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RNAplex specifications

Information


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

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Publication for RNAplex

RNAplex in publications

 (50)
PMCID: 5936019
PMID: 29728055
DOI: 10.1186/s12870-018-1288-3

[…] []. in this study, lncrnas were annotated by scanning regions within 2000 bp upstream and downstream of genes, and analyzing the complementary base-pairing between antisense lncrnas and mrnas using rnaplex software []., genes targeted by lncrnas were annotated using ncbi blast tools (version 2.2.8) in conjunction with the ncbi non-redundant protein sequences (nr) database, the arabidopsis […]

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

[…] lncrnas and nearest genes beyond 10 kb in downstream or upstream were picked out as cis-target genes. the top 20 lncrnas, with smallest fdr value, were used to predict the trans-regulated genes by rnaplex []., database for annotation, visualization and integrated discovery (david) v6.8 web tool (https://david.ncifcrf.gov/) were used to perform go and kegg enrichment analyses […]

PMCID: 5841072
PMID: 29675420
DOI: 10.1155/2018/3174352

[…] 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., several pairwise comparisons were carried out among […]

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

[…] 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 ., motifs were defined as given by regprecise (novichkov et al., ) for s. aureus […]

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

[…] knockdown of lncrna miat can overcome gefitinib resistance in lung cancer cells., 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 […]


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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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