User GuidesSnapGene User Guide Display Options for DNA SequencesShow or Hide Sequences Aligned to a Reference Sequence

Show or Hide Sequences Aligned to a Reference Sequence

How do I toggle display of aligned sequences view?

Show Alignment or Create an Alignment to the Reference sequence

The "Show Alignment" button allows you to view and edit sequences that have been aligned to your "reference" sequence. It also allows you to create a new alignment.

Click the "Show Alignment" button in the side toolbar to see the Aligned sequences panel.

Create An Alignment to the Reference

If the sequence has no aligned sequences then clicking the "Show Alignment" button the side toolbar will open a dialog to allow you to add sequences for alignment.

  • Select "Align imported sequences" then click Align to browse to and select sequences for alignment.
  • Select "Align copied sequence" the click Align to align a sequence that has been copied to the clipboard.
  • Select "Align Open sequences:" then click Align to align sequence files that are already open in SnapGene.

Click Cancel to dismiss the dialog and view the "Aligned Sequences" panel.

View an Alignment to the Reference

If a sequence already has associated "aligned sequences" then clicking the "Show Alignment" button will open the "Aligned Sequences" panel and show a list of aligned sequences. The aligned sequences will be shown as arrows in Map view.

Switch to Sequence view to see the alignment at the nucleotide level.

See the Aligning to a Reference DNA sequence video tutorial to learn about "Alignment to a reference".

See the Aligned Reads to a Reference Sequence User Guide article for detailed information on "Alignment to a reference".