Circular RNAs (circRNAs) are formed by joining the 3 and 5 ends of RNA molecules. Identification of circRNAs is an important part of circRNA research. The circRNA prediction methods can predict the circRNAs with start and end positions in the chromosome but cannot identify the full-length circRNA sequences. We present an R package FcircSEC (Full Length circRNA Sequence Extraction and Classification) to extract the full-length circRNA sequences based on gene annotation and the output of any circRNA prediction tools whose output has a chromosome, start and end positions, and a strand for each circRNA. To validate FcircSEC, we have used three databases, circbase, circRNAdb, and plantcircbase. With information such as the chromosome and strand of each circRNA as the input, the identified sequences by FcircSEC are consistent with the databases. The novelty of FcircSEC is that it can take the output of state-of-the-art circRNA prediction tools as input and is applicable for human and other species. We also classify the circRNAs as exonic, intronic, and others. The R package FcircSEC is freely available.

中文翻译：

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FcircSEC：用于全长circRNA序列提取和分类的R包。

通过连接3和5形成环状RNA（circRNA）RNA分子的末端。circRNA的鉴定是circRNA研究的重要组成部分。circRNA预测方法可以预测在染色体中具有起始和终止位置的circRNA，但无法识别全长circRNA序列。我们提出了一个R包FcircSEC（全长circRNA序列提取和分类），用于基于基因注释和任何circRNA预测工具的输出来提取全长circRNA序列，该工具的输出具有染色体，起始和终止位置，以及用于每个circRNA。为了验证FcircSEC，我们使用了三个数据库，即circbase，circRNAdb和plantcircbase。以每个circRNA的染色体和链等信息为输入，通过FcircSEC识别的序列与数据库一致。FcircSEC的新颖之处在于它可以将最新的circRNA预测工具的输出作为输入，适用于人类和其他物种。我们还将circRNA分类为外显子，内含子和其他。R软件包FcircSEC是免费提供的。