Freiburg RNA Tools
IntaRNA - Results
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IFF
IntaRNA 1972078

Input and runtime details for job 1972078 (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 1972078 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:13:56 CET 2020
?IntaRNA Started@ Mon Jan 27 14:16:07 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:17:05 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:18:21 CET 2020
?Job Completed@ Mon Jan 27 14:18:31 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1972078&toolName=IntaRNA ( 30 days expiry )

Description of the job

MicC - 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 p-value fdr gene annotation
b4496 8 31 MicC 39 64 -12.68 0.0048068 0.8384433 yedS pseudogene outer membrane protein homology putative outer membrane protein
b3128 -16 6 MicC 40 66 -12.58 0.0051283 0.853862 garD D-galactarate dehydrogenase
b4255 -59 -46 MicC 42 54 -12.39 0.0057958 0.9230441 rraB protein inhibitor of RNase E
b1667 45 59 MicC 41 55 -12.31 0.0061007 0.9311193 ydhR putative monooxygenase
b4328 60 71 MicC 53 65 -11.97 0.007574 0.9679271 iadA isoaspartyl dipeptidase
b0170 -75 -65 MicC 39 48 -11.94 0.007719 0.9679271 tsf translation elongation factor EF-Ts
b0763 57 71 MicC 41 55 -11.91 0.0078666 0.9679271 modA molybdate ABC transporter periplasmic binding protein chlorate resistance protein
b4473 52 67 MicC 39 54 -11.89 0.0079665 0.9679271 smf DNA recombination-mediator A family protein
b1119 57 75 MicC 42 58 -11.87 0.0080676 0.9679271 nagK N-acetyl-D-glucosamine kinase
b1535 -13 20 MicC 33 63 -11.71 0.0089209 0.9679271 dgcZ diguanylate cyclase zinc-sensing
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