UROBORUS

[…] that scores the achieved benefit of pairing one algorithm with any other algorithm (Figure ), e.g., the effect of pairing CIRI with ACSF is 0.27. Based on this it is evident that CIRI, find_circ, and Uroborus profit the most from combination with almost any other algorithm, while MapSplice seems to be the preferred complement to most algorithms. In addition, CIRI2, MapSplice, and the CIRCexplorers […]

[…] w circRNAs from RNA-seq data. Notable circRNA identification tools are find_circ [], MapSplice2 [], Segemehl [], circExplorer [], circRNA_finder [], CIRI [], ACFS [], KNIFE [], NCLscan [], DCC [] and UROBORUS []. Information regarding these tools is listed in . In addition, CircView, a platform visualization tool, is specifically developed to visualize circRNAs detected from these tools []. Furthe […]

[…] As described by Zeng et al. [], the tools that use the pseudo-reference-based approach to detect circRNAs include PTESFinder, KNIFE, and NCLscan, whereas circRNA_finder, CIRCexplorer, DCC, find_circ, UROBORUS, CIRI, MapSplice, and segemehl utilize the fragmented-based approach. In addition, several integrated tools aimed to identify circRNAs with a protein-coding potential have been developed, inc […]

[…] ase provides comprehensive information on circRNAs, including genome sequences and loci, and more importantly, this database also provides information for integrated ciRNA-miRNA-mRNA networks []. The UROBORUS database, developed by Song et al., contains the low expressed circRNAs from the total RNA-seq without RNase R treatment []. CIRCexplorer tools can detect candidate circRNAs in breast cancer […]

[…] ragmented-base or segmented read approach. In this approach, the software detects back-spliced sites based on reads mapped to alignment of multiple split reads against the genome. While find-circ and UROBORUS detect back-spliced sequences using the first and last 20 bp after mapping the sequences against the genomes, the rest of the detection tools generate splice alignment algorithms to identify […]

[…] the demand of comprehensive detection of circRNAs, several different pipelines with better performance in circRNA analysis have been developed, including find_circ, CIRI, circRNAFinder, CIRCexplorer, UROBORUS, etc., for further study of circRNAs. However, most of existing work on circRNA is based on bulk sequencing, in which individual cell properties and heterogeneities are hidden. Furthermore, a […]