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Fig. 1 | BMC Bioinformatics

Fig. 1

From: CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species

Fig. 1

Overview of CircMiMi. a Flowchart of the overall pipeline. b Schematic illustration of back-splicing events arising from ambiguous alignments with an alternative co-linear explanation (left) and multiple hits (right). For the left panel, the concatenated sequence of the back-splicing event has an alternative co-linear explanation on another chromosome. For the right panel, the concatenated sequence also non-co-linearly maps to another genomic region. c Schematic illustration of sequences flanking circularized exons and the corresponding RCSacross and RCSwithin. In this case, RCSacross = 5, RCSwithin = 4, and RCSacross—RCSwithin = 1. d The four main CircMiMi command lines: (1) collecting all required resources; (2) checking BSJ, alignment ambiguity, and RCS; (3) identifying circRNA-miRNA-mRNA interactions; and (4) generating a Cytoscape-executable file. For (2), “–dist” represents the considered length of the flanking sequences (± N nucleotides of the back-splice site; default value = 10,000). For (3), “–miranda-sc” represents the miRanda score threshold (default value = 155). For (2) and (3), “-p” represents the number of processor cores (default value = 1)

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