Peroxisome Primer Designer
We created a small software package to enable fast primer design for peroxisomal matrix import and matrix integration. The package uses primer3 to calculate the thermodynamic characteristics of the primer pair.
On the first screen you can paste the sequence of the protein you want to import or integrate into the peroxisome.
On the second screen you can choose the import or integration mechanism into the peroxisome. The C-terminal matrix import corresponds to PEX5 import, the N-terminal to PEX7. The N-terminal import should only be used when the protein is sensitive to C-terminal modifications. The C-terminal integration corresponds to the Pex3/Pex19-dependent pathway, the N-terminal integration to the ER-dependent pathway.
Furthermore the favored melting temperature can be set.
Finally the output screen shows the primer sequences, the respective melting and hairpin temperatures of the primers and the temperature for dimer formation. Note that the hairpin and dimer calculations are done without the added targeting sequences, as they can easily exceed the 60 bp limit for primer3.
Sadly we could not compile the software into a standalone software, but you can download the python file here.