Freiburg RNA Tools
IntaRNA - Results
IntaRNA 3189420

Input and runtime details for job 3189420 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Target RNA (long) in FASTA[.fa]

Output Parameters

? Number of (sub)optimal interactions1
? Suboptimal interaction overlap can overlap in query
? Max. absolute energy of an interaction0
? Max. delta energy above mfe of an interaction100

Seed Parameters

? Min. number of basepairs in seed7
? Max. Number of mismatches in seed0
? Maximal energy0
? Minimal unpaired probability (each)0
? Seed position (query)not provided
? Seed position (target)not provided

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 3189420 (server version 4.4.2)

?Job Submitted & Queued@ Tue Feb 21 12:08:08 CET 2017
?Processing Started@ Tue Feb 21 12:08:21 CET 2017
?IntaRNA Finished & Post-Processing@ Tue Feb 21 12:08:23 CET 2017
?Post-Processing Finished@ Tue Feb 21 12:08:23 CET 2017
?Job Completed@ Tue Feb 21 12:08:23 CET 2017
 DIRECT ACCESS: ( 30 days expiry )

The job description you specified

ncRNA-mRNA prediction

? Output download complete results [zip]

Downloadable files


? Identified Interactions

Select: 1-3 all
Sort by selecting a column name:
Target Position Query Position Energy
mRNA1 85 -- 95 ncRNA1 21 -- 32 -11.87820
mRNA2 86 -- 97 ncRNA1 20 -- 31 -8.16661
mRNA1 52 -- 58 ncRNA2 28 -- 34 -3.08778

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.
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 2.0.1 (wrapper 1.1.2) linking Vienna RNA package 2.3.1