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

BMC Bioinformatics

Software

Golam Rbbani¹  Jorge Galindo-Villegas¹  Prabhugouda Siriyappagouder¹  Jorge M. O. Fernandes¹  Joost A. M. Raeymaekers¹  Artem Nedoluzhko²  Fedor Sharko³ 

[1]Faculty of Biosciences and Aquaculture, Nord University, PB 1490, Universitetsalléen 11, 8049, Bodø, Norway

[2]Faculty of Biosciences and Aquaculture, Nord University, PB 1490, Universitetsalléen 11, 8049, Bodø, Norway

[3]Paleogenomics Laboratory, European University at Saint Petersburg, 6/1A Gagarinskaya st., 191187, Saint Petersburg, Russia

[4]Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33/2, 119071, Moscow, Russia

[5]Limited Liability Company ELGENE, Malaya Kalitnikovskaya 16, 109029, Moscow, Russia

[6]National Research Center “Kurchatov Institute”, 1st Akademika Kurchatova Square, 123182, Moscow, Russia

关键词: Circular RNAs;    RNA-sequencing;    circRNAs;    Primer design;    RT-PCR;    qPCR;    Validation;    PCR;    Web platform;    Prediction;   

DOI  :  10.1186/s12859-023-05331-y

 received in 2022-10-29, accepted in 2023-05-11,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundCircular 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.ResultsHere, 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.ConclusionsUser-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).

【 授权许可】

CC BY   
© The Author(s) 2023

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