SequenceSearchAdapter

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the sequence plugin. View source.

Example usage#

search is a regular expression matched against the assembly's own sequence, so a track needs no file of its own. This one finds canonical polyadenylation signals on both strands:

{
  type: 'FeatureTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'SequenceSearchAdapter',
    search: 'AATAAA',
  },
}

Example: one strand only#

Both strands are scanned by default. Turn one off where the motif is strand-specific, so the track does not report the reverse-complement hit as a second site:

{
  type: 'FeatureTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'SequenceSearchAdapter',
    search: 'GGTAAG',
    searchReverse: false,
  },
}

See the Config slots section below for all available configuration fields.

Note: don't set sequenceAdapter — JBrowse supplies it from the assembly the track is displayed against. Setting it by hand pins the scan to one sequence source and silently desyncs the track if the assembly's sequence changes.

Related links#

• Track: FeatureTrack
• Display: LinearArcDisplay
• Display: LinearBasicDisplay
• Display: LinearMultiRowFeatureDisplay
• Display: LinearScoreDisplay
• Guide: Supported file types

Config slots#

These slots go inside the track's adapter: "adapter": { "type": "SequenceSearchAdapter", ... }. This adapter has no uri shorthand — give it the location slots below. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.