Freiburg RNA Tools
IntaRNA - Results
IntaRNA 5724482

Input and runtime details for job 5724482 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Index first target position1

Output Parameters

? Number of interactions per RNA pair1
? Suboptimal interaction overlap can overlap in query
? Max. interaction lengthnot provided
? Max. absolute energy of an interaction0
? Max. delta energy above mfe of an interaction100
? No lonely base pairsyes
? No GU at helix endsyes

Seed Parameters

? Min. number of basepairs in seed7
? Max. Number of mismatches in seed0
? Maximal energy0
? Minimal unpaired probability (per RNA)0
? Seed position (query)not provided
? Seed position (target)not provided
? Ignore seeds with GU base pairsno
? Ignore seeds with GU endsyes

Folding Parameters

? Temperature for energy computation37.0
? Access. query: folding window size150
? Access. query: max. basepair distance100
? Access. target: folding window size150
? Access. target: max. basepair distance100
? Energy parameter set (Vienna package) Turner model, 2004

Job ID 5724482 (server version trunk)

?Job Submitted & Queued@ Fri Jan 07 21:02:52 CET 2022
?IntaRNA Started@ Fri Jan 07 21:03:17 CET 2022
?IntaRNA Finished & Post-Processing@ Fri Jan 07 21:03:17 CET 2022
?Post-Processing Finished@ Fri Jan 07 21:03:17 CET 2022
?Job Completed@ Fri Jan 07 21:03:18 CET 2022
 DIRECT ACCESS: ( 30 days expiry )

Description of the job

pairwise ncRNA-mRNA predictions

? Output [zip]

Downloadable files


? Identified Interactions

Sort by selecting a column name.
Target Start(T) End(T) Query Start(Q) End(Q) Energy
mRNA1 85 95 ncRNA1 21 32 -11.86
mRNA2 86 97 ncRNA1 20 31 -8.17
mRNA1 52 58 ncRNA2 28 34 -3.09

Details of Selected Interaction Download Interaction Details





Position-wise minimal energy profile

The following plots provide insights into the overall RNA-RNA interaction abundance. To this end, a minimal energy profile is provided for both sequences of each query-target pair considered. It visualizes for a given pair of sequences for each sequence position the minimal energy of any RNA-RNA interaction that can be formed between these two RNAs.
Furthermore, a combined plot that visualizes the minimal energy for each intermolecular index pair is provided in a heatmap style to track whether or not alternative interactions can be formed exclusively (overlapping regions) or in conjunction.
Note, since IntaRNA uses a heuristic to enable the low runtime, the provided energies are (close) upper bounds. Note further, only RNA-RNA interactions featuring a seed (according to the user parameters) are considered. Only interaction energies below or equal to 0 are visualized and missing data (subsequences without predicted interactions) are also depicted with an energy of 0.
Select a query-target sequence index combination for visualization:

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:
Feeds the job parameters to the input page to resubmit the job.

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When using IntaRNA please cite :

Results are computed with IntaRNA version 3.2.0 linking Vienna RNA package 2.4.14