Freiburg RNA Tools
IntaRNA - Results
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IFF
IntaRNA 2443602

Input and runtime details for job 2443602 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_002516
? 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 2443602 (server version trunk)

?Job Submitted & Queued@ Sat Feb 17 12:30:11 CET 2018
?Processing Started@ Sat Feb 17 12:30:29 CET 2018
?IntaRNA Finished & Post-Processing@ Sat Feb 17 13:39:13 CET 2018
?Post-Processing Finished@ Sat Feb 17 13:39:14 CET 2018
?Job Completed@ Sat Feb 17 13:39:19 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=2443602&toolName=IntaRNA ( 30 days expiry )

The job description you specified

PrrF1 - example

? Output download complete results [zip]

Downloadable files

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


heatmap

? Identified Interactions for NC_002516 Pseudomonas aeruginosa PAO1

Sort by selecting a column name:
p-value fdr value Target Position Query Position Energy Gene Annotation
8.2e-06 0.03888 PA3621 119 -- 130 PrrF1 71 -- 82 -19.76620 fdxA ferredoxin I
0.0002537 0.60039 PA5300 31 -- 49 PrrF1 99 -- 116 -16.60480 cycB cytochrome C5
0.0005342 0.69645 PA5164 62 -- 79 PrrF1 101 -- 122 -15.78150 rmlC dTDP-4-dehydrorhamnose 35-epimerase
0.0006923 0.69645 PA0007 72 -- 88 PrrF1 104 -- 120 -15.48190   'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
0.0007356 0.69645 PA1571 57 -- 69 PrrF1 96 -- 108 -15.41090   'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
0.0010054 0.70795 PA3255 2 -- 16 PrrF1 101 -- 115 -15.03850   'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
0.0011714 0.70795 PA0365 118 -- 127 PrrF1 101 -- 110 -14.85250   'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
0.0013051 0.70795 PA4756 127 -- 139 PrrF1 107 -- 119 -14.71950 carB carbamoyl phosphate synthase large subunit
0.0013559 0.70795 PA0112 35 -- 47 PrrF1 98 -- 110 -14.67210   'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
0.0014955 0.70795 PA4657 27 -- 44 PrrF1 105 -- 123 -14.55000   'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'

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