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Add Primers to the Primer Database

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How do I add primers to the SnapGene Primer database?

SnapGene 9.0 and later has a dedicated primer database for storing, labelling and reusing primers across projects. Import primers into your database from .CSV/.TSV files or SnapGene files, and organize your primers with labels, then use the primer database to annotate primers on other DNA sequences.

Access the Primer Database

  1. Expand the side panel if required.
  2. Click Databases.
  3. Select "All Primers" to view the primer database table as a tab.
  4. Click Add Primers or in the top toolbar, click Import → Import Primers.

Import Primers

In the dialog that opens, select either a CSV, TSV or SnapGene .dna file, then click Open.

If you have your primers in an Excel spreadsheet, then export first in either TSV or CSV format.

SnapGene can currently import primer name, sequence and description information.

For example in CSV format:

Name,Sequence,Description

M13-F (-20),GTAAAACGACGGCCAGT,Standard M13 forward sequencing primer

If you have other data you would like to import from your database then contact support and let us know.

In the "Import" window that opens, click the top check box to select all primers or use the check boxes to select specific primers, the click Add Primers.

SnapGene will warn if invalid primers are present. 

SnapGene will also warn if duplicate primers are present if in the list or if already in the database. 

Review, select appropriate primers for import, then click Add Primers.

Review the Primer Database 

All imported primers will be listed in the "All Primers" database.

Use Labels to Make Primer Sets

Create a Label

To create sets of primers add "labels" to primers to add them to the set.

To create a new "Label":

  1. Click Create New.
  2. Give the label a name.
  3. Click the color swatch and give the label a color.
  4. Click Create to make the new Label.

Add Labels to Primers

  1. Select All Primers.
  2. Select the primers you wish to label.
  3. Select the label you wish to assign to the selected primers.

Select the "Label" in the side panel to see all primers with that label.

Edit or delete Imported Primers

To edit a primer:

  1. Click the vertical ellipsis associated with a primer.
  2. Click "Edit primer" to make changes to the primer.
  3. Click "Labels" to add or remove labels associated with the primer.
  4. Click "Move to Trash" to remove the primer from the "All Primers" database.

In the "Edit Primer" dialog, edit the primer name , description, color or "Phosphorylation status" then click OK.

Use the Primer Database to Annotate a Sequence

To learn how to use the primer database to annotate your sequences see this article – Use the SnapGene Primer Database.

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