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RNAplex specifications


Unique identifier OMICS_09345
Name RNAplex
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


Publication for RNAplex

RNAplex citations


Long non coding RNAs of switchgrass (Panicum virgatum L.) in multiple dehydration stresses

BMC Plant Biol
PMCID: 5936019
PMID: 29728055
DOI: 10.1186/s12870-018-1288-3

[…] as annotated by scanning 2000 bp upstream or downstream of genes based on the switchgrass genomic database [–], and then analyzing complementary base-pairing between antisense lncRNAs and mRNAs using RNAplex software []. In this study, 4554 lncRNAs were annotated, and 9.7% (441) of these were differentially expressed (Table ; Fig. ). We analyzed the functions of the predicted target genes of all l […]


Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells

PLoS One
PMCID: 5892903
PMID: 29634734
DOI: 10.1371/journal.pone.0195468

[…] omosomes or distal regions)[], and lncRNA-mRNA interaction can affect mRNA level [,]. In this study, 20 DE-lncRNAs with the lowest FDR values were selected for prediction of their trans-target genes. RNAplex [] was used for searching interactions between above mentioned lncRNAs and differentially expressed mRNAs (DE-mRNAs). It showed that 20 DE-lncRNAs have 1098 potential trans-target mRNAs ().The […]


Regulation of Long Noncoding RNAs Responsive to Phytoplasma Infection in Paulownia tomentosa

Int J Genomics
PMCID: 5841072
PMID: 29675420
DOI: 10.1155/2018/3174352

[…] NA-mRNA duplex energy. First, BLASTN searches were performed to detect potential target mRNA sequences complementary to the lncRNA sequences with identity > 95% and E value < 1E − 5. Then we used the RNAplex software to calculate the complementary energy between the lncRNAs and their potential transregulated target genes with RNAplex − E −30. […]


Assessment of Bona Fide sRNAs in Staphylococcus aureus

Front Microbiol
PMCID: 5826253
PMID: 29515534
DOI: 10.3389/fmicb.2018.00228

[…] NApredator website (Eggenhofer et al., ) was used to predict sRNA-mRNA interactions between the sRNAs from Table and the NCTC8325 genome (accession # NC_007795). In the absence of conservation data, RNAplex program used by RNA predator is among the best predictor (Pain et al., ). Results are presented in Data Sheet . […]


Silencing of Long Non coding RNA MIAT Sensitizes Lung Cancer Cells to Gefitinib by Epigenetically Regulating miR 34a

Front Pharmacol
PMCID: 5816758
PMID: 29487526
DOI: 10.3389/fphar.2018.00082

[…] Bioinformatics analysis was used to search for the potential targeted microRNAs of lncRNA MIAT, such as MiRcode, RNAplex, catRAPID omics. Together, miR-34a was found to be a conserved target of lncRNA MIAT. To investigate if the predicted binding site of miR-34a to 3′UTR of lncRNA MIAT is responsible for this re […]


Competitive endogenous RNA networks: integrated analysis of non coding RNA and mRNA expression profiles in infantile hemangioma

PMCID: 5844720
PMID: 29552284
DOI: 10.18632/oncotarget.23946

[…] g sense transcripts. Transcripts that overlapped with LncRNAs on the opposite strand were also identified as lncRNA target genes, and the interactions between lncRNAs and transcripts were revealed by RNAplex []. […]


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RNAplex institution(s)
Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
RNAplex funding source(s)
This work was supported by siemens, by the Wiener Wissenschafts-, Technologie- und Forschungsfonds and by the Austrian GEN-AU projects bioinformatics integration network and non-coding RNA.

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