CircPrime: tool for circular RNA primer development

CircPrime is web-based platform, providing a user- friendly solution for DNA primer design and thermocycling conditions for circRNA identification with routine PCR methods.


The user-friendly CircPrime tool for circular RNA primer development is written in Python 3 and implemented on a web-based platform. It is freely available online:

CircPrime generates FASTA files using circRNA coordinates and reference genome from the National Center for Biotechnology Information database (NCBI). Then CircPrime extracts junction regions and develops primer sets with the recommended melting temperature (Tm) for each circRNA in the list (up to 100) using Primer3


Check out the Example usage and Parameters section for further information



This project is under active development.

Please cite CircPrime as follows:

Fedor Sharko, Golam Rbbani, Prabhugouda Siriyappagouder, Joost A.M. Raeymaekers, Jorge Galindo-Villegas, Artem Nedoluzhko, Jorge M.O. Fernandes: “CircPrime: a web-based platform for design of specific circular RNA primers. BMC Bioinformatics. Contact: Fedor Sharko (