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Feature sequence panel

TL;DR: The feature details panel can extract and display the sequence underlying a selected feature. For a gene or transcript, choose CDS, protein translation, cDNA, or genomic with introns (plus optional flanking bases); for any other feature type it shows the literal underlying sequence.

Gene features

For gene or transcript features, the feature details panel stitches the subfeature sequences together. The available types are:

  • CDS - the stitched-together coding sequences
  • Protein - protein translation of the CDS. The standard genetic code (NCBI table 1) is used by default, but if the CDS has a transl_table attribute in the GFF (e.g. transl_table=2 for vertebrate mitochondria) the matching alternative codon table is applied, including start-codon and transl_except handling
  • cDNA - the complementary DNA of the transcript, formed from the exon sequences
  • Genomic w/ full introns - the entire gene region including introns, with UTR and CDS highlighted
  • Genomic w/ full introns +/- Nbp up+down stream - the above plus N bases upstream and downstream
  • Genomic w/ Nbp intron - the exon sequence plus N intronic bases flanking each splice site
  • Genomic w/ Nbp intron +/- Nbp up+down stream - combines the upstream/downstream extension with the splice-site flanks

The sequence type is chosen from the dropdown at the top of the panel. The up/downstream extension defaults to 100bp and the intron flank to 10bp; both are configurable from the gear icon.

Sequence panel for the human SELENOP gene, color-coded by region: upstream/downstream (red), UTR (blue), CDS (yellow), and intronic (white). 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 hg38, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “NCBI RefSeq (GFF3Tabix)”.
  3. Track menu → Gene glyph → Representative transcript
  4. Drag the bar at the bottom edge of the track to resize it.
  5. Type your region of interest into the location box and press Enter.This figure is at chr11:5,224,000-5,228,500.

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%2Fconfig_demo.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr11%3A5%2C224%2C000-5%2C228%2C500%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ncbi_refseq_109_hg38_latest%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%2C%22height%22%3A200%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+feature_detail_sequence

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

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr11:5,224,000-5,228,500",
      "tracks": [
        {
          "trackId": "ncbi_refseq_109_hg38_latest",
          "type": "LinearBasicDisplay",
          "geneGlyphMode": "longestCoding",
          "height": 200
        }
      ]
    }
  ]
}

Loaded against config: test_data/config_demo.json

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

from jbrowse_anywidget import LinearGenomeView, fetch_hub

view = LinearGenomeView(
    assembly=fetch_hub("hg38"),
    location="chr11:5,224,000-5,228,500",
)

view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track",
    "name": "My track",
    "assemblyNames": ["hg38"],
    "adapter": {"type": "Gff3TabixAdapter", "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": "hg38",
      "loc": "chr11:5,224,000-5,228,500",
      "tracks": [
        {
          "trackId": "ncbi_refseq_109_hg38_latest",
          "type": "LinearBasicDisplay",
          "geneGlyphMode": "longestCoding",
          "height": 200
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/config_demo.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.

When the Protein type is selected, residues whose translation was overridden by a transl_except attribute are highlighted (amber) and summarized in a legend. The example below is SELENOP, whose ten in-frame UGA stop codons are annotated as transl_except=(...,aa:Sec) and translate to selenocysteine (U).

Protein translation of SELENOP: the ten selenocysteine (U) residues recoded via transl_except are highlighted amber, with a legend summarizing the overrides. 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 hg38, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “NCBI RefSeq (GFF3Tabix)”.
  3. Track menu → Gene glyph → Representative transcript
  4. Drag the bar at the bottom edge of the track to resize it.
  5. Type your region of interest into the location box and press Enter.This figure is at chr5:42,799,000-42,812,500.

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%2Fconfig_demo.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr5%3A42%2C799%2C000-42%2C812%2C500%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ncbi_refseq_109_hg38_latest%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%2C%22height%22%3A200%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+feature_detail_protein

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

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr5:42,799,000-42,812,500",
      "tracks": [
        {
          "trackId": "ncbi_refseq_109_hg38_latest",
          "type": "LinearBasicDisplay",
          "geneGlyphMode": "longestCoding",
          "height": 200
        }
      ]
    }
  ]
}

Loaded against config: test_data/config_demo.json

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

from jbrowse_anywidget import LinearGenomeView, fetch_hub

view = LinearGenomeView(
    assembly=fetch_hub("hg38"),
    location="chr5:42,799,000-42,812,500",
)

view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track",
    "name": "My track",
    "assemblyNames": ["hg38"],
    "adapter": {"type": "Gff3TabixAdapter", "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": "hg38",
      "loc": "chr5:42,799,000-42,812,500",
      "tracks": [
        {
          "trackId": "ncbi_refseq_109_hg38_latest",
          "type": "LinearBasicDisplay",
          "geneGlyphMode": "longestCoding",
          "height": 200
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/config_demo.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.

Choosing the sequence type for a volvox gene: the dropdown is set to 'Genomic w/ full introns +/- 100bp up+down stream', so the panel shows the upstream flank, the exons and introns, and the downstream flank. 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 one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “GFF3Tabix genes”.
  3. Drag the bar at the bottom edge of the track to resize it.
  4. Type your region of interest into the location box and press Enter.This figure is at ctgA:17200-23200.

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%3A17200-23200%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22gff3tabix_genes%22%2C%22height%22%3A300%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+upstream_downstream_details

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

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:17200-23200",
      "tracks": [
        {
          "trackId": "gff3tabix_genes",
          "height": 300
        }
      ]
    }
  ]
}

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:17200-23200",
)

view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track",
    "name": "My track",
    "assemblyNames": ["volvox"],
    "adapter": {"type": "Gff3TabixAdapter", "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:17200-23200",
      "tracks": [
        {
          "trackId": "gff3tabix_genes",
          "height": 300
        }
      ]
    }
  ]
}
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.

A volvox transcript selected, its feature sequence shown, and three types taken from the dropdown in turn: the coding sequence, its translation, and the genomic sequence with introns and flanks around it. Open the session this video starts in ↗

Other feature types

For non-gene features, the "Feature sequence" button shows the literal sequence underlying the feature, without subfeature stitching. The number of flanking bases is configurable from the gear icon.

See also