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 in publications

 (6)
PMCID: 5844931
PMID: 29556495
DOI: 10.3389/fcell.2018.00020

[…] et al., ). here, this analysis is extended by 6 additional algorithms: acsf (you et al., ), circexplorer2 (zhang et al., ), ciri2 (gao et al., ), dcc (cheng et al., ), knife (szabo et al., ), and uroborus (song et al., ) (see table ). overall, the sensitivity and specificity of predicted circrnas are compared by assessing the quantities of circrnas found by each algorithm as well […]

PMCID: 5748684
PMID: 29206165
DOI: 10.3390/genes8120366

[…] 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 []. […]

PMCID: 5748671
PMID: 29182528
DOI: 10.3390/genes8120353

[…] the other two software systems generate putative circrna sequences post-alignment with the genome or transcriptome [,,]. , circrna_finder, circexplorer, dcc, mapsplice, segemehl, find-circ, and uroborus detect circrna sequences based on the second approach for identification of circrna sequences which is the fragmented-base or segmented read approach. in this approach, the software detects […]

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

[…] 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, […]

PMCID: 5514102
PMID: 28717203
DOI: 10.1038/s41598-017-05922-9

[…] or rt-pcr artifacts. until recent years, due to the high throughput sequencing technologies coupled with exonuclease-based enrichment strategies and new bioinformatic tools, such as ciri, knife and uroborus, the identification, biogenesis and function of circrnas were widely reported in animals, such as human, mouse and drosophila –., in humans, circularized exons are typically bracketed […]


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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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