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miRProf specifications

Information


Unique identifier OMICS_14630
Name miRProf
Alternative name miRNA Profiler
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Input data A set of sRNA samples and a genome file.
Input format A results table in .csv format and a list of sRNAs matching known miRNAs.
Output format CSV, FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Java
Computer skills Medium
Version 2.0
Stability No
Maintained No

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Publication for miRNA Profiler

miRProf citations

 (21)
library_books

Roles of Non Coding RNA in Sugarcane Microbe Interaction

2017
PMCID: 5831913
PMID: 29657296
DOI: 10.3390/ncrna3040025

[…] (). the reads obtained from libraries of rep 2 are given in . conserved mirnas were identified based on matches with the mirbase database, release 21, allowing three mismatches. using the mirprof pipeline [], 1872 and 2313 unique sequences of conserved mirnas were identified in mock and infected libraries of rep 1 (). the remaining reads can be classified as putative sirna or novel […]

library_books

Altered miRNA expression network in locus coeruleus of depressed suicide subjects

2017
PMCID: 5491496
PMID: 28663595
DOI: 10.1038/s41598-017-04300-9

[…] group compared with the suicide group (t = 3.37, df = 18, p = 0.003). there were 2 females and 9 males in control group and 3 females and 6 males in the suicide group.table 1 , the tlda based mirna profiler is comprised of two plates: a and b. as detailed in the methods section, each plate assays 377 mirnas excluding 6 small rna related genes incorporated in each plate as normalizer and […]

library_books

Identification of Ice Plant (Mesembryanthemum crystallinum L.) MicroRNAs Using RNA Seq and Their Putative Roles in High Salinity Responses in Seedlings

2016
PMCID: 4977306
PMID: 27555850
DOI: 10.3389/fpls.2016.01143

[…] and t/r rna contamination. the filtered unique reads were compared to known mature plant mirna deposited in the mirbase database (http://www.mirbase.org; kozomara and griffiths-jones, ) using the mirprof tool (uea srna toolkit; http://srna-workbench.cmp.uea.ac.uk; stocks et al., ) with no more than two mismatches allowed. to identify the conserved and novel mirnas in ice plant, unique […]

library_books

Small RNA and PARE sequencing in flower bud reveal the involvement of sRNAs in endodormancy release of Japanese pear (Pyrus pyrifolia 'Kosui')

2016
PMCID: 4791883
PMID: 26976036
DOI: 10.1186/s12864-016-2514-8

[…] mirnas (data not shown)., as the relatively high stringent shortstack algorithm tended to produce false negative results [], blast-based strategies were also used to identify known mirnas with mirprof []. the clean reads were compared to a publicly available mirna database []. when only allowing perfect matches, a total of 137 unique sequences were annotated as known mirnas in the four […]

library_books

Identification and Expression Analyses of miRNAs from Two Contrasting Flower Color Cultivars of Canna by Deep Sequencing

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

[…] 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 (http://www.mirbase.org) [] and provided raw […]

library_books

Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis

2015
PMCID: 4667520
PMID: 26626050
DOI: 10.1186/s12864-015-2209-6

[…] the following parameters: minimal sequence length after adaptor removal was 16, maximal sequence length was 28 []. we used uea small rna workbench (version 2.5.0) for all mirna processing tasks []. mirprof calculated the expression of known mirnas. this program uses mirbase (version 20). we allowed 2 mismatches during the analysis. we grouped together mismatches, variants and mirnas […]


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miRProf institution(s)
School of Computing Sciences, University of East Anglia, Norwich, UK; School of Biological Sciences, University of East Anglia, Norwich, UK; The Sainsbury Laboratory, Norwich, UK
miRProf funding source(s)
This work was supported by the Biotechnology and Biological Sciences Research Council [grant number BB/E004091/1] and the Gatsby Charitable Foundation.

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