The recent discovery of circular RNAs (circRNAs) and characterization of their functional roles have opened a new avenue for understanding the biology of genomes. circRNAs have been implicated to play important roles in a variety of biological processes, but their precise functions remain largely elusive. Currently, a few approaches are available for novel circRNA prediction, but almost all these methods are intended for animal genomes. Considering that the major differences between the organization of plant and mammal genomes cannot be neglected, a plant-specific method is needed to enhance the validity of plant circRNA identification. In this study, we present CircPlant, an integrated tool for the exploration of plant circRNAs, potentially acting as competing endogenous RNAs (ceRNAs), and their potential functions. With the incorporation of several unique plant-specific criteria, CircPlant can accurately detect plant circRNAs from high-throughput RNA-seq data. Based on comparison tests on simulated and real RNA-seq datasets from Arabidopsis thaliana and Oryza sativa, we show that CircPlant outperforms all evaluated competing tools in both accuracy and efficiency. CircPlant is freely available at http://bis.zju.edu.cn/circplant.
环状RNA(circular RNA, circRNA)是一类具有共价闭合环结构的单链RNA分子。作为内源性非编码RNA的一员，circRNA与多种生物学过程相关，可以调控转录、影响可变剪接、沉默miRNA或蛋白质。目前，已有数十种环状RNA识别工具，但这些方法几乎都是为动物环状RNA而开发的。考虑到动植物基因组之间的差异和植物环状RNA的特性，需要植物特异性方法来增强植物circRNA识别的有效性。因此，我们开发了植物环状RNA整合分析工具CircPlant，该工具整合了植物特异性识别标准，不仅可以从高通量RNA-seq数据中准确检测植物circRNA，也适用于环状RNA和miRNA互作预测,ceRNA网络预测和环状RNA功能预测等后续分析。通过拟南芥和水稻的模拟数据和真实RNA-seq数据进行评估，发现CircPlant在模拟数据集中的敏感性和准确性均优于以前的工具，在真实数据中也取得很好的效果。CircPlant可以通过访问。





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