A free web tool to view a genome and everything annotated on it, at any zoom.
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Each row of data is a track; hundreds come pre-loaded per genome.
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Add your own data and share a live view, both later in this tutorial.
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Backed by databases at UCSC; nothing to install.
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+ Default view at BRAF (hg38): blue menu bar, search box, chromosome ideogram, and stacked tracks (genes, variants, expression, regulation, conservation).
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The home page & the blue menu bar
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The blue menu bar appears on every page.
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Genomes → jump to the Browser, or to the Gateway to pick an assembly.
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Tools · My Data (your tracks & sessions) · Downloads · Help.
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News on data/software changes & upcoming conferences.
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+ The Genomes drop-down.
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The Gateway: pick an assembly & search
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+ The Gateway: choose a genome on the left, set the assembly and enter a gene / position / term on the right, then press GO.
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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.
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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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Try it
+ Genomes → Human GRCh38/hg38. Search BRAF, press Enter.
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The search box takes more than gene names
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Gene symbol: BRAF
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A feature within a gene: SOX2 exon 2
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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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A pasted DNA sequence (runs BLAT)
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ClinVar / RefSeq / GENCODE accessions
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Two ways to search
+ Quick jump: pick the gene from the drop-down. Full search: press Enter / “Search” to scan all tracks & the whole site.
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The “Examples” link by the box lists every accepted format.
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+ Searching BRAF: the quick-jump drop-down offers matches; pressing Enter runs a full search.
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Navigation & viewing controls
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1 Search bar, accepts various formats
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2 Examples of accepted formats
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3 Current viewing size
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4 Current position/range (click to copy)
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5 Move to a different position on the chromosome
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6 Change the viewing size (zoom in / out)
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7 Click "Base" to zoom to nucleotides at center of current view
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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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Alt-drag (Windows) / Option-drag (Mac) adds a highlight directly.
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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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Try it
+ Shift-drag over a BRAF exon → Add Highlight, pick a colour.
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+ Shift-drag → Drag-and-select: zoom to the region, or highlight it in a colour that persists across views.
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Tracks & display
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Tracks and display modes
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The track image is where every annotation is drawn.
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Right-click a track for options: visibility, configure, reorder, hide others.
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Each track controls its own height/detail via its visibility mode.
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Try it
+ Right-click a track name to open its menu.
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+ The right-click menu: hide / dense / squish / pack / full, plus Hide all others, Move to top/bottom, Configure, View image.
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Visibility modes: “feature” tracks
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hide: off
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dense: all on one line
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squish: thin, many per line
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pack: one labelled item per row
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full: one row per feature
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Right-click a track to set its mode, configure, or reorder. (Same GENCODE region, four modes →)
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+ dense
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Visibility modes: “signal” tracks
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Quantitative / “signal” tracks (wiggles, conservation, coverage) use the same menu; here it sets how the data is drawn:
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dense: single heat-style line
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squish / pack: compact
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full: full-height plot with a value axis
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Get information out of a track
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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 the track name → docs & configuration.
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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.
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+ mouse-over (hover)
+ click → details page
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Mouse-over for quick descriptions
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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.
Below the image, every track sits in a labelled group, your menu of data:
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Genes & Gene Predictions GENCODE, RefSeq, MANE
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Phenotype, Variants & Literature ClinVar, COSMIC, CIViC…
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Variation dbSNP, gnomAD
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Expression · Single Cell · Regulation
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Comparative Genomics · Repeats
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+ 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.
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 →
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Sessions: save & share
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turn any view into a stable, shareable link
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Sessions: save & share a live view
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My Data → My Sessions → name it → Submit.
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Captures position, every track setting, your custom tracks & hubs.
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Stable short link: genome.ucsc.edu/s/user/Name
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Drop it into emails, papers, figure legends, posters, class handouts.
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+ Public Sessions: researchers share snapshots: each is a full Browser view (tracks, position, custom data) behind one link.
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Sessions = collaboration & teaching
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Some of you want to teach with the Browser: a link gives every student the same starting view.
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The BRCA·ENIGMA expert-panel set (Tutorial 3) shared its whole analysis as a session.
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Try it
+ Save your current view as a session and copy its short link.
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What you can now do
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Navigate the Browser and read any track & gene model.
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Set track visibility, use the track groups, and reset to defaults.
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Extract DNA, query the Table Browser, and place a sequence with BLAT.
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Load your own data as custom tracks and hubs, and save & share a session.
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Next
+ Tutorial 2 (Cancer Data) tours the clinical databases; Tutorial 3 puts them to work on real variants.
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