Freiburg RNA Tools
IntaRNA - Results
BIF
IFF
IntaRNA 4421343

Input and runtime details for job 4421343 (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 4421343 (server version trunk)

?Job Submitted & Queued@ Wed Sep 27 16:46:16 CEST 2017
?Processing Started@ Wed Sep 27 16:46:21 CEST 2017
?IntaRNA Finished & Post-Processing@ Wed Sep 27 18:54:12 CEST 2017
?Post-Processing Finished@ Wed Sep 27 18:54:13 CEST 2017
?Job Completed@ Wed Sep 27 18:54:17 CEST 2017
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=4421343&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
8.7e-06 0.0396 STM0369 77 -- 144 GcvB 31 -- 91 -27.12990 prpC 2-methylcitrate synthase
0.0001769 0.25029 STM3251 71 -- 114 GcvB 45 -- 87 -23.66120   ribokinase family sugar kinase
0.0002515 0.25029 STM1098 7 -- 48 GcvB 56 -- 90 -23.19350 hpaC 4-hydroxyphenylacetate 3-monooxygenase reductase subunit
0.0003054 0.25029 STM3630 33 -- 74 GcvB 51 -- 92 -22.92940 dppA dipeptide ABC transporter substrate-binding protein DppA
0.0003657 0.25029 STM3344 6 -- 47 GcvB 57 -- 102 -22.68010 rpsI 30S ribosomal protein S9
0.0003757 0.25029 STM4398 2 -- 53 GcvB 38 -- 82 -22.64240 cycA D-alanine/D-serine/glycine permease
0.0003849 0.25029 STM1107 80 -- 136 GcvB 36 -- 81 -22.60860 hpaX 4-hydroxyphenylacetate permease
0.0005078 0.28896 STM3909 41 -- 63 GcvB 66 -- 89 -22.21560 ilvC ketol-acid reductoisomerase
0.0008369 0.4233 STM0399 44 -- 99 GcvB 36 -- 81 -21.48290 brnQ branched-chain amino acid transport system 2 carrier protein
0.0010381 0.47254 STM2768 83 -- 124 GcvB 36 -- 79 -21.15700   transposase

Details of Selected Interaction Download Interaction Details

Target

Query

		

		

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Results are computed with IntaRNA version 2.0.5 (wrapper 1.1.2) linking Vienna RNA package 2.3.1