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

Sharko, F.; Rbbani, G.; Siriyappagouder, P.; Raeymaekers, J. A. M.; Galindo-Villegas, J.; Nedoluzhko, A.; Fernandes, J. M. O.

2022-12-20 bioinformatics
10.1101/2022.12.20.521155 bioRxiv
Show abstract

BackgroundCircular RNAs (circRNAs) are covalently closed-loop RNAs with critical regulatory roles in cells. The tenth 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 (NCBI).

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The top 8 journals account for 50% of the predicted probability mass.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.