Freiburg RNA Tools
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IntaRNA 6571257

Input and runtime details for job 6571257 (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 6571257 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:18:03 CET 2020
?Processing Started@ Mon Jan 27 14:20:22 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:21:19 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:22:25 CET 2020
?Job Completed@ Mon Jan 27 14:22:35 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=6571257&toolName=IntaRNA ( 30 days expiry )

The job description you specified

Spot42 - E. coli


? Output download complete results [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) Start(seed-Q) Energy p-value fdr gene annotation
b1927 -50 -39 Spot42 48 59 -13.13 0.0025285 0.9238006 amyA cytoplasmic alpha-amylase
b2935 63 75 Spot42 52 64 -12.34 0.003983 0.9238006 tktA transketolase 1 thiamine triphosphate-binding
b0307 57 71 Spot42 48 60 -10.37 0.0122776 0.9238006 ykgF ferridoxin-like LutB family protein putative electron transport chain YkgEFG component
b1300 -28 -13 Spot42 44 58 -9.81 0.0168668 0.9238006 puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase succinate semialdehyde dehydrogenase
b0511 -28 10 Spot42 18 58 -9.6 0.0189931 0.9238006 ybbW putative allantoin transporter
b1792 -68 -32 Spot42 40 73 -9.23 0.0234 0.9238006 yeaO DUF488 family protein
b0559 38 49 Spot42 46 58 -9.04 0.0260389 0.9238006 ybcW DLP12 prophage uncharacterized protein
b0367 -75 -66 Spot42 52 61 -10.23 0.0132937 0.9238006 tauC taurine ABC transporter permease
b1385 21 37 Spot42 55 71 -11.57 0.006193 0.9238006 feaB phenylacetaldehyde dehydrogenase
b1391 56 67 Spot42 55 66 -10.65 0.0104701 0.9238006 paaD ring 12-phenylacetyl-CoA epoxidase subunit
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