Navigation
This page covers how you move around the genome in a project's browser panel, how the separate public landing browser differs, and how the assistant changes the view.
Where you are
The browser header always shows the genome and the current locus, for example:
Genome Browser hg38 · chr4:73380000-73460000
The locus uses the form chr:start-end with a 1-based start. It updates as you pan and zoom.
Searching for a gene
The Gene symbol box in the browser header jumps to a gene.
- Start typing a gene symbol. After three characters, and a short pause (250 ms), a list of matching symbols appears. While it loads you see "Searching...".
- Pick a symbol from the list (the first one is highlighted when the list appears, so Enter picks it), or click Search to search for exactly what you typed.
- A second list shows each matching transcript (isoform); while it loads you see "Loading...". Each entry shows the transcript name, its collection (for example refGene or GENCODE), the strand, its coordinates, a small exon diagram and, where available, a description.
- Pick a transcript. The browser jumps to that transcript's span.
Keys in the gene search box:
| Key | Action |
|---|---|
| ↓ / ↑ | Move through the suggestions or transcripts. |
| Enter | Choose the highlighted entry, or search for the typed text if nothing is highlighted. |
| Esc | Close the list. |
Clicking outside the box also closes the list.
Messages you may see:
| Message | Meaning |
|---|---|
| "Could not load gene suggestions." | The suggestion request failed. |
| "Could not find gene "X"" | No transcript matched the exact search. |
| "Could not load gene "X"." and a "Gene search failed." toast | The exact search request failed. |
| "Gene not available in current region set view." (toast) | The transcript lies outside the chromosomes the browser can show. |
| "Genome browser is still loading." (toast) | Try again once the tracks appear. |
The Gene symbol box accepts gene symbols only. If you type coordinates such as chr8:127,700,000-127,760,000, they are treated as a gene name and nothing is found. In the project workspace, move to coordinates by dragging and zooming, or ask the assistant to navigate (see below).
Gene search uses the gene-annotation service at lambda.epigenomegateway.org/v3, the same service that supplies the gene tracks. It is a browser feature only; the assistant does not use it.
Zooming
The header has two zoom buttons. They zoom around the centre of the current view, and the label on each button changes while you hold a modifier key:
| Button label | How | Zoom factor |
|---|---|---|
| +1 / -1 | Click | In 2× (half the span) / out 2× (double the span) |
| +1/3 / -1/3 | Hold Shift and click | In to 2/3 of the span / out to 4/3 of the span |
| +5 / -5 | Hold Option (macOS) or Alt and click | In to 1/5 of the span / out 5× |
The tooltip reads "Zoom in 1-fold. Hold Shift for 1/3-fold or Option/Alt for 5-fold." If you hold both modifiers, Option/Alt wins.
Panning
Drag left or right inside the tracks to pan. The browser panel always uses the drag tool; there are no pan buttons in the project workspace.
Limits on the view
The project browser always shows a single chromosome. If a zoom, drag or stored view would span more than one chromosome, the browser shows the whole of the chromosome that covers the largest share of that span. Zooming out past the whole chromosome therefore shows the whole chromosome.
Full Screen
Click Full Screen to open the browser in a large overlay. The overlay has the gene search box, the zoom buttons and Close. Clicking the dimmed area outside the overlay also closes it. The full-screen browser shows the same project state, so changes you make there are kept when you close it. If you export an image while the overlay is open, the overlay's browser is exported.
Refresh
Refresh in the browser header reloads the browser state (tracks, hidden tracks and position) from the project. Window → Refresh Data (Cmd+Alt+Shift+R) reloads the project's data more broadly, including the Track Manager's copy of the tracks.
What is not available
The project browser does not currently provide:
- a coordinate (locus) input box,
- back and forward history of views,
- region highlighting,
- multi-region (split) views,
- a chromosome ideogram, cytoband track or overview minimap.
In earlier testing, the browser's first draw after loading a project could fill only part of the labelled region. The first zoom or window resize corrects it. See Limitations.
The public landing browser
A static web deployment of Genie can show a public browser at / (hg38) and /browser/hg19. It is separate from projects: it uses Genie's native renderer rather than eg3, offers hg38 and hg19 only, shows the default tracks, and does not save anything.
Its toolbar has:
- an hg38 / hg19 toggle,
- a Region box (placeholder
chr7:27053397-27373765) with a Go button; Enter also jumps, - Pan Left and Pan Right, which move by one full window,
- Zoom In (half the span) and Zoom Out (double the span).
You can also scroll horizontally (for example with a trackpad) to pan.
Coordinate syntax in the Region box
The Region box is forgiving about separators and commas:
| You type | Interpreted as |
|---|---|
chr7:27,053,397-27,373,765 | chr7, 1-based start 27,053,397, end 27,373,765 |
chr7:27053397-27373765 | the same |
chr7 27053396 27373765 | chr7, 0-based start 27,053,396, end 27,373,765 (no colon, so the start is not shifted) |
chr7 | a 6 bp window at the centre of chr7 |
Commas are removed before parsing. If the text contains a colon, the start is treated as 1-based. Errors appear under the toolbar, for example "Could not parse interval" or "Location unavailable in this context".
How the assistant navigates
In Genome mode, the assistant moves the browser with the genome_navigate tool. Give it coordinates:
- a locus such as
chr8:127,700,000-127,760,000, or - a chromosome with start and end.
After the tool finishes, the browser panel reloads and shows the new region. The assistant can read the current region with genome_get_current_region.
Gene symbols do not move the viewport. The tool's description mentions gene symbols, but a symbol such as MYC is stored without coordinates, so the browser does not go to the gene (it falls back to the genome's default region). Ask for coordinates, or use the Gene symbol box yourself and then continue the chat.
See Tools for the full tool reference.