Freiburg RNA Tools
IntaRNA - RNA-RNA interaction
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IntaRNA

IntaRNA - RNA-RNA interaction

IntaRNA is a program for the fast and accurate prediction of interactions between two RNA molecules. It has been designed to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs), but it can also be used to predict other types of RNA-RNA interactions. Precomputed results for Enterobacteria: ChiX, CyaR, FnrS, GcvB, MicC, RyhB, Spot42, and for Non-enteric bacteria: LhrA2, PrrF1, Yfr1.
Furthermore, IsaR target prediction on the PCC6803 genome.

Note, in contrast to this server, the stand-alone IntaRNA software does not limit the problem size, provides enhanced functionality, and offers a batch processing-friendly command line interface. For this reasons, you might consider to install IntaRNA locally

For articles describing the tool refer to the reference section below. Please cite us when using our tools.
For more information check the help page.

Try IntaRNA with these examples:

Note: the IntaRNA webserver will be offline for maintenance from 25/07/2017 to 26/07/2017.

Due to construction work at the computing center of the University of Freiburg, we have to temporarily stop the Freiburg RNA tools service. We will restart the service as soon as possible.

We apologize for the inconvenience.

Sequence Parameters

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Note, if the number of query-target combinations (product of respective numbers) is below or equal to 10, minimal energy profiles will be generated for each query-target pair (see example output), which enables a detailed investigation of interaction alternatives.

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When using IntaRNA please cite :

Results are computed with IntaRNA version 2.0.2 (wrapper 1.1.2) linking Vienna RNA package 2.3.1