Freiburg RNA Tools
IntaRNA - Results
BIF
IFF
IntaRNA 4255663

Input and runtime details for job 4255663 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_003197
? All repliconsyes
? Extract sequences aroundstart codon
? nt up (1-300)75
? nt down (1-300)75

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 4255663 (server version trunk)

?Job Submitted & Queued@ Sat Feb 17 12:27:58 CET 2018
?Processing Started@ Sat Feb 17 12:28:13 CET 2018
?IntaRNA Finished & Post-Processing@ Sat Feb 17 14:03:10 CET 2018
?Post-Processing Finished@ Sat Feb 17 14:03:11 CET 2018
?Job Completed@ Sat Feb 17 14:03:16 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=4255663&toolName=IntaRNA ( 30 days expiry )

The job description you specified

GcvB - example

? Output download complete results [zip]

Downloadable files

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heatmap

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

Sort by selecting a column name:
p-value fdr value Target Position Query Position Energy Gene Annotation
6.96e-05 0.11872 STM0849 50 -- 68 GcvB 139 -- 162 -18.27770 yliB glutathione ABC transporter substrate-binding protein GsiB
8.82e-05 0.11872 STM3089 130 -- 149 GcvB 156 -- 175 -18.11060 yqgD similar to E. coli orf hypothetical protein (AAC75978.1) Blastp hit to AAC75978.1 (83 aa) 52% identity in aa 1 - 78
9.16e-05 0.11872 STM2818 56 -- 67 GcvB 153 -- 164 -18.08340 gshA glutamate--cysteine ligase
0.0001119 0.11872 STM3707 41 -- 53 GcvB 147 -- 159 -17.93730 yibD putative glycosyltransferase
0.0001596 0.11872 STM0283 116 -- 135 GcvB 152 -- 169 -17.67010    
0.0001789 0.11872 STM4398 31 -- 53 GcvB 38 -- 60 -17.58140 cycA D-serine/D-alanine/glycine transporter
0.0001831 0.11872 STM1498 22 -- 39 GcvB 75 -- 92 -17.56310   dimethyl sulfoxide reductase subunit A
0.0006106 0.34639 STM0510 41 -- 55 GcvB 66 -- 80 -16.54580 sfbA metal ABC transporter substrate-binding protein
0.0007577 0.38204 STM3495 127 -- 139 GcvB 181 -- 193 -16.34700 yrfF Intracellular growth attenuator protein igaA
0.0009323 0.41449 STM2355 19 -- 37 GcvB 72 -- 91 -16.15080 argT histidine ABC transporter substrate-binding protein HisJ

Details of Selected Interaction Download Interaction Details

Target

Query

		

		

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Results are computed with IntaRNA version 2.1.0 (wrapper 1.1.3) linking Vienna RNA package 2.4.3