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IntaRNA 1972078

Input and runtime details for job 1972078 (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 1972078 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:13:56 CET 2020
?IntaRNA Started@ Mon Jan 27 14:16:07 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:17:05 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:18:21 CET 2020
?Job Completed@ Mon Jan 27 14:18:31 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1972078&toolName=IntaRNA ( 30 days expiry )

Description of the job

MicC - 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
b4664 -70 -61 MicC 56 65 -10.92 0.0145348 0.9679271 ibsD toxic membrane protein
b0002 27 37 MicC 50 60 -12.71 0.0047142 0.8384433 thrA Bifunctional aspartokinase/homoserine dehydrogenase 1
b3996 -15 -6 MicC 45 54 -9.78 0.02869 0.9679271 nudC NADH pyrophosphatase
b1833 43 54 MicC 7 18 -10.92 0.0145348 0.9679271 yebS inner membrane PqiA domain protein
b0126 30 44 MicC 40 52 -9.79 0.028523 0.9679271 can carbonic anhydrase
b0354 -12 7 MicC 50 67 -10.71 0.0165104 0.9679271 yaiL DUF2058 family protein
b2091 4 16 MicC 50 62 -10.87 0.0149839 0.9679271 gatD galactitol-1-phosphate dehydrogenase Zn-dependent and NAD(P)-binding
b0553 14 23 MicC 49 58 -10.68 0.0168124 0.9679271 nmpC DLP12 prophage truncated outer membrane porin (pseudogene)IS phage Tn Phage or Prophage Related outer membrane porin protein locus of qsr prophage
b2550 -75 -62 MicC 43 56 -13.61 0.0026038 0.7974595 yphH putative DNA-binding transcriptional regulator
b2573 48 57 MicC 56 65 -10.66 0.0170166 0.9679271 rpoE RNA polymerase sigma E factor
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


		

		

		

		

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

			

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
			

		
 
		
		

		
		

		
		

			

		

		
		

	

	
	
	
	
	
	
	




			 
	





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



		 
	

			





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