DARIO protocols

View DARIO computational protocol

DARIO statistics

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DARIO specifications

Information


Unique identifier OMICS_00356
Name DARIO
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Steve Hoffmann <>

Publication for DARIO

DARIO in pipeline

2014
PMCID: 4153649
PMID: 25184567
DOI: 10.1371/journal.pone.0106434

[…] nc_010612 for m. marinum, nc_008596 for m. smegmatis and al123456 for m. tuberculosis) and the host genome (hg19 for human genome and mm9 for mouse genome) by bowtie and analyzed by samtools and dario , . rna secondary structures were predicted by mfold . sequence data are available at the sequence read archive, http://www.ncbi.nlm.nih.gov/sra (srp042180)., to confirm expression […]


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DARIO in publications

 (4)
PMCID: 5814818
PMID: 29155959
DOI: 10.1093/nar/gkx1115

[…] included the execution of blockbuster (), took ∼15 min and used nearly 30 gb of memory. additionally, we compared the performance of serpent against the supervised version of blockclust and against dario (), using a cross-fold validation approach (). using small rna-seq data from mcf-7 cells () (gsm769510) for the three methods, serpent shows overall higher precision in all tested sncrna […]

PMCID: 5615367
PMID: 28925938
DOI: 10.3390/genes8090234

[…] small rna expression by means of ngs approaches, downstream data analysis might be performed using different tools: small rna toolkit [], mirdeep [] and mirdeep2 [], miranalyzer [,], seqbuster [], dario [] uea srna workbench [] and shortstack []. in certain cases, some of these tools include other prediction tools for novel micrornas or isoforms of mirnas (isomirs) quantification. however, […]

PMCID: 4453482
PMID: 26090362
DOI: 10.3389/fbioe.2015.00077

[…] the first integrated tool ever developed for the analysis and prediction of several classes of small ncrnas on rna-seq data originating from arbitrary sequencing platforms is the web service dario (fasold et al., ). the software provides a straighforward interface which allows users to quantify ncrnas in a completely platform independent way. dario annotates reads with information […]

PMCID: 4153649
PMID: 25184567
DOI: 10.1371/journal.pone.0106434

[…] nc_010612 for m. marinum, nc_008596 for m. smegmatis and al123456 for m. tuberculosis) and the host genome (hg19 for human genome and mm9 for mouse genome) by bowtie and analyzed by samtools and dario , . rna secondary structures were predicted by mfold . sequence data are available at the sequence read archive, http://www.ncbi.nlm.nih.gov/sra (srp042180)., to confirm expression […]


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DARIO institution(s)
Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany; LIFE, Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
DARIO funding source(s)
LIFE - Leipzig Research Center for Civilization Diseases, Universität Leipzig. European Social Fund and the Free State of Saxony

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