MiRPara protocols

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MiRPara specifications

Information


Unique identifier OMICS_00380
Name MiRPara
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for MiRPara

MiRPara in pipeline

2017
PMCID: 5209728
PMID: 28051166
DOI: 10.1038/srep39742

[…] reads were then mapped to the m. sympodalis genome (zhu y et al., manuscript submitted) using the bowtie alignment software package., to predict potential small rna features, a modified version of mirpara was used to parse the generated sam alignment files and examine the proximity of mapped reads to annotated coding regions. reads that mapped to non-coding regions (i.e. outside regions […]


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MiRPara in publications

 (10)
PMCID: 5608193
PMID: 28934224
DOI: 10.1371/journal.pone.0183163

[…] by the enzymes drosha and dicer [, ]. thus, we aligned lncrnas to mirbase [] to detect potential pre-mirnas by selecting those with a hit coverage greater than 90%., the svm-based software mirpara [] was also used to predict probable mirnas. in addition, rfam divides non-coding rnas into families based on evolution from a common ancestor. to better annotate novel lncrnas […]

PMCID: 5591252
PMID: 28887500
DOI: 10.1038/s41598-017-11487-4

[…] the reference sequence perfectly and one mismatch was allowed in the first 32 bases of the read when mapping to the genome. no indels were allowed in the mapping. novel mirnas were predicted using mirpara and mirbase and isomirs were detected using deanniso with default settings defined in ref. . the cut-off for isomirs listed in the supplementary table  was set to 100 counts. putative novel […]

PMCID: 5552708
PMID: 28848525
DOI: 10.3389/fmicb.2017.01515

[…] all the oshv-1 orfs as query. the resulting hits were extracted and further inspected., two ab-initio tools for the detection of mirna precursors were tested on malacoherpesviridae genomes, namely mirpara (wu et al., ) and vmir (grundhoff et al., ). briefly, mirpara is a support vector machine tool that provides 76 parameters predictive of putative hairpin regions on the basis […]

PMCID: 5504012
PMID: 28694521
DOI: 10.1038/s41598-017-05279-z

[…] downstream of a gene. these lncrnas likely regulate transcription of neighbouring genes. the lncrnas were aligned to mirbase to detect potential pre-mirna, and hit coverage above 90% were selected. mirpara were used to predict probable mirna. the predicted novel lncrnas were categorized into different non-coding rna families using infernal, which classifies noncoding rnas, their conserved […]

PMCID: 5679755
PMID: 29087294
DOI: 10.7554/eLife.28932.039

[…] from the dataset revealed distinct peaks representing microrna (~18–22 nt). putative micrornas not in standard mirbase or rfam classification were identified based on the prediction algorithm mirpara and are included with the sequencing data in the geo file (). expression levels were quantified in tags per million (tpm) (unadjusted data and batch-adjusted data available in ). tpm […]


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MiRPara institution(s)
Bioinformatics Group, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Science, China

MiRPara reviews

 (2)
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Anonymous user #153

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Desktop
you need to download the UNAFold software separately from
http://mfold.rna.albany.edu/?q=DINAMelt/software
Anonymous user #152's avatar image No country

Anonymous user #152

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Desktop
It works as expected. I did face a few hiccups while installing it due to my own limited knowledge of Linux. However, Mr. Yoggan Wu was immensely helpful in guiding me through the process.
Thank you for the wonderful tool !!