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Set the Display Preferences for New and Imported RNA Sequences

  • Updated

How do I set the default appearance for newly created or imported RNA sequences?

Restriction enzyme sites are not shown on RNA sequences, as restriction enzymes cannot cut ssRNA or dsRNA. Convert your RNA sequence to dsDNA if you want to see enzyme cut sites. See Convert RNA to DNA.

Open Preferences

Click SnapGene → Preferences (macOS) or Edit → Preferences (Windows or Linux), and select "RNA" in the sidebar.

Set the Default Visibility for Features and Primers

Toggle the "Show features" to display or hide features.

Set the Default Appearance for Translations

Toggle the "Show translations" button to display or hide predicted translations for new or imported DNA sequences.

  • Use the drop-down menu to choose "ORFs only" or specific reading frame combinations.
  • Use the drop-down menu to select a preset minimum length for an ORF, or use the field to enter a custom minimum length.
  • Check or uncheck the box to control whether start codons are required for predicted ORFs.
    • Use the drop-down menu to specify the allowed start codons.
    • Check the box labeled "except at RNA ends" to show truncated ORFs that begin at DNA ends.

Set the Default Map View Options for New or Imported RNA Sequences

  1. Toggle the "Show features on the RNA line" button to determine whether features are placed on the RNA line.
  2. Toggle the "Show feature labels" button to show or hide feature labels. Use the associated drop-down menu to choose between display of "Internal and external" labels, or "Internal" labels only.
  3. Toggle the "Show locations" button to show or hide locations (coordinates) for primers.

Set the Default Sequence View Options

  1. Toggle the "Minimap" button to show or hide a minimap at the top of the window.
  2. Toggle the "Use an Alternative format" button and use the associated dropdown menu to display sequence in "Blocks of 10", "Blocks of 3" and "Compact" Format. See
  3. Toggle the "Use 3-letter amino acid codes" button to show translations as either 1-letter or 3-letter codes.  See View Sequence in Blocks of 3 or 10 and Display  Sequence as Plain Text for more information on these alternative formats.
  4. Toggle the "Fixed line width" button to use a fixed line width or to fit the window width.  See Adjust Line Width in Sequence View for more information on this option.

Set the Default Structure View Options

Toggle the button to show or hide base index labels on predicted ssRNA structures in RNA Structure View. See View Predicted RNA Secondary Structure to learn about structure labels.

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