RNAhybrid protocols

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RNAhybrid specifications

Information


Unique identifier OMICS_00416
Name RNAhybrid
Interface Web user interface, Application programming interface
Restrictions to use None
Input data A miRNA sequence or a RNA sequence.
Computer skills Basic
Version 2.1.2
Stability Stable
Source code URL https://bibiserv.cebitec.uni-bielefeld.de/applications/rnahybrid/resources/downloads/RNAhybrid-2.1.2.tar.gz
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster

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Maintainer


  • person_outline Marc Rehmsmeier <>

Additional information


https://bibiserv.cebitec.uni-bielefeld.de/rnahybrid?id=rnahybrid_manual_manual

Information


Unique identifier OMICS_00416
Name RNAhybrid
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Source code URL https://bibiserv.cebitec.uni-bielefeld.de/applications/rnahybrid/resources/downloads/RNAhybrid-2.1.2.tar.gz

Taxon


  • Invertebrates
    • Drosophila melanogaster

Download


Versioning


Add your version

Maintainer


This tool is not maintained anymore.

Additional information


https://bibiserv.cebitec.uni-bielefeld.de/rnahybrid?id=rnahybrid_manual_manual

Publications for RNAhybrid

RNAhybrid in pipelines

 (11)
2017
PMCID: 5579249
PMID: 28860459
DOI: 10.1038/s41598-017-10207-2

[…] test the possible impact of these snps on the regulation of gene expression mediated by mirnas, as previously described. the prediction tools funcpred, mirwalk, mirsnp, mrsnp, mirdsnp, mirnasnp and rnahybrid were used to select mirnas which binding sites in plcb1 is potentially affected by these snps. we chose the best predictions for each snp: for rs1047383, hsa-mir-124-1, hsa-mir-139, […]

2017
PMCID: 5596602
PMID: 29048434
DOI: 10.1038/cddis.2017.426

[…] with euclidean distances, treating samples independently each other. differentially expressed mirnas between any two samples were calculated by ebseq. target genes of mirnas were predicted using rnahybrid. gene ontology (go) analysis and kyoto encyclopedia of genes and genomes (kegg) pathway analysis of differentially expressed genes were performed using the database for annotation […]

2017
PMCID: 5733040
PMID: 29312175
DOI: 10.3389/fmicb.2017.02463

[…] transcripts and spätzle was found to be a target of dme-mir-998-3p. to assess the stability of predicted mirna-mrna interactions, we estimated minimum free energy level of mirna-mrna duplexes using rnahybrid (rehmsmeier et al., ). this tool provides energetically favorable sites for mirna and its target transcript and takes into account potential intra-molecular hybridization within the target […]

2016
PMCID: 4993730
PMID: 27610292
DOI: 10.1186/s40064-016-2902-1

[…] the normalized expression of a certain mirna was all lower than 1 in two libraries, further differential expression analysis was conducted without this mirna for the reason of its low expression., rnahybrid software was performed to predict target gene of mirna in the sequencing. go enrichment analysis in our study was successful at predicted target gene candidates of all differentially […]

2015
PMCID: 4411651
PMID: 25922662
DOI: 10.1186/s13578-015-0009-y

[…] below 0.05. mirnas with log2-fold changes higher than 1 were designated as significantly up-regulated, and those with log2-fold changes less than -1 were designated as significantly down-regulated., rnahybrid and smvlight were used to predict the targets of the mirnas (p value < 0.05, prediction-value > 1, a minimum free energy (mfe) < -20.0 kcal/mol, one g:u mismatch was permitted […]

RNAhybrid in publications

 (836)
PMCID: 5957056
PMID: 29785127
DOI: 10.2147/OTT.S165147

[…] expression in gc tumor tissues (n = 30, r = −0.504, p = 0.0039; ). furthermore, we performed a search for mirnas that have complementary base pairing with gaplinc, using online software program rnahybrid (https://bibiserv.cebitec.uni-bielefeld.de/rnahybrid/). the results demonstrated that mir-378 could form complementary base pairing with gaplinc (). we also observed the expression levels […]

PMCID: 5941680
PMID: 29739336
DOI: 10.1186/s12864-018-4670-5

[…] rna and 45.5% (2,018/4,438) had higher expression of the linear rna., given the potential mirna regulatory function of circrnas, we next used the mirna target prediction algorithms miranda [] and rnahybrid [] to predict the mirna targets of the circrnas detected in ten or more samples by at least one of the circrna prediction algorithms (n = 10 circrna candidates). using a list of 2588 […]

PMCID: 5940789
PMID: 29739971
DOI: 10.1038/s41598-018-25103-6

[…] took part in several biological processes in the chicken ovary., based on the data for differentially expressed protein-coding transcripts, mirna, and lncrna transcripts, we used three softwares rnahybrid(v2.1.2) + svm_light(v6.01), miranda(v3.3a) and targetscan(version:7.0) to identify biological targets of each mirna from the protein-coding and lncrna transcripts that showed […]

PMCID: 5941466
PMID: 29739335
DOI: 10.1186/s12864-018-4728-4

[…] bayesian approach was applied for the statistical analysis of the data []., to test for significant associations between genes, mirnas, pathways and go terms, the prediction software targetscan and rnahybrid, together with the differentially expressed genes in the l. vannamei hemocytes transcriptome data (genebank accession numbers: prjna385392) were used. the relatedness or anticorrelation […]

PMCID: 5930509
PMID: 29716627
DOI: 10.1186/s13048-018-0410-3

[…] ubiquitously expressed in the ovarian follicle and important in reproductive performance [], were selected for functional analysis. the secondary structure of mir-424 and mir-503 was predicted by rnahybrid (http://bibiserv.techfak.uni-bielefeld.de/rnahybrid)., bovine ovaries as sources of bgcs were collected from a local slaughterhouse. ovaries were processed to obtain follicular fluid […]

RNAhybrid institution(s)
Center for Biotechnology, CeBiTec, Universität Bielefeld, Bielefeld, Germany
RNAhybrid funding source(s)
Supported by the Deutsche Forschungsgemeinschaft, Bioinformatics Initiative.

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