CircPrime

CircPrime designs DNA primers for polymerase chain reaction (PCR) validation of circular RNAs (circRNAs) predicted from high-throughput RNA sequencing and bioinformatic predictors.

Key Features:

• circRNA-specific primer design: Designs DNA primers tailored for detection of covalently closed-loop circular RNAs (circRNAs).
• Thermocycling recommendations: Provides optimal thermocycling conditions for PCR-based identification of circRNAs.
• Input compatibility: Accepts circRNA coordinates and integrates outputs from popular bioinformatic predictors.
• Reference genome selection: Uses reference genomes available in the National Center for Biotechnology Information (NCBI) database for primer design.

Scientific Applications:

• PCR cross-validation of predicted circRNAs: Confirms circRNAs predicted by bioinformatic tools.
• Validation of RNA-seq discoveries: Enables PCR validation of circRNAs identified from high-throughput RNA sequencing datasets.
• Experimental planning for circRNA studies: Supports design of PCR assays to increase reliability of circRNA identification prior to publication.

Methodology:

Accepts circRNA coordinates and outputs from bioinformatic predictors, retrieves selected reference genomes from NCBI, and designs DNA primers with associated thermocycling condition recommendations for PCR validation.