Freiburg RNA Tools
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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
b2215 -67 -15 MicC 1 70 -21.53 5.2e-06 0.0190476 ompC outer membrane porin protein C
b4403 -8 11 MicC 1 21 -13.87 0.0021857 0.7974595 yjtD putative methyltransferase
b1385 -3 20 MicC 1 21 -10.7 0.0166105 0.9679271 feaB phenylacetaldehyde dehydrogenase
b1771 -14 4 MicC 2 19 -11 0.0138425 0.9679271 ydjG methylglyoxal reductase NADH-dependent
b3334 -68 -23 MicC 4 55 -9.85 0.0275399 0.9679271 gspM general secretory pathway component cryptic
b0333 51 74 MicC 6 28 -11.71 0.0089209 0.9679271 prpC 2-methylcitrate synthase
b3619 59 71 MicC 6 18 -9.81 0.0281917 0.9679271 hldD ADP-L-glycero-D-mannoheptose-6-epimerase NAD(P)-binding
b1833 43 54 MicC 7 18 -10.92 0.0145348 0.9679271 yebS inner membrane PqiA domain protein
b2118 34 64 MicC 7 42 -10.57 0.0179646 0.9679271 yehI DUF4132 domain-containing protein
b3673 -10 11 MicC 7 25 -9.9 0.0267449 0.9679271 emrD multidrug efflux system protein
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