sRNAbench protocols

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sRNAbench specifications

Information


Unique identifier OMICS_29052
Name sRNAbench
Alternative name miRanalyzer
Interface Web user interface
Restrictions to use None
Biological technology Illumina
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Michael Hackenberg <>
  • person_outline Danijela Koppers-Lalic <>

Information


Unique identifier OMICS_29052
Name sRNAbench
Alternative name miRanalyzer
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainers


  • person_outline Michael Hackenberg <>
  • person_outline Danijela Koppers-Lalic <>

Publications for sRNAbench

sRNAbench in pipelines

 (9)
2018
PMCID: 5882837
PMID: 29643765
DOI: 10.3389/fnmol.2018.00090

[…] sequence. sequencing 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 […]

2017
PMCID: 5355888
PMID: 28303893
DOI: 10.1038/srep44132

[…] (for other noncoding rna), and repbase (for repetitive elements) to remove reads corresponding to transcribed sequences that were not mirnas. the remaining reads were used to predict new mirnas with miranalyzer. miranalyzer employs a machine learning approach based on the random forest method. with the default parameter setting, miranalyzer can obtain the area under the curve value of 97.9% […]

2017
PMCID: 5558978
PMID: 28813447
DOI: 10.1371/journal.pone.0182629

[…] using nucleotide blast []., the unique (non-redundant) 18 to 26 nt sequences with accompanying copy numbers, across all six libraries (representing the six biological samples), were submitted to miranalyzer [] (http://bioinfo5.ugr.es/miranalyzer/miranalyzer.php) for known mirna analysis, allowing one mismatch. all reads that mapped to other non-coding rnas (ncrnas) in rfam […]

2016
PMCID: 4813251
PMID: 26999121
DOI: 10.3390/ijms17030396

[…] the trimming. reads longer than 26 nt were trimmed using the fastx toolkit v0.6.1. the trimmed reads ranging in sized from 17–26 nt were grouped for unique sequences using scripts provided by the miranalyzer web tool, aligned using bowtie2 [], and the aligned reads were classified as mirna, refseq genes, refseq coding regions and rrna using bedtools v2.14.2. of the mirna counts […]

2016
PMCID: 5111516
PMID: 27882350
DOI: 10.1172/jci.insight.89631

[…] to the manufacturer’s instructions. rnaseq was performed on a hiseq 2500 (illumina, single-end 50-bp read length), using equimolar amounts for each sample. sequencing analysis was done by using the srnabench package as described previously (). briefly, after adapter trimming and unique read grouping, reads were aligned to the human genome (ucsc hg19) using bowtie 1.1.2. to provide annotations […]


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sRNAbench in publications

 (102)
PMCID: 5913337
PMID: 29686252
DOI: 10.1038/s41598-018-24765-6

[…] and removal of all contaminants with endogenous sequences, the software aligned the remaining sequences to exogenous small rnas. reads not mapped to any exogenous small rnas were aligned again using srnabench to the complete set of viral mirna sequences available in mirbase., a detailed description of this procedure was previously provided. briefly, reverse transcription was performed using […]

PMCID: 5894187
PMID: 29636028
DOI: 10.1186/s12864-018-4646-5

[…] hiseq 2000 sequencing system (illumina). small rna libraries were prepared using 5 μl of rna extract. raw sequencing data, available on the geo database (accession gse84871 []), were analysed using srnabench 1.0 [, ]. briefly, the software was run in genome mode using default settings, with the bovine genome (bostau4) and mirbase 21 as reference (accessed on 30 april 2015 [, ]) in order […]

PMCID: 5912193
PMID: 29696074
DOI: 10.1080/20013078.2018.1446660

[…] (illumina). rnaseq was performed on a hiseq 2500 (illumina) pair-end 125 nucleotide length read, using equimolar amounts for each sample. sequencing reads analysis was performed by using the srnabench analysis package as described previously []. briefly after adaptor trimming and unique reads grouping, reads were aligned to the human genome (ucsc hg19) using the bowtie 1.1.2. to provide […]

PMCID: 5837101
PMID: 29505615
DOI: 10.1371/journal.pone.0193527

[…] the reference databases and approach used in this study differ from the pipeline followed in two of the most recent publications on circulating small rnas: freedman et al. 2016 (excerpt, based on srnabench) [] and yeri et al. 2017 (srnabench) []. in srnabench, reads are first mapped to mirna, and remaining reads are mapped to other small rnas using ensembl 75. for isomirs characterization, 3’ […]

PMCID: 5832017
PMID: 29636786
DOI: 10.1155/2018/8025062

[…] for annealing and extension. u6 was used as a reference gene. three independent experiments were performed., the expression of mirnas in each library was estimated using the free web-server tool srnabench, where the normalized read count of each mirna was shifted by the following formula: rpm = (mirnas read number/total map reads) × 1,000,000. evaluation of differential expression (de) […]


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sRNAbench institution(s)
Department of Genetics, University of Granada, Campus de Fuentenueva, Granada, Spain; Bioinformatics Group, Biomedical Research Center (CIBM), Granada, Spain; Genomics and Bioinformatics Platform of Andalusia (GBPA), Edificio INSUR, Sevilla, Spain; Biology Centre, Academy of Sciences of Czech Republic, Budweis, Czech Republic; Australian Centre for Plant Functional Genomics, the University of Adelaide, Adelaide, SA, Australia; Department of Pathology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands
sRNAbench funding source(s)
Supported by the Spanish Government (FIS2012-36282) and Basque country ‘AE’ grant.

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