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inteRNA specifications


Unique identifier OMICS_23839
Name inteRNA
Alternative name Agile inteRNA
Software type Application/Script
Interface Web user interface
Restrictions to use None
Input data RNA sequences, target mRNA and antisense RNA.
Input format FASTA
Output data A file that contains the base-pair information of the joint secondary structure, an image file that can help visualize the joint secondary structure prediction of the input RNAs and a file reporting the calculated free energy of the predicted joint secondary structure.
Output format TXT+JPEG
Computer skills Basic
Version 3.3
Stability Stable
Source code URL
Maintained No


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Publications for inteRNA

inteRNA citations


A comprehensive benchmark of RNA–RNA interaction prediction tools for all domains of life

PMCID: 5408919
PMID: 27993777
DOI: 10.1093/bioinformatics/btw728

[…] RNA families such as specialized miRNA algorithms (reviewed in ), specialized snoRNA target prediction algorithms and comparative bacterial sRNA prediction methods (reviewed in , ). We also excluded inteRNA (), IRIS (), piRNA () and biRNA (), as they are either no longer supported or obsolete.In summary, our final list of selected tools used for further analyses consisted of RIsearch (), IntaRNA […]


RNA RNA interaction prediction using genetic algorithm

PMCID: 4122056
PMID: 25114714
DOI: 10.1186/1748-7188-9-17

[…] int secondary structure prediction of our algorithm, GRNAs, in Matthews Correlation Coefficient []. It is also compared to the state-of-the-art methods such as PETcofold [], the sparsified version of inteRNA [], Pairfold [], RactIP[] and RNAcofold []. The MCC evaluates the joint structure, i.e. both the binding sites between the two RNAs and the secondary structure of each single RNA. In two pairs […]


Predicting sRNAs and Their Targets in Bacteria

PMCID: 5054197
PMID: 23200137
DOI: 10.1016/j.gpb.2012.09.004

[…] ssing complex) between two RNA molecules. To address this problem, Alkan et al. presented inteRNA based on joint structure of two RNA molecules. When applied in CopA-CopT and OxyS-fhlA interactions, inteRNA detected the loop-loop interactions successfully. Thereafter, multiple programs such as piRNA , inRNA , rip , RactIP , ripalign and PETcofold have been presented based on joint structure of […]


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inteRNA institution(s)
Laboratory for Computational Biology, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada; Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universitat, Freiburg, Germany
inteRNA funding source(s)
Supported by SFU-CTEF funded Bioinformatics for Combating Infectious Diseases Project, the German Research Foundation (DFG grant BA 2168/3-1), MITACS, NSERC, the CRC program and the Michael Smith Foundation for Health Research, the German Research Foundation (DFG grant BA 2168/2-1 SPP 1258) and the German Federal Ministry of Education and Research (BMBF grant 0313921 FRISYS).

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