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IntaRNA specifications

Information


Unique identifier OMICS_03819
Name IntaRNA
Interface Web user interface
Restrictions to use None
Input data Some ncRNA or target RNA.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • SHAPE

Maintainer


  • person_outline Martin Raden

Publications for IntaRNA

IntaRNA citations

 (97)
library_books

LncRNA OIP5 AS1 is overexpressed in undifferentiated oral tumors and integrated analysis identifies as a downstream effector of stemness associated transcription factors

2018
Sci Rep
PMCID: 5935738
PMID: 29728583
DOI: 10.1038/s41598-018-25451-3

[…] were performed and retrieved from targetscan, miranda, mircode, starbase and diana online prediction tools. for prediction of rna-rna interactions and rna-rna binding protein (rbps) interaction, intarna, and clipdb online tools were employed. individual study for assessment of the association of mirnas in various human cancers was collected from public databases pubmed using mesh terms […]

library_books

RNA Seq profiling of circular RNAs in human laryngeal squamous cell carcinomas

2018
Mol Cancer
PMCID: 5930968
PMID: 29716593
DOI: 10.1186/s12943-018-0833-x

[…] using the diana-mirpath v.3 platform, which has been reported in previous study [], the candidate circrna(s) were matched against the seed sequences of predicted target mirna candidate(s) using the intarna platform to predict interactions between rna molecules. the settings that were applied to the diana-mirpath v.3 platform included: 0 suboptimal interactions, 5 minimum number of basepairs […]

library_books

Regulation Mechanism Mediated by Trans Encoded sRNA Nc117 in Short Chain Alcohols Tolerance in Synechocystis sp. PCC 6803

2018
Front Microbiol
PMCID: 5946031
PMID: 29780373
DOI: 10.3389/fmicb.2018.00863

[…] confirmed by pcr and sequencing analysis. pcr primers for mutant construction were listed in table ., after determination of the end of trans-encoded srna nc117, target prediction was performed by intarna software (), and only the top 100 predictions obtained from intarna with a free-energy cut-off of -15 kcal/mol were retained to remove potential false positive targets., the wt and nc117 […]

library_books

An sRNA and Cold Shock Protein Homolog Based Feedforward Loop Post transcriptionally Controls Cell Cycle Master Regulator CtrA

2018
Front Microbiol
PMCID: 5928217
PMID: 29740411
DOI: 10.3389/fmicb.2018.00763

[…] may contribute to the regulation of ctra levels., computational predictions of srna-mrna interactions, either using mrna or srna as query sequences, was performed at a genome-wide scale applying intarna and coprarna with standard parameters (). the full-length gspr homologous sequences from s. meliloti 1021 (nc_003047, our reference genome), s. meliloti bl225c (nc_015590), sinorhizobium […]

library_books

Ribosome dependent conformational flexibility changes and RNA dynamics of IRES domains revealed by differential SHAPE

2018
Sci Rep
PMCID: 5882922
PMID: 29615727
DOI: 10.1038/s41598-018-23845-x

[…] rna has been suggested as a mechanism used by viral ires elements to recruit the 40s subunit,. potential base pairs between the fmdv ires and the 18s rna positions 815–1193 were predicted using intarna (table ). in particular, the sequences within domain 2 sharing complementarity with 18s positions were also predicted to interact with the hcv ires. for 28s rna, a higher number […]

library_books

Mechanism of translation control of the alternative Drosophila melanogaster Voltage Dependent Anion selective Channel 1 mRNAs

2018
Sci Rep
PMCID: 5871876
PMID: 29593233
DOI: 10.1038/s41598-018-23730-7

[…] 6,3 kcal/mol (fig. ). similarly, 1b(δ16–31)-vdac mrna can pair with 18s rrnay at the 1306–1331 sequence, producing only a short dsrna structure with a low hybridisation energy value (fig. ).figure 6, intarna software was also used to predict interactions between d. melanogaster 18s ribosomal rna (18s rrnad) and 1a-, 1b- or 1b(δ16–31)-5′ utrs. this additional analysis showed that the 2–116 sequence […]


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IntaRNA institution(s)
Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany; Center for Biological Signaling Studies (BIOSS), University of Freiburg, Germany
IntaRNA funding source(s)
Supported by Bundesministerium fur Bildung und Forschung [031A538A RBC, 031L0106B] and Deutsche Forschungsgemeinschaft [BA 2168/14-1, BA 2168/16-1].

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