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) Energy p-value fdr gene annotation
b2506 -51 -37 Spot42 55 68 -11.81 0.0053979 0.9238006 yfgI nalidixic acid resistance protein putative periplasmic protein
b0973 67 75 Spot42 48 56 -11.79 0.0054601 0.9238006 hyaB hydrogenase 1 large subunit
b4311 -27 -16 Spot42 1 12 -11.59 0.0061225 0.9238006 nanC N-acetylnuraminic acid outer membrane channel protein
b1385 21 37 Spot42 55 71 -11.57 0.006193 0.9238006 feaB phenylacetaldehyde dehydrogenase
b4553 -64 -42 Spot42 53 74 -11.45 0.006633 0.9238006 ysaB uncharacterized protein
b4621 -48 -41 Spot42 1 8 -11.15 0.0078733 0.9238006 yjbS uncharacterized protein
b3685 -51 -36 Spot42 54 68 -11.08 0.0081942 0.9238006 yidE putative transporter
b1901 -37 -30 Spot42 1 8 -11.04 0.0083834 0.9238006 araF L-arabinose ABC transporter periplasmic binding protein
b1596 63 73 Spot42 56 66 -10.86 0.0092897 0.9238006 ynfM putative arabinose efflux transporter
b2659 -45 -24 Spot42 1 24 -10.83 0.0094499 0.9238006 csiD carbon starvation 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