Freiburg RNA Tools
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IntaRNA 3508279

Input and runtime details for job 3508279 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_002516
? 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 3508279 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:22:03 CET 2020
?Processing Started@ Mon Jan 27 14:24:19 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:25:34 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:26:51 CET 2020
?Job Completed@ Mon Jan 27 14:27:04 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=3508279&toolName=IntaRNA ( 30 days expiry )

The job description you specified

PrrF1 - Pseudomonas aeruginosa


? Output download complete results [zip]

Downloadable files

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


heatmap

? Identified Interactions for NC_002516 Pseudomonas aeruginosa PAO1

Sort by selecting a column name
Target Start(T) End(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
PA3621 44 55 PrrF1 71 82 -19.78 5.17e-05 0.165795 fdxA ferredoxin I
PA0119 53 73 PrrF1 101 121 -19.45 7e-05 0.165795 C4-dicarboxylate transporter DctA
PA2831 -26 -6 PrrF1 99 118 -18.5 0.0001609 0.2469872 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA1103 -16 54 PrrF1 38 102 -17.95 0.0002544 0.2469872 flagellar assembly protein FliH
PA1571 -33 -7 PrrF1 96 121 -17.92 0.0002607 0.2469872 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA5300 -45 -27 PrrF1 99 116 -16.71 0.0006757 0.5334651 cycB cytochrome C5
PA2715 44 55 PrrF1 71 82 -16.49 0.0007976 0.5397473 ferredoxin
PA5490 -20 41 PrrF1 67 120 -16.18 0.0010037 0.5780432 cc4 cytochrome C4
PA5351 -10 22 PrrF1 71 99 -15.79 0.0013327 0.5780432 rubA1 rubredoxin
PA2659 -9 17 PrrF1 75 99 -15.78 0.0013423 0.5780432 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
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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When using IntaRNA please cite :

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