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CircPrime: a web-based platform for design of specific circular RNA primers
Fedor Sharko1,2,3, Golam Rbbani4, Prabhugouda Siriyappagouder4
1Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33/2, 119071, Moscow, Russia.
BMC Bioinformatics
|May 19, 2023
Summary
CircPrime is a web platform that designs DNA primers for identifying circular RNAs (circRNAs) using standard PCR. It simplifies the validation of circRNAs predicted by bioinformatics tools.
Area of Science:
- Molecular Biology
- Bioinformatics
Background:
- Circular RNAs (circRNAs) are regulatory molecules with critical cellular roles.
- High-throughput sequencing and bioinformatics have identified numerous circRNAs.
- Polymerase chain reaction (PCR) validation is crucial for published circRNA studies.
Purpose of the Study:
- To present CircPrime, a web-based platform for designing PCR primers and thermocycling conditions for circRNA identification.
- To offer a user-friendly solution for validating circRNAs predicted by bioinformatics tools.
Main Methods:
- Development of a web-based platform, CircPrime.
- Integration with outputs from popular circRNA bioinformatics predictors.
- Utilizing circRNA coordinates and National Center for Biotechnology Information (NCBI) reference genomes.
Main Results:
- CircPrime provides a user-friendly interface for primer design.
- The platform suggests specific thermocycling conditions for PCR-based circRNA identification.
- Facilitates the essential cross-validation step in circRNA research.
Conclusions:
- CircPrime is a valuable tool for researchers studying circRNAs.
- The platform streamlines the design of specific primers for circRNA validation.
- It supports circRNA research by simplifying experimental validation using routine PCR methods.
