miRPlant protocols

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miRPlant specifications

Information


Unique identifier OMICS_05325
Name miRPlant
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data Raw RNA sequencing data
Input format FASTQ, FASTA, BAM, SAM, RESULT
Output data A table of identified miRNAs
Output format EPS, PDF, SVG
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Version 5.0
Stability Stable
Requirements
JDK
Maintained Yes

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Publication for miRPlant

miRPlant in pipelines

 (3)
2017
PMCID: 5447065
PMID: 28611800
DOI: 10.3389/fpls.2017.00873

[…] (de) analysis by normalization to total reads for each sample (robinson et al., ). mirnas with false discovery ration (fdr) < 0.05 were defined as de-mirnas., novel mirna were first predicted by mirplant v5 with cut off score over 0. their secondary structures were predicted by psrobot with the criteria of having large stem loop; mismatches in small rna region between 0 and 7, and maximal […]

2017
PMCID: 5447065
PMID: 28611800
DOI: 10.3389/fpls.2017.00873

[…] duplex. only mirnas that meet at least two criteria and showed consistent hairpin shaped secondary structures predicted by psrobot (wu et al., ), mfold (http://mfold.rna.albany.edu/?q= mfold), and mirplant v5 were selected as final candidates., mirna targets were also predicted by psrobot (wu et al., ). our criteria included: (1) penalty score threshold = 2 (the penalty score of each candidate […]

2017
PMCID: 5831935
PMID: 29657290
DOI: 10.3390/ncrna3020019

[…] conversion. after quality filtration, other contaminating rnas such as rrna, trna, sn and snornas are removed by alignment with bowtie []. the filtered small rna sequences were analysed through mirplant []. since the a. esculentus genome sequence is not available, we used g. raimondii, arabidopsis and o. sativa as reference genomes to find out the conserved as well as novel mirnas […]


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miRPlant in publications

 (11)
PMCID: 5744193
PMID: 29312421
DOI: 10.3389/fpls.2017.02192

[…] novel mirnas were mapped against mirbase and sequences that matched known plant mirnas with up to three mismatches were excluded. the novelty of potato specific mirnas was verified with the mirplant version 5 (an et al., ) using default parameters and additionally rechecked against the latest releases of rfam (nawrocki et al., ; http://rfam.xfam.org/), trna (chan and lowe, ; […]

PMCID: 5673675
PMID: 29017967
DOI: 10.1016/j.gpb.2017.01.007

[…] substitution frequency; svm, support vector machine., note: rna-seq, rna sequencing; csf, codon substitution frequency; svm, support vector machine., according to srna sequencing (srna-seq) data, mirplant , miranalyzer , mira and mirdeep-p could be used to predict new mirnas; whereas based on target data, semirna could be used to search for mirnas., a great number of programs […]

PMCID: 5632664
PMID: 29046688
DOI: 10.3389/fpls.2017.01719

[…] containing 3.1 million scaffolds longer than 500 bases and a n50 of 43.5 kbp; pg29 v3, 20gb divided into 30 mb per file) (warren et al., ) and the arabidopsis genome (tair10), respectively, using mirplant (an et al., ) at default settings with a sequence length cutoff of 18~24 nt. as the size of our p. glauca sequence libraries exceeded the maximal single load on mirplant, we divided […]

PMCID: 5624873
PMID: 28970509
DOI: 10.1038/s41598-017-12249-y

[…] to increase the accuracy of mirna identification, we combined all read data and the publicly available genome assembly of n. tabacum k326 as a reference to mine the mirna candidates with mirplant software (version 4). after removing rrnas, trnas and snornas from among the candidates by using blastn tool, we identified 403 mirnas (fig. ) belonging to 200 mirna families (table ). […]

PMCID: 5716067
PMID: 29036674
DOI: 10.1093/nar/gkx834

[…] compared mirvial with six existing mirna prediction methods. three of them focus on animal species – mirdeep2 (), mirtrap () and mirena () – and the other three are tailored to plans – mirdeep-p (), mirplant () and mira (). if the six tools have parameters similar to the ones in mirvial, we used the same values as in mirvial. running scripts and parameters can be found in (available […]


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miRPlant institution(s)
Australian Prostate Cancer Research Centre, Brisbane Australia; Princess Alexandra Hospital, Brisbane, Queensland, Australia
miRPlant funding source(s)
This project was funded by the Prostate Cancer Foundation of Australia (PCFA PG25)

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