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IntaRNA 4935127

Input and runtime details for job 4935127 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_003197
? 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 4935127 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:12:23 CET 2020
?IntaRNA Started@ Mon Jan 27 14:14:40 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:16:11 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:17:25 CET 2020
?Job Completed@ Mon Jan 27 14:17:35 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4935127&toolName=IntaRNA ( 30 days expiry )

Description of the job

GcvB - E. coli

? Output [zip]

Downloadable files

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


heatmap

? Identified Interactions for NC_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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) Query Start(Q) End(Q) ED(Q) Energy p-value fdr gene annotation
STM3598 58 75 GcvB 62 79 -15.15 0.0086358 0.7799855 putative L-asparaginase
STM0022 -74 -55 GcvB 127 147 -14.36 0.0140165 0.7904009 bcfB fimbrial chaperone protein
STM3600 -75 -47 GcvB 155 182 -15.65 0.0062731 0.7419678 fructoselysine 6-kinase
STM0604 4 22 GcvB 62 80 -15.71 0.0060327 0.7419678 ybdM similar to E. coli orf hypothetical protein (AAC73702.1) Blastp hit to AAC73702.1 (209 aa) 77% identity in aa 5 - 209
STM1822 43 69 GcvB 162 185 -14.36 0.0140165 0.7904009 yoaB similar to E. coli orf hypothetical protein (AAC74879.1) Blastp hit to AAC74879.1 (130 aa) 92% identity in aa 17 - 130
STM3083 -36 -6 GcvB 130 160 -15.04 0.009252 0.7883581 fructuronate reductase
STM1257 -35 -12 GcvB 166 189 -13.92 0.018166 0.8371189 peptide ABC transporter permease
STM3909 -34 -14 GcvB 67 88 -21.24 6.85e-05 0.2036716 ilvC ketol-acid reductoisomerase
STM2179 -46 -27 GcvB 69 90 -14.7 0.0114137 0.7904009 4-hydroxybenzoate transporter
STM0689 -9 15 GcvB 66 90 -16.13 0.0045687 0.6975035 citA citrate-proton symporter
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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