sRNAtoolbox protocols

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sRNAtoolbox specifications

Information


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

Subtools


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

Maintainer


  • person_outline Michael Hackenberg <>

Additional information


http://bioinfo2.ugr.es:8080/srnatoolbox/

Publication for sRNAtoolbox

sRNAtoolbox in pipeline

2018
PMCID: 5882837
PMID: 29643765
DOI: 10.3389/fnmol.2018.00090

[…] reads <15 nucleotides which could not be mapped on the genome were discarded. duplicate reads >15 nucleotides were collapsed into unique sequences and analyzed with the srnabench tool on the srnatoolbox server (http://bioinfo5.ugr.es/srnatoolbox) to build individual mirna expression profiles (rueda et al., ). this server used the mirbase database version 21 (http://www.mirbase.org) […]


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sRNAtoolbox in publications

 (14)
PMCID: 5766573
PMID: 29330429
DOI: 10.1038/s41598-017-18945-z

[…] the illumina hiseq v4 kit in a single read 50 bp (1 × 50) run., the alignment of sequences from the libraries obtained in the previous step and the quantification of mirnas was performed using the srnatoolbox webserver according to rueda et al.. statistical analyses of differentially expressed mirnas was performed using edger using the glm model and pairing samples by patient. mirnas […]

PMCID: 5751329
PMID: 29258192
DOI: 10.3390/ijms18122728

[…] mirbase was utilized to identify the small rnas of interest in l. decemlineata samples using red flour beetle tribolium castaneum reference databases []. the mirnas were annotated using srnabench in srnatoolbox []. small rnas unique reads were mapped to mirnas (26,447 for control and 24,221 for imidacloprid-treated). snrnas (4735 for control and 3616 for imidacloprid-treated), snrnas (4705 […]

PMCID: 5615367
PMID: 28925938
DOI: 10.3390/genes8090234

[…] are mirtools 2.0 [], which includes a target prediction and a functional analysis module, uea srna workbench which includes a visualization tool and srnabench for multi-species analysis []. srnatoolbox is a set of independent but interconnected tools for expression profiling from high-throughput sequencing data, consensus differential expression, target gene prediction, visual […]

PMCID: 5567286
PMID: 28831113
DOI: 10.1038/s41598-017-09515-4

[…] reference. due to difference in sensitivity and specificity of different target prediction algorithms, targets were predicted using 3 tools: miranda, pita and targetspy in small rna analysis server srnatoolbox. if the same target site is predicted by all 3 tools it was considered a potential microrna target. for pita, prediction parameters chosen were: seed length 6–8 nts, no g:u wobble allowed […]

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

[…] 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 [] (http://bioinfo5.ugr.es/srnatoolbox/srnabench), 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 […]


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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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