Primer 3 Implementation for plugin

Pedro Fernandez

• February 26, 2025 15:30

I'm currently developing a plugin using the Geneious devkit and would like to integrate Primer3 for primer design. However, I haven't been able to find documentation on how to call the Primer3 API from within Geneious. I understand that Primer3 is used for melting temperature calculations, and I’d like to leverage it as part of my plugin for designing primers for synthetic genome assembly.

I've already implemented the program in Python, but I’m now working on translating it into Java for integration as a Geneious plugin. I'm having trouble finding the appropriate method in Java to call the Primer3 function. Would anyone be able to provide guidance on how to do this?

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  Richard Moir

  • February 27, 2025 21:15

  Check out this previous post: https://help.geneious.com/hc/en-us/community/posts/360068914912-API-access-to-primer3-calculations

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  Pedro Fernandez

  • February 27, 2025 23:12

  Hey Richard, thank you for your reply! I had seen that post, but I'm struggling to see where I could input the buffer composition for the sake of the Tm calculation with primer3. my plugin is for a method that utilizes a specific buffer so I want to ensure the melting temperature is calculated with the right concentrations of di and monovalent salts, DTT etc... would you be able to direct me to some documentation where I could find that? 

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  Richard Moir

  • March 03, 2025 21:03

  The setValue method can be used like this:

  annealingCharacteristicOptions.setValue("saltConcentrationOptions.dntpConcentration", 99);

  To see a complete list of available options call annealingCharacteristicOptions.toString()

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  Pedro Fernandez

  • March 06, 2025 18:36

  Hey Richard, Thanks again for the response. I'm having a hard time getting the annealingCharacteristicOptions.toString() to to work. its not showing the method at all, when I go into the com.biomatters.plugins.primerDesign folder within the geneious files there is no src code there or any way to look at the documentation.
  because of this its not allowing me to look at the list of options for it. when I go into the primer3 documentation it shows different names for the values. 
  would I be able to find the documentation for the primer3 plugin implementation for this? 

  thanks

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  Richard Moir

  • March 09, 2025 22:06

  Hi Pedro, to see the values you'll have to do inspect the return value of annealingCharacteristicOptions.toString() at runtime. The easiest way would be:

  System.out.println(annealingCharacteristicOptions.toString());

  Unfortunately we don't have any documentation for the plugin.

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