miRDeep-P protocols

View miRDeep-P computational protocol

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miRDeep-P specifications

Information


Unique identifier OMICS_00375
Name miRDeep-P
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for miRDeep-P

miRDeep-P in pipelines

 (3)
2017
PMCID: 5649071
PMID: 29052505
DOI: 10.1186/s12864-017-4209-1

[…] to be conserved mirnas. to reveal conserved and novel mirna precursors, the unique sequences that have 10 or more counts were aligned to the s. aralocaspica mrna transcriptome database using mirdeep-p with default parameters []. blastx [] was used to match the sequences to nr database, the putative precursors conserved in other plant species were removed. mfold [] was used to predict […]

2016
PMCID: 5066498
PMID: 27729476
DOI: 10.1093/jxb/erw346

[…] sequences analysed from each alignment read. the secondary structures of novel mirnas were predicted using rnafold software, and genome mapping of mirnas was processed using the plant-specific mirdeep-p core algorithm (). the mirna sequence data have been submitted to the ncbi sra database under the bioproject ‘translational research on transgenic rice’ (accession no. prjna307629)., […]

2012
PMCID: 3445533
PMID: 23028583
DOI: 10.1371/journal.pone.0044696

[…] conserved mirnas in l. chinense. for the abundance analysis of mirnas, the number of the read (read count) acquired by solexa gaii was used., the de novo prediction of novel mirna was performed by mirdeep-p (http://faculty. virginia.edu/lilab/mirdp/) and mirnafinder(http://bioinfo3.noble.org/mirna/). the putative novel mirnas were screened in our sequencing data. the putative mirnas […]


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miRDeep-P in publications

 (38)
PMCID: 5944317
PMID: 29774043
DOI: 10.3389/fpls.2018.00589

[…] mapping was performed with bowtie software (v. 1.0.1; langmead et al., ) and up to three mismatches were allowed in alignments., mirna prediction was performed with mirdeep-p (v. 1.3; yang and li, ), a modified version of the mirdeep algorithm (friedländer et al., ) that incorporates an adapted scoring system for plant mirna biogenesis. non-annotated small rna […]

PMCID: 5649071
PMID: 29052505
DOI: 10.1186/s12864-017-4209-1

[…] expression profiles to promote dimorphic seed germination. 194 conserved mirnas comprising 40 families and 21 novel mirnas belonging to 20 families in suaeda aralocaspica were identified using mirdeep-p and mfold. the expression of mirnas in black seed was suppressed at imbibition stage. among the identified mirnas, 59 conserved and 13 novel mirnas differentially expressed during seed […]

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

[…] 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 and algorithms have been applied […]

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 […]

PMCID: 5604955
PMID: 28971115
DOI: 10.1016/j.dib.2017.08.037

[…] curcuma longa (zingiberaceae family) transcriptome sequence (the whole genome or transcriptome sequence of cardamom was not available at the time of the study) to predict putative novel mirnas using mirdeep-p software satisfying mayer's criteria of mirna prediction (). using the identified mirnas we also performed the differential expression analysis, target prediction and gene ontology (go) […]


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miRDeep-P institution(s)
Department of Biology, University of Virginia, Charlottesville, VA, USA

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