The bioinformatics toolbox for circRNA discovery and analysis

• Published in: Briefings in bioinformatics Vol. 22; no. 2; pp. 1706 - 1728
• Main Authors: Chen, Liang, Wang, Changliang, Sun, Huiyan, Wang, Juexin, Liang, Yanchun, Wang, Yan, Wong, Garry
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 22.03.2021; Oxford Publishing Limited (England)
• Subjects: Annotations; Bioinformatics; Biomarkers; Data mining; Gene sequencing; Network analysis; Review; Ribonucleic acid; RNA; Splicing; text mining; circRNA; non-coding RNA; next generation sequencing; bioinformatics tools; disease biomarker
• ISSN: 1477-4054; 1467-5463; 1477-4054
• DOI: 10.1093/bib/bbaa001

Abstract Circular RNAs (circRNAs) are a unique class of RNA molecule identified more than 40 years ago which are produced by a covalent linkage via back-splicing of linear RNA. Recent advances in sequencing technologies and bioinformatics tools have led directly to an ever-expanding field of types and biological functions of circRNAs. In parallel with technological developments, practical applications of circRNAs have arisen including their utilization as biomarkers of human disease. Currently, circRNA-associated bioinformatics tools can support projects including circRNA annotation, circRNA identification and network analysis of competing endogenous RNA (ceRNA). In this review, we collected about 100 circRNA-associated bioinformatics tools and summarized their current attributes and capabilities. We also performed network analysis and text mining on circRNA tool publications in order to reveal trends in their ongoing development.