IntaRNA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool IntaRNA

Tool usage distribution map

This map represents all the scientific publications referring to IntaRNA per scientific context
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Associated diseases

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IntaRNA specifications


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




  • person_outline Martin Raden

Publications for IntaRNA

IntaRNA citations


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

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

[…] gets 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 such a […]


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

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

[…] 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 medic […]


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

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

[…] somal 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 of complementa […]


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

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

[…] for prediction of RNA secondary structure. A similar pattern of secondary structures with comparable hybridisation energies was obtained for both D. melanogaster VDAC mRNAs.Furthermore, IntaRNA software ( was used to predict the interactions between yeast 18S ribosomal RNA (18S rRNAy) and 1A-VDAC or 1B-VDAC mRNA. The 1B-(Δ16–31) […]


The Small RNA ncS35 Regulates Growth in Burkholderia cenocepacia J2315

PMCID: 5760752
PMID: 29359187
DOI: 10.1128/mSphere.00579-17

[…] Putative targets of ncS35 were predicted with CopraRNA (Comparative Prediction Algorithm for sRNA Targets) (). The underlying IntaRNA parameters for implementation of the CopraRNA algorithm are a seed length of 7, a target folding window size of 150, and a maximum base pair distance of 100 (). Interactions were predicted for […]


Gene network analysis identifies a central post transcriptional regulator of cellular stress survival

PMCID: 5869019
PMID: 29537368
DOI: 10.7554/eLife.33684.044

[…] IntaRNA version 2.0.2 is a program within the Freiberg RNA Tools collection (). To predict likely RNA-RNA associations between predicted unstructured regions within GsrN and its RNA targets, we input […]

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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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