IVA Prime

About IVA Prime

IVA Prime is a web application that allows you to import plasmid files (.gb and .dna), and then easily generate primers for IVA cloning as you edit your plasmid file. The primers can be then easily exported to a read-to-order format and the altered plasmid file can be saved.

The primer design technique is originally based on the work by García-Nafría et al.: DOI: 10.1038/srep27459.

The source code for IVA Prime can be found in the GitHub repository.

How to use

Importing

1. Click on Import File to import either a .gb or .dna file. (Or click Try Demo File to import an empty pET-28a(+) vector.)

2. Navigate using the sequence grid on the right or by clicking on a specific feature in the sidebar.
3. Import more plasmids by clicking Import File again.

Insertions

1. Left click at the position you would like to insert a sequence.

   

2. Right-click to open the context menu and select Insert here.

   

3. Enter a DNA or amino acid sequence to insert.
4. Select a target organism for codon optimisation (Escherichia coli, human, yeast etc.).
5. Press Create Primers.

Deletions

1. Select a region to be deleted.

   

2. Right-click to open the context menu and select Delete selection.

   

Mutations & Replacements

1. Select a region to be mutated/replaced.

   

2. Right-click to open the context menu and select Mutate selection or Mutate selection.

   

3. Enter a DNA or amino acid sequence.
4. Select a target organism for codon optimisation (Escherichia coli, human, yeast etc.).
5. Press Create Primers.

Subcloning

1. To subclone navigate to your region of interest and select it.

   

2. Right-click to open the context menu and select Mark selection for subcloning. A highlight color advanced dashed lines demarcate your marked sequence.
3. Now open the destination plasmid, navigate to where the marked sequence will be inserted.
4. To subclone into a region between bases, left-click at desired position to set the cursor, then right click and choose Subclone into selection
5. If you wish to at the same time insert additional sequences adjacent to the subcloned sequence at the destination, choose Subclone with insertion into selection. This will open a window where you can specify the additional sequences that will be included at the 5' and 3' prime ends individually. Once you are done, press Create Primers.

Saving the primers and modified plasmid to file

• To export the generated primers, click on the downwards arrow next to the plasmid name ▼. This will open a dropdown menu where you can choose your desired format for the primer list.
• To save the modified plasmid file, click on the downwards arrow next to the plasmid name ▼. This will open a dropdown menu where you can choose your desired format for plasmid file.

Privacy policy

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