A free web tool to view a genome and everything annotated on it, at any zoom.
Each row of data is a track; hundreds come pre-loaded per genome.
Add your own data and share a live view, both later in this tutorial.
Backed by databases at UCSC; nothing to install.
Default view at BRAF (hg38): blue menu bar, search box, chromosome ideogram, and stacked tracks (genes, variants, expression, regulation, conservation).
The home page & the blue menu bar
The blue menu bar appears on every page.
Genomes → jump to the Browser, or to the Gateway to pick an assembly.
Tools · My Data (your tracks & sessions) · Downloads · Help.
News on data/software changes & upcoming conferences.
The Genomes drop-down.
The Gateway: pick an assembly & search
The Gateway: choose a genome on the left, set the assembly and enter a gene / position / term on the right, then press GO.
Left: popular species, a box to search thousands of assemblies, and your Recent Genomes and connected hub assemblies. “Show species tree” opens the full tree.
Right: the assembly drop-down and a search box for a gene, position, or sequence. Over 50,000 assemblies in all.
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We use hg38; hg19 is still common clinically — pick the right build first.
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We use hg38, but hg19 is still common clinically, so pick the right build first.
Try itGenomes → Human GRCh38/hg38. Search BRAF, press Enter.
The search box takes more than gene names
Gene symbol: BRAF
A feature within a gene: SOX2 exon 2
Position: chr7:140,753,300-140,753,400
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dbSNP: rs113488022 · HGVS: NM_004333.6:c.1799T>A
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dbSNP: rs113488022
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HGVS: NM_004333.6:c.1799T>A
A pasted DNA sequence (runs BLAT)
ClinVar / RefSeq / GENCODE accessions
Two ways to searchQuick jump: pick the gene from the drop-down. Full search: press Enter / “Search” to scan all tracks & the whole site.
The “Examples” link by the box lists every accepted format.
Searching BRAF: the quick-jump drop-down offers matches; pressing Enter runs a full search.
Navigation & viewing controls
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1 Search bar, accepts various formats
2 Examples of accepted formats
3 Current viewing size
4 Current position/range (click to copy)
5 Move to a different position on the chromosome
6 Change the viewing size (zoom in / out)
7 Click "Base" to zoom to nucleotides at center of current view
Shift + drag to zoom or highlight
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Shift + drag across the image opens the Drag-and-select dialog: Zoom In to that range, or add a coloured highlight you can keep.
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Shift + drag across the image opens the Drag-and-select dialog: Zoom In to that range, or add a colored highlight you can keep.
Alt-drag (Windows) / Option-drag (Mac) adds a highlight directly.
Ctrl-drag (Windows) / Cmd-drag (Mac) zooms straight to the selected range.
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Clear highlights via View → Clear Highlights.
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Clear highlights via View → Remove all highlights.
Try it
- Shift-drag over a BRAF exon → Add Highlight, pick a colour.
+ Shift-drag over a BRAF exon → Add Highlight, pick a color.
- Shift-drag → Drag-and-select: zoom to the region, or highlight it in a colour that persists across views.
+ Shift-drag → Drag-and-select: zoom to the region, or highlight it in a color that persists across views.
Tracks & display
Tracks and display modes
The track image is where every annotation is drawn.
Right-click a track for options: visibility, configure, reorder, hide others.
Each track controls its own height/detail via its visibility mode.
Try it
Right-click a track name to open its menu.
The right-click menu: hide / dense / squish / pack / full, plus Hide all others, Move to top/bottom, Configure, View image.
Visibility modes: “feature” tracks
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A feature is a single item drawn in a track, such as a gene, an exon, or a variant. Feature tracks draw these one at a time based on their chromosome start position, and the visibility mode sets how they stack:
hide: off
dense: all on one line
squish: thin, many per line
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pack: one labelled item per row
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pack: each row can contain multiple features
full: one row per feature
Right-click a track to set its mode, configure, or reorder. (Same GENCODE region, four modes →)
densesquishpackfull
Visibility modes: “signal” tracks
Quantitative / “signal” tracks (wiggles, conservation, coverage) use the same menu; here it sets how the data is drawn:
dense: single heat-style line
squish / pack: compact
full: full-height plot with a value axis
densesquishpackfull
Get information out of a track
Mouse-over a feature for a quick tooltip.
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Click a feature → details page (significance, links, colour key).
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Click a feature → details page (significance, links, color key).
Click the track name → docs & configuration.
Try it, ▶ open the BRAF V600E session
Click the BRAF V600E ClinVar variant; read its details page. We work through this variant closely in Tutorial 3.
mouse-over (hover)click → details page
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Mouse-over for quick descriptions
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Mouse-over a track name for a description
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Hover a track name (in the controls) → a one-line description of what it is.
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Hover a feature → its key facts without clicking.
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The fast way to learn an unfamiliar track before turning it on.
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Hover a track name in the controls under the image (not a feature in the image itself) → a one-line description of what that track is.
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The fast way to learn an unfamiliar track before you turn it on.
Below the image, every track sits in a labelled group, your menu of data:
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Below the image, every track sits in a labeled group, your menu of data:
Genes & Gene Predictions GENCODE, RefSeq, MANE
Phenotype, Variants & Literature ClinVar, COSMIC, CIViC…
Variation dbSNP, gnomAD
Expression · Single Cell · Regulation
Comparative Genomics · Repeats
- The track-controls area under the image: each track has a visibility dropdown, organised by group. Don’t panic at the volume. The Recommended Track Sets (next) help.
+ The track-controls area under the image: each track has a visibility dropdown, organized by group. Don’t panic at the volume. The Recommended Track Sets (next) help.
Note: not all track groups will be available for all assemblies, especially non-human and non-mouse
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Track documentation pages
Reach it two ways: click the track's name in the controls under the image, or right-click the track → Configure.
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Shows the track's description: data, methods & references, and the colour key.
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Shows the track's description: data, methods & references, and the color key.
The same page holds the track's settings (next slide).
Try it
Click the GENCODE track name; skim its description.
- A track’s documentation page: methods, references, colour key, and configuration controls.
+ A track’s documentation page: methods, references, color key, and configuration controls.
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Container tracks: folders of subtracks
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Many entries (like NCBI RefSeq or GTEx) are really a group of related tracks — a single line in the controls that holds a set of subtracks.
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Many entries (like NCBI RefSeq or GTEx) are really a group of related tracks: a single line in the controls that holds a set of subtracks.
Open the container (click its name, or right-click → Configure) to switch its subtracks on or off and set each one’s display mode.
Turn the container off to hide all its subtracks at once, or on to reveal them and choose individually.
Example
- NCBI RefSeq is one container holding RefSeq Curated, Predicted, MANE, HGMD and more — here only RefSeq Curated is on.
+ NCBI RefSeq is one container holding RefSeq Curated, Predicted, MANE, HGMD and more. Here, only RefSeq Curated is on.
A container track’s settings: check or uncheck each subtrack to choose what is drawn.
Configure a track: display & filters
- ClinVar’s settings page: the display mode, the boxed Filter items by controls, and colour options.
+ ClinVar’s settings page: the display mode and the boxed Filter items by controls.
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Set the display mode (hide → full) and track colours.
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Filter what’s shown — here by clinical significance, variant type, allele origin, molecular consequence, and size.
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Set the display mode (hide → full).
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Filter what’s shown, here by clinical significance, variant type, allele origin, molecular consequence, and size.
Container tracks (a folder grouping related tracks) list their subtracks to switch on or off individually.
Submit applies your changes; Reset to defaults undoes them.
Try it
Open ClinVar’s settings and filter to Pathogenic variants only.
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Reset all tracks
Changed too many tracks and lost your place?
Genome Browser → Reset All User Settings restores the default set.
Note
Reset clears your track choices, custom tracks, and connected hubs (but not your saved sessions); gives you a clean slate.
After Reset All User Settings: the curated default set of tracks is back.
Viewing and extracting the DNA sequence
Want the actual bases of a gene/region? View → DNA.
Returns the sequence for whatever is currently in view.
Try it
Zoom to a BRAF exon → View → DNA → Get DNA.
View → DNA Sequence returns the bases for the current window.
Viewing DNA: options
The DNA output page: reverse-complement option, extension controls, and the retrieved sequence.
Reverse complement for a (–)-strand gene, then Get DNA.
Extend the output up- / down-stream to grab flanking sequence.
Feeds primer design, BLAT, cloning…
Tools: Table Browser & BLAT
get the data out, and find a sequence in the genome
Table Browser: get the data out
Tools → Table Browser: a graphical interface to all the underlying Genome Browser data.
Get the data behind any track, as a table.
Restrict to a region, filter by field, intersect two tracks.
Download BED/CSV, send to Galaxy, or save as a custom track.
New: free hosting: Hub Space 2026
- No web server? Upload bigBed / bigWig / BAM / VCF directly on the Browser: Track Hubs → Hub Space tab (10 GB to start — email us if you need more). Announcement →
+ No web server? Upload bigBed / bigWig / BAM / VCF directly on the Browser: Track Hubs → Hub Space tab (10 GB to start; email us if you need more). Read the announcement.
Sessions: save & share
turn any view into a stable, shareable link
Sessions: save & share a live view
My Data → My Sessions → name it → Submit.
Captures position, every track setting, your custom tracks & hubs.
Stable short link: genome.ucsc.edu/s/user/Name
Drop it into emails, papers, figure legends, posters, class handouts.
Public Sessions: researchers share snapshots: each is a full Browser view (tracks, position, custom data) behind one link.
Sessions = collaboration & teaching
Some of you want to teach with the Browser: a link gives every student the same starting view.
The BRCA·ENIGMA expert-panel set (Tutorial 3) shared its whole analysis as a session.
Try it
Save your current view as a session and copy its short link.
What you can now do
Navigate the Browser and read any track & gene model.
Set track visibility, use the track groups, and reset to defaults.
Extract DNA, query the Table Browser, and place a sequence with BLAT.
Load your own data as custom tracks and hubs, and save & share a session.
NextTutorial 2 (Cancer Data) tours the clinical databases; Tutorial 3 puts them to work on real variants.
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