Welcome to the IVA Prime repository!
IVA Prime 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 then be exported to a ready-to-order format, and the altered plasmid file can be saved.
IVA Prime is described in detail in our recent publication: Leonte et al. (2025)
The primer design technique is originally based on the work by García-Nafría et al.:
Tip
You can use IVA Prime in your browser or as a desktop app:
- Online Web App: ivaprime.com
- Desktop App: Download the latest release
Note
The latest version of IVA Prime is available online at ivaprime.com.
For local installation, see Installation.
Plasmid files can be imported using either the "Import File" button or by dragging them onto the page. IVA Prime currently supports the .gb, .gbk, .dna, and .fasta file formats. Alternatively, a new file can be generated from a DNA sequence by pressing the "New File" button. By clicking on "Try Demo File", a pET-28a plasmid will be loaded for users to try out features.
Once a plasmid file has been imported, its DNA sequence can be edited similarly to editing a text document.
For simple insertions, the position where the new sequence should be inserted can be selected by left clicking. The currently selected position is indicated by a vertical line. Then, right-click anywhere in the sequence to bring up the context menu. Select Insert here. A window will pop up to ask for a DNA or AA sequence. If an AA sequence is provided, it will be optimized for the selected organism.
Select a region in the DNA sequence by pressing left-click and dragging the mouse while holding left-click. The selection can be adjusted by dragging the cursors on each side. Once the region to be mutated is selected, right-click to open the context menu and select Mutate selection. The DNA or AA sequence to replace the selected bases can then be specified. If an AA sequence is provided, it will be optimized for the selected organism.
Select the region to be deleted as described in the previous section. Right-click and select Delete selection in the context menu.
For subcloning, import the two plasmid files on the same browser page. In the plasmid containing the region to be subcloned, select the sequence. Then right-click and select Mark selection for subcloning. Switch over to the target vector. If the sequence to be subcloned should be inserted a specific position, left-click at the wanted position. If the sequence to be subcloned should replace a region in the target vector, select that region. Right-click and select Subclone into selection.
Additionally, insertions can be added to the subcloning target in the same operation. In the last step, select instead Subclone with insertion into selection. In the window that pops up, DNA or AA sequences can be specified which will be added to either the 5' or 3' end of the subcloning target. If an AA sequence is provided, it will be optimized for the selected organism.
Just download the installer for your platform from the latest releases page:
- Windows:
.exe - macOS:
.dmg- For Intel Macs: download the
macos-intelversion - For Apple Silicon (M1/M2): download the
macos-armversion
- For Intel Macs: download the
- Linux:
.AppImage.deb.rpm
Run the installer and follow the on-screen instructions.
If you want to build the Tauri app from source, you’ll need Node.js, Rust, and the Tauri prerequisites. Then run:
git clone https://github.com/RaduLeonte/IVA-Prime
cd IVA-Prime/tauri/iva-prime
npm install
npm run tauri buildIVA Prime can be installed locally using Git and Docker.
Note: On some systems, Docker Desktop does not include
docker-compose. Make sure it is installed.
Once Docker is ready, open your terminal and run:
git clone https://github.com/RaduLeonte/IVA-Prime
cd IVA-Prime/docker
docker-compose up --buildThe web app is now running locally on your computer and can be accessed by going the following address in your web browser:
https://localhost:8000
Note
The web app must be relaunched after rebooting.
If you use IVA Prime in your research, please cite our recent publication describing the tool:
Leonte et al. (2025)
You may also reference the original primer design method:
García-Nafría et al. (2016)