sRNAtoolbox statistics

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Citations per year

Number of citations per year for the bioinformatics software tool sRNAtoolbox

Tool usage distribution map

This map represents all the scientific publications referring to sRNAtoolbox per scientific context
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Associated diseases


Popular tool citations

chevron_left Normalization miRNA target prediction Differential expression Bioinformatics workflows IsomiR detection ncRNA identification Mature miRNA sequence prediction chevron_right
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sRNAtoolbox specifications


Unique identifier OMICS_09043
Name sRNAtoolbox
Software type Toolkit/Suite
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • miRNAconsTarget
  • miRNAgFree
  • sRNAblast
  • sRNAde
  • sRNAfuncTargets
  • sRNAfuncTerms
  • sRNAhelper
  • sRNAjBrowser
  • sRNAjBrowserDE


  • person_outline Michael Hackenberg

Additional information

Publication for sRNAtoolbox

sRNAtoolbox citations


Circulating microRNAs and Bioinformatics Tools to Discover Novel Diagnostic Biomarkers of Pediatric Diseases

PMCID: 5615367
PMID: 28925938
DOI: 10.3390/genes8090234

[…] ins the following tools:sRNAbench: expression profiling of small RNAs, prediction of novel microRNAs, analysis of isomiRs, genome mapping and read length statistics. Samples are analyzed individually.sRNAde: detection of differentially expressed small RNAs based on three commonly used programs: DESeq [], edgeR [] and NOISeq [].sRNAblast: aimed at determining the origin of unmapped or unassigned re […]


The use of high throughput small RNA sequencing reveals differentially expressed microRNAs in response to aster yellows phytoplasma infection in Vitis vinifera cv. ‘Chardonnay’

PLoS One
PMCID: 5558978
PMID: 28813447
DOI: 10.1371/journal.pone.0182629

[…] l).For novel miRNA predictions, sRNA library files of the 18 to 26 nt reads, from all six libraries, were grouped into a single file that served as input for sRNAbench v0.9 [] (, and Shortstack v0.4.1 [], using the default parameters of the respective packages. sRNAbench was also used for the discovery of sequence variants of known miRNAs, also known as […]


Thiourea priming enhances salt tolerance through co ordinated regulation of microRNAs and hormones in Brassica juncea

Sci Rep
PMCID: 5382540
PMID: 28382938
DOI: 10.1038/srep45490

[…] sing two independent methods by comparative cross-mapping of reads to Brassica rapa Chiifu-401 v1.2 assembly available from Phytozome ( using bowtie and Shortstacks and using sRNAtoolbox. For both novel and conserved miRNAs, 20–24 nt length threshold were kept. Subsequently, all putative hairpins and identified microRNAs were analyzed for structural analysis using RNAFold. […]


Plant genome and transcriptome annotations: from misconceptions to simple solutions

Brief Bioinform
PMCID: 5952960
PMID: 28062412
DOI: 10.1093/bib/bbw135

[…] A) tools would itself warrant a complete review, so for the purposes of this article, we will restrict our discussion to tools relevant to detection and analysis of microRNA (miRNA) with reference to sRNAtoolbox [], which offers a selection of user-friendly tools from expression profiling to target gene prediction.miRNAs are a class of RNA that are involved in gene regulation. Though similar in ma […]


Illumina Sequencing Reveals Aberrant Expression of MicroRNAs and Their Variants in Whitefish (Coregonus lavaretus) Liver after Exposure to Microcystin LR

PLoS One
PMCID: 4938405
PMID: 27391076
DOI: 10.1371/journal.pone.0158899

[…] nd in all groups. On the other hand, there were several miRNAs that were only found in certain groups of samples (). In all, 223 mature miRNAs were detected for differential expression analysis using sRNAde software []. shows numbers of differentially expressed miRNAs obtained with three different methods: EdgeR, DeSeq and NoiSeq. The three methods yielded somewhat different results with respect […]


Circulating microRNA Profiles during the Bovine Oestrous Cycle

PLoS One
PMCID: 4920432
PMID: 27340826
DOI: 10.1371/journal.pone.0158160

[…] e submitted to 36-base single-end sequencing using the Illumina HiSeq 2000 platform. The raw sequencing data are available on the GEO database under accession GSE81050. Raw reads were processed using sRNAtoolbox 1.0; initially reads with no adaptor and/or with undetermined bases (N) were removed []. The bovine genome (assembly UMD 3.1, []) was used as reference; trimmed and quality-controlled read […]

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sRNAtoolbox institution(s)
Genomics and Bioinformatics Platform of Andalusia (GBPA), Edificio INSUR, Calle Albert Einstein, Sevilla, Spain; Centro de Genómica e Investigaciones Oncológicas, Pfizer-Universidad de Granada-Junta de Andalucía, Granada, Spain; Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, Granada, Spain; Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, Granada, Spain
sRNAtoolbox funding source(s)
Ministerio de Economía y Competitividad from the Spanish Government [AGL2013-49090-C2-2-R]

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