JGI Genome Portal Help: The Genome Viewer

The Genome Viewer displays tracks (colored, horizontal rows of sequence data) that represent the scaffold, JGI-predicted genes (gene models), and other relevant sequences all aligned by base position. Each track is shown in a specific color and with an identifying label.

Manipulating Tracks

A set of buttons to the left of the tracks in the Genome Viewer allows you to manipulate tracks.

Previous/Next arrows

When you expand a track, the track label will include black arrows to the left and right of the label name (as shown above on either side of Contigs in Scaffolds). These arrows allow you to navigate to the and features for the current track and on the current scaffold/chromosome only.

The left-side arrow moves you to the feature, and the right-side arrow move you to the feature. The or track feature will be centered in the browser along with a 20% padding on each side, causing the zoom to automatically adjust.

If you are currently viewing the first feature in a track, using the previous feature icon will result in recentering around the same feature. Similarly, using the next feature icon when viewing the last feature in a track will cause the browser to recenter around the same feature.

Base Position

The Base Position row is a scale showing the nucleotide base position along the scaffold. To center the Genome Viewer on a certain nucleotide, click the Base Position row at that number. The browser behavior is determined by the Tool Bar's Browser Options. If the Recenter Options is set to:

The Scaffold Track

The black track at the top of the Genome Viewer represents the scaffold. When viewed in full mode (the default), black areas indicate contigs, and red lines or rectangles indicate gaps. The track label shows the scaffold number (e.g., "Scaffold_1"). Small gaps may not be evident when zoomed out.

When zoomed in to a shorter range on the browser, the scaffold track also includes the 3-frame amino acid translation (AA) or at a closer range, the 3-frame amino acid translation with nucleotide bases (NA).

Quick Tips

To view scaffold information, click anywhere along the scaffold track or its label. The Scaffold Info page shows contigs and gaps and allows you to retrieve scaffold and contig sequences in FASTA format.
To view the 3-frame translation of the scaffold, click the Zoom +3x button several times until the 3-frame translation is visible, OR select either the NA or AA button in the Browser Navigation Controls frame.

Other Tracks

In dense mode, a track fits on one row. Though it may not be apparent without zooming, dense tracks other than the scaffold track are broken into features (genes, loci, or proteins) that can be studied more closely when the track is expanded to full mode. Features are shown as rectangles joined by lines. In full mode, each feature appears on its own row and contains arrowheads indicating the read direction of its sequence.

Quick Tips

To toggle a track between full and dense mode, click on the track, the track label, or the + or - button to the left of the track. If the track does not appear to expand, try zooming in.
To view descriptive information about a feature, expand the track, then place your cursor over the feature row. Information should appear in the Feature text box of the Navigation Controls or in a pop-up window.
To move a track up or down in the Genome Viewer, click the up or down arrow to the left of the track.

Loci Tracks

For some organisms, loci are shown in a "Loci" track. Each feature in such a track represents a locus. To view the annotation area for a locus, click the Loci track to expand it to full mode, then click the feature row for the locus of interest.

Gene Model Tracks

JGI-predicted genes appear in a track below the scaffold track, usually labeled "Gene Models" or "" User-created gene models may be shown further down the list of tracks.

On Gene Model tracks, each feature represents a single gene model. Rectangles represent exons, and the connecting lines represent introns.

Quick Tip

To view the Protein Page for a gene model of interest, click on a gene model track to expand it into feature rows, then click the feature row that corresponds to the gene model.

Nucleotide Tracks

Tracks for nucleotide sequences are shown below the gene models. These can include ESTs, clones, reads, and BLAT or BLAST data for related organisms.

On nucleotide tracks, each feature represents an alignment. Rectangles represent high-scoring pairs (HSPs), and connecting lines represent gaps in the alignment.

Quick Tip

To view the Alignment Details page for a nucleotide alignment of interest, click on a nucleotide track to view it in full mode, then click the feature row that corresponds to the alignment.

Repeat Tracks

In repeat sequence tracks (usually shown in black near the bottom of the screen), each feature represents a repetitive region on the scaffold.

Quick Tip

To view a repeat of interest, click on the repeat track to view it in full mode, then click the feature row that corresponds to the repeat.

VISTA Tracks

When expanded, the full VISTA curve is displayed showing a percent of conservation where regions colored in blue correspond to exonic regions within the predicted gene model set and red represents all other regions. Only regions exceeding a predefined minimum percent of conservation threshold are colored red/blue, all other regions remain uncolored (or white).

Quick Tip

To go directly to the VISTA text-based alignment browser, click on the expanded curve.