export of a limited number of tracks (typically represented by simple box glyphs representing genes, transcripts, cDNAs, etc.). Many custom FlyBase graphics, such as the layered "Topoview" representation of RNA-Seq data, the exon junctions, DNA/GC content, RNA editing sites and transgenic insertion sites are not supported in the high-resolution SVG format. For such tracks, the low-resolution PNG export option is available, but honestly, you're better off zooming into the web page and using a standard screen grab (e.g., command+shift+4 on a MAC OS) to get a higher resolution PNG.

Ruler

Clicking on the orange ruler icon in the top left corner of the "Details" panel brings up a vertical "ruler" that can be dragged across the GBrowse display and used to gauge the relative positions of features in different tiers. The coordinate corresponding to the central line of the ruler is displayed at the top of the ruler.

Download Sequence File

Select "Download Sequence File" from the drop-down menu at the top right of the browser and click on "Configure" to obtain genomic sequence of the region displayed in the browser. Select the type of output desired (GFF3, FASTA, GenBank, EMBL, GCG, or Raw Sequence) and the type of output (text, html/xml, or Save to Disk). Click on "Go" to obtain the sequence in the desired format. The Feature Fasta option is not functional.

Download HTML table view

Select "Download HTML table view" from the drop-down menu at the top right of the browser and click on "Configure" to obtain a tabular representation of all the feature data for the region displayed in the genome viewer. You can choose to dump all features or just the features corresponding to the selected tracks. Then click on "GO". A table is generated which is labeled with the date and sequence span at the top. Under this, the features from the chosen tracks are separated by feature type and listed along with symbol/name/ID, sequence location, strand information, and notes.

Download GFF File

Select "Download GFF File" from the drop-down menu at the top right of the browser and click on "Configure" to choose among options for creating a GFF file of the genomic region. Files containing all or selected features can be created in GFF versions 2, 2.5. or 3 in genome coordinates or in local coordinates (starting with 1 at the beginning of the segment). The data can be viewed directly, saved to a file, or edited (if a helper application is installed). DNA sequence can be embedded in the GFF file or not. Click on Go to obtain specified GFF file.

Download Decorated FASTA

Select "Download Decorated FASTA File" from the drop-down menu at the top right of the browser and click on "Go" to obtain genomic sequence in FASTA format for the region displayed in the browser. The option to "decorate" the file from the "Configure" menu by choosing separate colors for different features of the sequence, e.g. CDS, is not working.

Links to report pages

Clicking on most genomic features displayed in the GBrowse genomic viewer leads to a detailed report of curated information connected to that feature; reports on the relevant genes, alleles, insertions, aberrations, and sequence features can be accessed in this way. cDNAs and ESTs link to GenBank sequence accession reports.

Highlighting

If you have accessed GBrowse from a report page the feature in question is highlighted in the browser. For example, if you enter GBrowse from the hh gene report, the hh gene will be highlighted in the browser. This behavior is also seen for other mapped features including sequence features, insertions, point mutations and aberrations.

To clear the highlighting click the 'Clear Highlighting' button at the bottom of the browser.

It is also possible to manually highlight features using the options in the Preferences tab.

Accessing previous versions of the genome

The link "Go to Dmel R5.57 Archive Server" above the top right corner of the browser goes to the last FlyBase release containing genome Release 5 (R5) data. Clicking on the GBrowse link at the archived FlyBase site leads to a genome browser with the genomic data displayed relative to R5 coordinates. Previous releases can always be accessed from the Archive tab at the top of the page.