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Protocols

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

Download


debian.png

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


download.png
download.png
debian.png

Versioning


No version available

Maintainer


This tool is not maintained anymore.

Additional information


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

Publications for RNAhybrid

RNAhybrid citations

 (840)
library_books

Long noncoding RNA GAPLINC promotes gastric cancer cell proliferation by acting as a molecular sponge of miR 378 to modulate MAPK1 expression

2018
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 […]

library_books

Circular RNA expression and regulatory network prediction in posterior cingulate astrocytes in elderly subjects

2018
BMC Genomics
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 […]

library_books

Acute Hepatopancreatic Necrosis Disease (AHPND) related microRNAs in Litopenaeus vannamei infected with AHPND causing strain of Vibrio parahemolyticus

2018
BMC Genomics
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 […]

library_books

Whole transcriptome analysis of atrophic ovaries in broody chickens reveals regulatory pathways associated with proliferation and apoptosis

2018
Sci Rep
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 […]

library_books

MicroRNA 424/503 cluster members regulate bovine granulosa cell proliferation and cell cycle progression by targeting SMAD7 gene through activin signalling pathway

2018
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 […]

library_books

Virulent duck enteritis virus infected DEF cells generate a unique pattern of viral microRNAs and a novel set of host microRNAs

2018
PMCID: 5923184
PMID: 29704894
DOI: 10.1186/s12917-018-1468-2

[…] 33 vac-encoded mirnas, only 13 mirna sequences and 22 “seed sequences” of mirna were identical, and 8 novel viral mirnas were detected and confirmed by stem-loop rt-qpcr in this study. using rnahybrid and pita software, 38 chv-encoded mirnas were predicted to target 41 viral genes and formed a complex regulatory network. dual luciferase reporter assay (dlra) confirmed that viral […]


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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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