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UROBORUS specifications

Information


Unique identifier OMICS_11196
Name UROBORUS
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages Perl
License MIT License
Computer skills Advanced
Version 0.0.1
Stability Stable
Requirements
TopHat, samtools, Bowtie
Maintained Yes

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Maintainer


  • person_outline Xiaofeng Song

Publication for UROBORUS

UROBORUS citations

 (10)
library_books

Improved circRNA Identification by Combining Prediction Algorithms

2018
PMCID: 5844931
PMID: 29556495
DOI: 10.3389/fcell.2018.00020

[…] 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 […]

library_books

Current Research on Non Coding Ribonucleic Acid (RNA)

2017
Genes
PMCID: 5748684
PMID: 29206165
DOI: 10.3390/genes8120366

[…] 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 […]

library_books

Circular RNAs: Biogenesis, Function, and a Role as Possible Cancer Biomarkers

2017
Int J Genomics
PMCID: 5733622
PMID: 29349062
DOI: 10.1155/2017/6218353

[…] 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 […]

library_books

Circular RNAs: clinical relevance in cancer

2017
Oncotarget
PMCID: 5787450
PMID: 29416705
DOI: 10.18632/oncotarget.22846

[…] 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 […]

library_books

Circular RNAs (circRNAs) in Health and Disease

2017
Genes
PMCID: 5748671
PMID: 29182528
DOI: 10.3390/genes8120353

[…] 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 […]

library_books

Heterogeneous circRNA expression profiles and regulatory functions among HEK293T single cells

2017
Sci Rep
PMCID: 5663837
PMID: 29089539
DOI: 10.1038/s41598-017-14807-w

[…] 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 […]


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UROBORUS institution(s)
Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China; Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA; Department of Gynecology and Obstetrics, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China; USC Norris Comprehensive Cancer Center, Department of Neurology and Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA; Zilkha Neurogenetic Institute, Department of Psychiatry and Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
UROBORUS funding source(s)
National Natural Science Foundation of China [61171191, 61571223, 81270700]; Specialized Research Fund for the Doctoral Program of Higher Education [20133218110016]; ‘Six Talent Peak’ Project of Jiangsu Province [SWYY-021]; China Scholar Council [201203070162]

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