Freiburg RNA Tools
IntaRNA - Results
BIF
IFF

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

IntaRNA 6571257

Input and runtime details for job 6571257 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_000913
? All repliconsyes
? Extract sequences aroundstart codon
? nt upstream (1-300)75
? nt downstream (1-300)75
? Index first target position-75

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 6571257 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:18:03 CET 2020
?IntaRNA Started@ Mon Jan 27 14:20:22 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:21:19 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:22:25 CET 2020
?Job Completed@ Mon Jan 27 14:22:35 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6571257&toolName=IntaRNA ( 30 days expiry )

Description of the job

Spot42 - E. coli

? Output [zip]

Downloadable files

[csv]
[png] [pdf]
[png] [pdf]
[txt]
[html] [pdf] [png]


heatmap

? Identified Interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Show rows: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 all
Sort by selecting a column name.
Target Start(T) End(T) ED(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
b3934 -56 -44 Spot42 41 56 -10.45 0.0117318 0.9238006 cytR Anti-activator for CytR-CRP nucleoside utilization regulon
b1862 13 20 Spot42 1 8 -9.04 0.0260389 0.9238006 yebB DUF830 family protein
b3224 -61 -50 Spot42 1 12 -16.33 0.0003958 0.8439588 nanT sialic acid transporter
b1623 -58 -51 Spot42 1 8 -9.03 0.0261856 0.9238006 add adenosine deaminase
b1385 21 37 Spot42 55 71 -11.57 0.006193 0.9238006 feaB phenylacetaldehyde dehydrogenase
b0369 -53 -46 Spot42 1 8 -8.81 0.0296259 0.9238006 hemB 5-aminolevulinate dehydratase (porphobilinogen synthase)
b3311 17 25 Spot42 1 9 -9.59 0.0191007 0.9238006 rpsQ 30S ribosomal subunit protein S17
b4174 -75 -61 Spot42 42 57 -9.36 0.0217476 0.9238006 hflK modulator for HflB protease specific for phage lambda cII repressor
b0559 38 49 Spot42 46 58 -9.04 0.0260389 0.9238006 ybcW DLP12 prophage uncharacterized protein
b0878 64 73 Spot42 47 56 -9.01 0.0264814 0.9238006 macA macrolide transporter membrane fusion protein (MFP) component
Rows: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 all

Details of Selected Interaction Download Interaction Details 

Target

Query


		

		

		

		

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

			

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
			

		
 
		
		

		
		

		
		

			

		

		
		

	

	
	
	
	
	
	
	




			 
	





	
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.
			
		

	


	





	
de.NBI 
		usability assessment

	

		

			
				
				
			 
		

		

			Please 
			support us 
			by filling this 
			short quality survey 
			for evaluating this
			de.NBI
			service.
		

	





	





	
	
		 
		
When using IntaRNA please cite :







		 
	
	
	
		 
		



Results are computed with IntaRNA version 3.1.3 linking Vienna RNA package 2.4.14



		 
	

			





	About this web server
	  | 
	version 5.0.9
	  | 
	Copyright © 2012 - 2024 Bioinformatics Group Freiburg
	  | 
	de.NBI
	  | 
	Imprint and Disclaimer