UEA sRNA toolkit protocols

View UEA sRNA toolkit computational protocol

UEA sRNA toolkit statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Read quality control Bioinformatics workflows chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

UEA sRNA toolkit specifications

Information


Unique identifier OMICS_00369
Name UEA sRNA toolkit
Software type Pipeline/Workflow
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License MIT License
Computer skills Advanced
Version 4.5
Stability Stable
Maintained Yes

Download


Versioning


Add your version

Maintainer


  • person_outline Vincent Moulton <>

Additional information


http://srna-workbench.cmp.uea.ac.uk/tutorials/ https://sourceforge.net/projects/srnaworkbench

Publications for UEA sRNA toolkit

UEA sRNA toolkit in pipelines

 (4)
2017
PMCID: 5590963
PMID: 28886174
DOI: 10.1371/journal.pone.0184528

[…] nature of viroids. small rnas were searched for similarity against the hop transcriptome, using two tools designed to identify possible targets of srnas action with default parameters: 1) the uea srna toolkit [], which was used as a standalone application (version may 18, 2012) and 2) the plant small rna target analysis server (psrna target) [], which was used as a www application […]

2016
PMCID: 4723037
PMID: 26799570
DOI: 10.1371/journal.pone.0147499

[…] the reads matching with other rnas, including rrna, trna, snrna and snorna were excluded and remaining reads were designated as filtered reads. the filtered reads were submitted to the uea srna toolkit-plants version, mirprof pipeline (http://srna-workbench.cmp.uea.ac.uk/tools/analysis-tools/mirprof/) [] at default parameters which aligned the sequences to mirbase 19.0 […]

2014
PMCID: 4168055
PMID: 25194793
DOI: 10.1186/1471-2164-15-766

[…] l log2 (hs/ct). the statistical analysis (fisher exact test) was performed with a p-value cutoff < 0.05 and bonferroni correction., novel mirnas were identified in the maize libraries using the uea srna toolkit (plant version) mircat pipeline. sequences were mapped to the maize genome (b73 refgen_v2) to find clusters of srna. the most abundant srna read within a cluster was chosen […]

2012
PMCID: 3511302
PMID: 23226347
DOI: 10.1371/journal.pone.0050663

[…] match. as mirna precursors have a characteristic hairpin structure, the next step to select candidate sequences was secondary structure analysis by rnafold using an annotation algorithm from the uea srna toolkit . in addition, perfect stem-loop structures should have the mirna sequence at one arm of the stem and a respective antisense sequence at the opposite arm. finally, precursor […]


To access a full list of citations, you will need to upgrade to our premium service.

UEA sRNA toolkit in publications

 (32)
PMCID: 5755913
PMID: 29304061
DOI: 10.1371/journal.pone.0190691

[…] near the target site (approximately 1000 bp) was used for gene annotation using the cucumber genome website (http://www.icugi.org/), softberry software (http://linux1.softberry.com/) and the uea srna toolkit (http://srna-tools.cmp.uea.ac.uk/). finally, gene-specific primers were designed to analyze gene abundance in the two cultivars (). for the multicopy gene, only one pair of primers […]

PMCID: 5744193
PMID: 29312421
DOI: 10.3389/fpls.2017.02192

[…] mirna sample preparation kit (seqmatic llc, fremont, ca) and sequenced on the illumina hiseq 2000 sequencing system at seqmatic llc., the raw reads were quality filtered using filter tool of the uea srna toolkit (moxon et al., ) by discarding low complexity reads (containing at most two distinct nucleotides), reads shorter than 18 nt and longer than 25 nt, reads matching trna/rrna sequences […]

PMCID: 5831913
PMID: 29657296
DOI: 10.3390/ncrna3040025

[…] [] under accession number gse42628., small rna reads were trimmed and filtered if they had an exact full-length match to known plant trna or rrna sequences or low-complexity sequences. using the uea srna toolkit—plant version filter pipeline (http://srna-tools.cmp.uea.ac.uk/) [] with three different databases (plant t/rrnas from rfam, arabidopsis trnas from the genomic trna database, […]

PMCID: 5590963
PMID: 28886174
DOI: 10.1371/journal.pone.0184528

[…] nature of viroids. small rnas were searched for similarity against the hop transcriptome, using two tools designed to identify possible targets of srnas action with default parameters: 1) the uea srna toolkit [], which was used as a standalone application (version may 18, 2012) and 2) the plant small rna target analysis server (psrna target) [], which was used as a www application […]

PMCID: 5398497
PMID: 28426683
DOI: 10.1371/journal.pone.0175178

[…] reads of various lengths were extracted from the reference genome and hairpin structures were prepared through rnafold [] and analyzed for the identification of potential mirna precursor using uea srna toolkit []. for the identification of conserved mirnas, predicted rkn mirna sequences were aligned with known mirna sequences in the mirbase v21 depository []. the criteria used […]


To access a full list of publications, you will need to upgrade to our premium service.

UEA sRNA toolkit institution(s)
School of Computing Sciences, University of East Anglia, Norfolk, UK; School of Biological Sciences, University of East Anglia, Norfolk, UK
UEA sRNA toolkit funding source(s)
Supported by the Biotechnology and Biological Sciences Research Council (grant BBSRC BB/L021269/1).

UEA sRNA toolkit reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review UEA sRNA toolkit