MirPlex protocols

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MirPlex specifications

Information


Unique identifier OMICS_11465
Name MirPlex
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages Java
Computer skills Advanced
Version 0.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Dr. Daniel Mapleson <>

Publication for MirPlex

MirPlex in pipeline

2017
PMCID: 5245829
PMID: 28103286
DOI: 10.1371/journal.pone.0168817

[…] yield a dataset of 848,129 sequences and removed those present in less than 5 copies. we also removed sequences that could be assembled together to form longer contigs, mimicking what is done by the mirplex pipeline []. the remaining 94,239 sequences contained 53 different small rnas that were able to form duplexes with the 2 base 3’ overhangs expected for mirnas, and most of these were 22 […]


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MirPlex in publications

 (3)
PMCID: 5245829
PMID: 28103286
DOI: 10.1371/journal.pone.0168817

[…] bases and contained only reads in the same direction. these 948 assemblies indicated the small rnas contributing to them did not have the defined ends expected for bone fide mirnas, so as with the mirplex pipeline [], they were also removed leaving a final dataset of 94,239 potential mirna candidates. to test if any of the 94,239 sequences could form rna duplexes with 2 base 3’ overhangs, […]

PMCID: 4306309
PMID: 25674563
DOI: 10.3389/fbioe.2015.00007

[…] overall, the most abundant and conserved mirnas were identified in this study, but the approach might be less successful for species that do not have closely related species with genome sequences., mirplex is a tool that requires only srna datasets as input with no genome sequences needed (mapleson et al., ). it uses a multi-stage process to identify genuine mirna duplexes. first, […]

PMCID: 4307313
PMID: 25580537
DOI: 10.3390/ijms16011466

[…] based on the analysis of a hold-out test set. using experimental data, we also show that our approach can detect about an order of magnitude or more known mirnas than the mature mirna predictor, mirplex., non-coding rnas (ncrnas) are functional rna transcripts that do not translate into proteins. the small ncrna class consists of ncrnas of lengths of about 20 to 30 nucleotides (nt). two […]


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MirPlex institution(s)
University of East Anglia, Norwich, UK

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