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Sequence track

TL;DR: The sequence track appears automatically when an assembly is loaded, showing the reference sequence and a six-frame translation (three frames per strand), visible only at base resolution. If the view is horizontally flipped, the sequence is shown reverse-complemented and the forward/reverse strand rows swap places.

By default the translation uses the standard genetic code (NCBI table 1). If the assembly config maps a reference sequence to a different genetic code (for example a mitochondrial contig), the translation rows for that sequence use the matching codon table. See Configuring alternative genetic codes for how to set this up.

You can also extract or copy the sequence underlying selected features; see the Feature sequence panel guide.

The sequence track showing the reference sequence (top row) and six-frame translation (three frames per strand) at single-base resolution. Open this view in JBrowse ↗

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses volvox, loaded from a .2bit genome.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “volvox_refseq” track.
  3. Type your region of interest into the location box and press Enter.This figure is at ctgA:20000-20050.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fvolvox%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22volvox%22%2C%22loc%22%3A%22ctgA%3A20000-20050%22%2C%22tracks%22%3A%5B%22volvox_refseq%22%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+sequence_track

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:20000-20050",
      "tracks": [
        "volvox_refseq"
      ]
    }
  ]
}

Loaded against config: test_data/volvox/config.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

from jbrowse_anywidget import LinearGenomeView, make_assembly

view = LinearGenomeView(
    assembly=make_assembly("volvox", "https://your-server/your-genome.fa.gz"),
    location="ctgA:20000-20050",
)

view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track",
    "name": "My track",
    "assemblyNames": ["volvox"],
    "adapter": {"type": "BamAdapter", "uri": "https://your-server/your-file"},
})

view  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:20000-20050",
      "tracks": [
        "volvox_refseq"
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/volvox/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Searching the reference sequence for a pattern, CRISPR guide, or restriction site is a view-level feature; see Sequence search.

Getting the sequence out

The track menu's Launch → Get sequence (visible region) opens the sequence for the window as FASTA, with reverse and complement toggles and a download. A rubberband selection opens the same panel for a span narrower than the window.

See also