CircPrime: a web-based platform for design of specific circular RNA primers

BACKGROUND: Circular RNAs (circRNAs) are covalently closed-loop RNAs with critical regulatory roles in cells. Tens of thousands of circRNAs have been unveiled due to the recent advances in high throughput RNA sequencing technologies and bioinformatic tools development. At the same time, polymerase c...

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Detalles Bibliográficos
Autores principales: Sharko, Fedor, Rbbani, Golam, Siriyappagouder, Prabhugouda, Raeymaekers, Joost A. M., Galindo-Villegas, Jorge, Nedoluzhko, Artem, Fernandes, Jorge M. O.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10197314/
https://www.ncbi.nlm.nih.gov/pubmed/37208611
http://dx.doi.org/10.1186/s12859-023-05331-y
Descripción
Sumario:BACKGROUND: Circular RNAs (circRNAs) are covalently closed-loop RNAs with critical regulatory roles in cells. Tens of thousands of circRNAs have been unveiled due to the recent advances in high throughput RNA sequencing technologies and bioinformatic tools development. At the same time, polymerase chain reaction (PCR) cross-validation for circRNAs predicted by bioinformatic tools remains an essential part of any circRNA study before publication. RESULTS: Here, we present the CircPrime web-based platform, providing a user-friendly solution for DNA primer design and thermocycling conditions for circRNA identification with routine PCR methods. CONCLUSIONS: User-friendly CircPrime web platform (http://circprime.elgene.net/) works with outputs of the most popular bioinformatic predictors of circRNAs to design specific circular RNA primers. CircPrime works with circRNA coordinates and any reference genome from the National Center for Biotechnology Information database). SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-023-05331-y.

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