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

Sharko F 1 , Rbbani G 2 , Siriyappagouder P 2 , Raeymaekers JAM 2 , Galindo-Villegas J 2 , Nedoluzhko A 3 Show all authors , Fernandes JMO 4

Affiliations 

  • 1 Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33/2, 119071, Moscow, Russia
  • 2 Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, PB 1490, 8049, Bodø, Norway
  • 3 Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, PB 1490, 8049, Bodø, Norway. nedoluzhko@gmail.com
  • 4 Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, PB 1490, 8049, Bodø, Norway. jorge.m.fernandes@nord.no
BMC Bioinformatics, 2023 May 19;24(1):205.
PMID: 37208611 DOI: 10.1186/s12859-023-05331-y

Abstract

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).

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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