Artem Nedoluzhko1, Fedor Sharko2, Golam Rbanni3, Anton Teslyuk4, Ioannis Konstantinidis5, Jorge M.O. Fernandes6
1Nord University, artem.nedoluzhko@nord.no
2NRC \”Kurchatov Institute\”, fedosic@gmail.com
3Nord University, golam.rbbani@nord.no
4NRC \”Kurchatov Institute\”, anthony.teslyuk@gmail.com
5Nord University, ioannis.konstantinidis@nord.no
6Nord University, jorge.m.fernandes@nord.no
Circular RNAs (circRNAs) are long noncoding RNAs that play a significant role in various biological processes, including embryonic development and stress responses. A number of circRNA de novo and host gene prediction tools are available to date, but their ability to accurately predict circRNA host genes is limited in the case of low-quality genome assemblies or annotations.
Here we describe CircParser, a novel, easy to use and Unix/Linux pipeline for circular RNAs host gene and orthologue prediction using the blastn program and the freely available bedtools software. CircParser is most useful for circRNA host gene prediction analysis in whole transcriptomic datasets for low-quality assembled as well as poorly annotated genomes.
We demonstrate the prediction capacity of CircParser on a recently published transcriptomic data set from the wild and domesticated females of Nile tilapia (Oreochromis niloticus) fast muscle using the five most popular circRNAs in silico prediction tools – CIRI, CIRI2, CircExplorer2, find_circ, and circFinder (Fig. 1).
The Perl implementation of CircParser is available at https://github.com/SharkoTools/CircParser