EasyPrimer assists primer design in difficult contexts, e.g. on an alignment of hundreds of sequences and/or on hypervariable genes.

The tool uses as input the fasta sequence of an alignment and identifies the best regions for primer design: two low variable regions flanking a highly variable one

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Accepted file extention are:
.fasta, .FASTA, .fas, .ffn, .txt, .fna, .fa
No space character accepted in the file's name
Sequences must be in fastA format
(see the example in the textbox below)
Maximium allowed sequence length (for the on-line version) is 2500bp


HRM takes into account only the "HRM detectable" SNP, ALL takes into account any kind of nuclotide change

Shows more advanced settings, we advise to use the default ones first

By clicking "Submit" EasyPrimer will start to run and a summary of your request will be sent to your email address

Download the stand-alone UNIX version of EasyPrimer tool from GitHub

Download an EXAMPLE FASTA FILE to try EasyPrimer
Download here an example of the EASYPRIMER PDF OUTPUT

EasyPrimer is also on GitHub https://github.com/MatteoPS/EasyPrimer

To report bugs please contact matteo.perini@unimi.it

If you are using EasyPrimer for an article or scientfic publication please cite:
Perini, M., Piazza, A., Panelli, S. et al. EasyPrimer: user-friendly tool for pan-PCR/HRM primers design. Development of an HRM protocol on wzi gene for fast Klebsiella pneumoniae typingSci Rep101307 (2020). https://doi.org/10.1038/s41598-020-57742-z