Viewing and managing primers

Meghan Bosch
Meghan Bosch
  • Updated

Primers saved to projects can be used across multiple entities. They can be mapped to sequences, linked in pairs, and used in other tools, like in silico PCR. This article explains viewing, attaching, and detaching primers and primer pair creation and visibility.

Access saved primers

To view existing primers:

  1. Click the lens icon in the Home menu to open global search.
  2. Click Filters under the search bar.
  3. Click + Add filters, then select DNA Oligo from the drop-down menu. 

Viewing_saved_primers.png

Tip: View sequences the primer is bound to in the Relevant Items section of the primer entity’s Metadata tab.

Attach and detach primers 

You can attach new or existing primers to sequences. 

To attach new primers to a sequence, create a primer manually or with the Primer Wizard tool. Primers automatically attach to the sequence they are created on. 

To attach existing primers to a sequence:

  1. In a sequence, click the arrows icon in the right-side menu to open the Primers panel.
  2. Click Attach Existing to open the Find Binding Sites tab. 
  3. In the Find binding sites drop-down menu, select how you want to search for existing primers. 
  4. Complete the search parameters and click Find Binding Sites.
  5. In the Primers Search Results that display at the bottom, select the primer(s) you want to attach.
  6. Click Attach Selected Primers in the top-right corner. A toast displays when the attachment is completed. Attach_primers.png

To detach primers from a sequence, open the Primers panel and select Detach. Alternatively, you can detach multiple primers by selecting Detach All Primers.

Detach_primers.png

Link and create primer pairs

Manage primer pairs and conduct in silico PCR by linking two primers on a sequence. 

To link primers: 

  1. Select the first primer, then press Shift and click to select the second primer.
  2. Right-click the highlighted region between the primers and click Link Primers.

Alternatively, you can link primers from the Primers panel. In the panel, click the Primer Pairs tab and click Link Primers.Primer_visibility_on_sequences.gif

To unlink primers: 

  1. In the Primers panel, click the Primer Pairs tab.
  2. Select the primer pair to unlink. 
  3. Click Unlink.

Note: Unlinked primers will remain on the sequence and can be re-linked if needed. 

Manage visibility of primers on sequences

To view your primers on your sequence:

  1. Click the gear icon in the sequence map toolbar.
  2. In the drop-down menu, check Primers.
  3. [Optional] Check Primer Bases to display primer bases on your sequence.

Link_primer_pairs.gif

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