Input and runtime details for job 5724482 (precomputed example)

Sequence Parameters

	Query ncRNA (short) in FASTA		[.fa]
	Index first query position		1
	Target RNA (long) in FASTA		[.fa]
	Index first target position		1

Output Parameters

	Number of interactions per RNA pair		1
	Suboptimal interaction overlap		can overlap in query
	Max. interaction length		not provided
	Max. absolute energy of an interaction		0
	Max. delta energy above mfe of an interaction		100
	No lonely base pairs		yes
	No GU at helix ends		yes

Seed Parameters

	Min. number of basepairs in seed		7
	Max. Number of mismatches in seed		0
	Maximal energy		0
	Minimal unpaired probability (per RNA)		0
	Seed position (query)		not provided
	Seed position (target)		not provided
	Ignore seeds with GU base pairs		no
	Ignore seeds with GU ends		yes

Folding Parameters

	Temperature for energy computation		37.0
	Access. query: folding window size		150
	Access. query: max. basepair distance		100
	Access. target: folding window size		150
	Access. target: max. basepair distance		100
	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: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5724482&toolName=IntaRNA ( 30 days expiry )

Description of the job

pairwise ncRNA-mRNA predictions

Output [zip]

Downloadable files

IntaRNA result table:

[csv]

Identified Interactions

Sort by selecting a column name.

Target	Start(T)	End(T)	Start(seed-T)	End(seed-T)	ED(T)	Query	Start(Q)	End(Q)	Start(seed-Q)	End(seed-Q)	ED(Q)	Energy	E(hybrid)	E_norm	RRI subseqs	RRI details	Seq(T)	Seq(Q)
mRNA1	85	95	88	94	4.54	ncRNA1	21	32	22	28	1.94	-11.86	-18.34	-1.2809	GUGGUGAGGAG&CUCCUCACACAC	(((((((((((&)))))))).)))	UUUAAAUUAAAAAAUCAUAGAAAAAGUAUCGUUUGAUACUUGUGAUUAUACUCAGUUAUACAGUAUCUUAAGGUGUUAUUAAUAGUGGUGAGGAGAAUUUAUGAAGCUUUUCAAAAGCUUGCUUGUGGCACCUGCAACUCUUGGUCUUUUAGCACCAAUGACCGCUACUGCUAAU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU
mRNA2	86	97	86	92	4.09	ncRNA1	20	31	25	31	1.88	-8.17	-14.14	-0.882372	UGUGUGACGAGU&ACUCCUCACACA	(((((((.((((&)))).)))))))	UGCUUCUUAGUAAUGGCCAGCUCGGGGAUUUGGAACUGGUGGUUGUUAAUUCUAGGCAAAUAGAUUAAAAUUAAAUUACUCAAAUUGUGUGACGAGUUUUAUGAAGCUUUUUAAAAGCUUGUUGGUAGCUCCAGCAACGAUUGGGCUACUAGCUCCAUUUUCAACGUUUGCUGGC	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU
mRNA1	52	58	52	58	1.13	ncRNA2	28	34	28	34	3.06	-3.09	-7.28	-0.343584	UCAGUUA&UGACUGA	(((((((&)))))))	UUUAAAUUAAAAAAUCAUAGAAAAAGUAUCGUUUGAUACUUGUGAUUAUACUCAGUUAUACAGUAUCUUAAGGUGUUAUUAAUAGUGGUGAGGAGAAUUUAUGAAGCUUUUCAAAAGCUUGCUUGUGGCACCUGCAACUCUUGGUCUUUUAGCACCAAUGACCGCUACUGCUAAU	ACUGAGGUACGAUCGUGGCAGGGCCUUUGACUGACUUUCGUACUUU

Details of Selected Interaction Download Interaction Details

Target

Query

Energy

Hybridization Energy

Unfolding Energy - Target

Unfolding Energy - Query

Position - Target

Position - Query

Position Seed - Target

Position Seed - Query

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: Query: Target:

Job resubmission

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

usability assessment

Please support us by filling this short quality survey for evaluating this

service.

When using IntaRNA please cite :

Martin Mann, Patrick R. Wright, and Rolf Backofen
IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions
Nucleic Acids Research, 2017, 45 (W1), W435–W439.
Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Anke Busch, Andreas S. Richter, and Rolf Backofen
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
Bioinformatics, 2008, 24 (24), 2849-56.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching