How to add primers to Geneious Prime

Primers are a special file type in Geneious Prime. A primer file will have a green arrow icon Screen_Shot_2019-01-23_at_1.41.37_PM.png in the Document Table.  A primer normally comprises a binding region, which is denoted by the “Binding region” annotation, and optional 5’ extension which may include adaptor sequence, restriction sites or a combination of elements.  

When primers are added to Geneious, it is important to ensure that they are formatted as a primer document, as otherwise they will not be available for primer-associated operations (such as testing against a new sequence).

This article describes the ways in which you can get existing primers into Geneious Prime, either by manually entering them or importing from external sources. 

1. Manual entry of individual primer sequences

If you want to enter a primer sequence, for example a published primer sequence, go to File → New → Sequence. This will open the New Sequence window, just enter the primer sequence and set Type to Primer. If the primer has an extension, select the region corresponding to the binding region, then hit the Binding region: button to set the binding region start point.


Hit OK and the new primer file will be created.


Alternately, you can add the extension after the primer is created. To do this, create a primer as above but do not include the extension. Once the primer is created, select the new primer and go Primers → Add 5′ Extension. This will allow you to add annotated extension elements, such as restriction sites or Gateway sites, to your primer.

2. Importing multiple primers from a spreadsheet or delimited text file.

You can easily import primer sequences from spreadsheets or delimited text documents, either using the Import option under the File menu, or by copying and pasting from your file. At a minimum the tabular data should have two columns, the first column for the primer name, the second for the primer sequence (5′-3′).

To import from the File menu… If you have a collection of primers in an Excel spreadsheet then you can save the file in either tab-delimited (.tsv) or comma-delimited (.csv) format. Then either import via the menu File → From File…, or simply drag the delimited file into the Geneious Prime window. Geneious will identify that you are importing tabular data and ask you to confirm the import format. Once you have confirmed the format the Import Sequences window will open.  

To import by copy and paste... If you have primers in an Excel spreadsheet or a delimited text file then you can simply Copy (CTRL-c or command-c) the column data from the spreadsheet, go to Geneious Prime and Paste (CTRL-v or command-v). Geneious  will detect that you are importing tabular delimited data and ask you to confirm the import format. Once you have confirmed the format the Import Sequences window will open.

The Import Sequences window, shown in the screenshot below, displays a preview of how the sequences will be imported into Geneious.  Ensure the type is set to Primer, and configure the fields so that Name, Sequence, Description and Primer Extension (if required) are set to the correct columns from your delimited file (the Clipboard Contents box shows the columns contained in your file).  Note that if you have primer extensions, these must be listed in a separate column to the binding region in your text file so that they can be correctly identified. Then click OK to finish the import.


3. Add primers to sequence.

This operation under the Primers menu should be used when you want to test whether a published primer sequence (that is not currently in your Geneious database) matches a particular sequence in your database.  Just type or paste your sequence in, configure any mismatch allowances required, and click OK.


If a match is found, the primer will be annotated on your sequence, and you can then extract it into your database if you wish.  

Note that this operation is currently only suitable for primers without extensions. 


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