Circular RNAs (circRNAs) represent an abundant group of noncoding RNAs in eukaryotes and are emerging as important regulatory molecules in physiological and pathological processes. However, the precise mechanisms and functions of most of circRNAs remain largely unknown.
We developed three stand-alone computational softwares, including circSeeker, circAnno and clipSearch, to identify and annotate circRNAs and their interactions with microRNAs (miRNAs) from large-scale CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, eCLIP, irCLIP, CLASH) and RNA-seq data.
In addition, we developed interactive Web applications to evaluate circRNA-miRNA interactions identified from CLIP-Seq data and discover the miRNA-sponge circRNAs.
The software (Source Codes) and platform are available at http://starbase.sysu.edu.cn/circTools.php.
The paper and the protocol described these software has been published in Methods Mol Biol.