Freiburg RNA Tools
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IntaRNA 4596356

Input and runtime details for job 4596356 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_000913
? 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 4596356 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:10:48 CET 2020
?IntaRNA Started@ Mon Jan 27 14:13:48 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:14:50 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:16:49 CET 2020
?Job Completed@ Mon Jan 27 14:17:02 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4596356&toolName=IntaRNA ( 30 days expiry )

Description of the job

FnrS - E. coli

? Output [zip]

Downloadable files

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


heatmap

? Identified Interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Sort by selecting a column name.
Target Start(T) End(T) Query Start(Q) End(Q) Energy RRI subseqs p-value fdr gene annotation
b3755 -17 -3 FnrS 47 60 -10.02 0.0254359 0.9422174 yieP putative transcriptional regulator
b3106 -28 -17 FnrS 48 59 -10.14 0.0235457 0.9422174 yhaK redox-sensitive bicupin
b3441 -6 15 FnrS 41 58 -12.05 0.0063372 0.9422174 yhhY aminoacyl nucleotide detoxifying acetyltransferase
b4552 21 44 FnrS 38 61 -11.14 0.0120834 0.9422174 yrhC pseudogene fragment
b4236 56 68 FnrS 37 49 -12.7 0.0039014 0.9422174 cybC pseudogene truncated cytochrome b562 cytochrome b(562)
b3892 -16 -1 FnrS 31 49 -10.14 0.0235457 0.9422174 fdoI formate dehydrogenase-O cytochrome b556 subunit
b4040 -14 8 FnrS 34 59 -12.6 0.0042095 0.9422174 ubiA p-hydroxybenzoate octaprenyltransferase
b1476 -31 -17 FnrS 42 57 -11.48 0.0095365 0.9422174 fdnI formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible
b3136 -57 -18 FnrS 4 49 -11.04 0.012942 0.9422174 agaS tagatose-6-phosphate ketose/aldose isomerase
b1526 -16 3 FnrS 71 89 -10.44 0.0193611 0.9422174 yneJ putative DNA-binding transcriptional regulator
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