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MotifListAdapter

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

Example usage

{
  type: 'FeatureTrack',
  trackId: 'restriction_enzymes',
  name: 'Restriction enzymes',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'MotifListAdapter',
    motifs: 'EcoRI\tG^AATTC\nBamHI\tG^GATCC',
  },
}

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

Scans the reference for a list of named motifs, e.g. restriction enzyme recognition sites.

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.

Config slots

These slots go inside the track's adapter: "adapter": { "type": "MotifListAdapter", ... }. 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.

SlotDescription
motifs
text = ''		Newline-separated list of named motifs in REBASE notation, e.g. EcoRI G^AATTC or, for a type IIS enzyme that cuts downstream of its site, BsaI GGTCTC(1/5). The name is optional, ^ marks the top-strand cut, and (n/m) gives the top and bottom cuts counted from the site's 3' end. Blank lines and # comments are ignored.
sequenceAdapter
frozen = null		discouraged: leave unset. JBrowse supplies the assembly's sequence adapter automatically; this override exists only for the rare case of scanning a sequence other than the one the track is displayed against.
searchForward
boolean = true		ignored for palindromic motifs, which match both strands at once
searchReverse
boolean = true		ignored for palindromic motifs, which match both strands at once