IntaRNA protocols

View IntaRNA computational protocol

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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 in pipelines

 (7)
2018
PMCID: 5869019
PMID: 29537368
DOI: 10.7554/eLife.33684.044

[…] pipeline (; ). together, these two quantification strategies identified several mrna, srnas, and untranslated regions enriched in the gsrn(37)::pp7hp pull-down fraction ( and ). we applied intarna 2.0.2 () to identify potential binding sites between gsrn and the enriched co-purifying rnas. of the 67 analyzed enriched genes and regions, 32 of the predicted rna-rna interactions involved […]

2018
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 (http://rna.informatik.uni-freiburg.de/intarna/input.jsp) was used to predict the interactions between yeast 18s ribosomal rna (18s rrnay) and 1a-vdac or 1b-vdac mrna. […]

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

[…] values were normalized against an endogenous control mrna rpl11 (5′-gtgctgggtaggccag and 5′- ttctgctggaaccagcg). the comparative cycle threshold (ct) method was used to quantify the results., intarna was used to predict rna-rna long-range base pairings incorporating the accessibility of target sites under default parameters (minimum seed size 7, mismatches 0). this approach computes […]

2017
PMCID: 5465533
PMID: 28595592
DOI: 10.1186/s13062-017-0183-4

[…] tcc library in bioconductor []., we previously developed a series of computational pipelines including various computational tools for sequence analysis, such as raccess [], tantan [], last [, ], intarna [], and ractip [], for predicting human lncrna-rna interactions []. furthermore, all predicted human lncrna-rna interactions are available from our database […]

2017
PMCID: 5511505
PMID: 28717590
DOI: 10.7717/peerj.3461

[…] in bacterial genomes although their significance is not fully understood (). finally, edge-pro and deseq was used to estimate differential gene expression levels for the srnas/sorfs., targetrna2 and intarna were used to identify potential srnas targets (; ). using srna sequences as queries, the programs searches for complementary regions in 5′ regions of mrnas. only targets predicted […]


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IntaRNA in publications

 (96)
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 […]

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 […]

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 […]

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 […]

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 […]


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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, Freiburg, Germany
IntaRNA funding source(s)
Supported by Bundesministerium fr Bildung und Forschung [031A538A RBC, 031L0106B] and Deutsche Forschungsgemeinschaft [BA 2168/14-1, BA 2168/16-1].

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