Freiburg RNA Tools
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IntaRNA 7069096

Input and runtime details for job 7069096 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_000913
? All repliconsyes
? Extract sequences aroundstart codon
? nt up (1-300)75
? nt down (1-300)75

Output Parameters

? Number of (sub)optimal interactions1
? Suboptimal interaction overlap can overlap in query
? Max. absolute energy of an interaction0
? Max. delta energy above mfe of an interaction100

Seed Parameters

? Min. number of basepairs in seed7
? Max. Number of mismatches in seed0
? Maximal energy0
? Minimal unpaired probability (each)0
? Seed position (query)not provided
? Seed position (target)not provided

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 7069096 (server version trunk)

?Job Submitted & Queued@ Sat Feb 17 12:29:12 CET 2018
?Processing Started@ Sat Feb 17 12:29:27 CET 2018
?IntaRNA Finished & Post-Processing@ Sat Feb 17 13:16:27 CET 2018
?Post-Processing Finished@ Sat Feb 17 13:16:27 CET 2018
?Job Completed@ Sat Feb 17 13:16:31 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=7069096&toolName=IntaRNA ( 30 days expiry )

The job description you specified

Spot42 - example

? Output download complete results [zip]

Downloadable files

[csv]
[txt]
[png] [pdf] [ps]
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heatmap

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

Sort by selecting a column name:
p-value fdr value Target Position Query Position Energy Gene Annotation
7.41e-05 0.28728 b3224 15 -- 26 Spot42 1 -- 12 -16.32220 nanT sialic acid transporter
0.0009946 0.89934 b1398 66 -- 74 Spot42 1 -- 9 -13.15580 paaK phenylacetyl-CoA ligase
0.0010176 0.89934 b1927 26 -- 37 Spot42 48 -- 59 -13.12620 amyA cytoplasmic alpha-amylase
0.0010588 0.89934 b1212 90 -- 103 Spot42 43 -- 56 -13.07480 prmC RF-1 and RF-2 N5-glutamine methyltransferase
0.0012808 0.89934 b2801 37 -- 47 Spot42 46 -- 56 -12.82700 fucP L-fucose transporter
0.0027795 0.89934 b0973 142 -- 150 Spot42 48 -- 56 -11.79560 hyaB hydrogenase 1 large subunit
0.0032453 0.89934 b4311 49 -- 60 Spot42 1 -- 12 -11.58490 nanC N-acetylnuraminic acid outer membrane channel protein
0.0035539 0.89934 b4174 1 -- 15 Spot42 42 -- 57 -11.46060 hflK modulator for HflB protease specific for phage lambda cII repressor
0.0039351 0.89934 b1302 41 -- 57 Spot42 43 -- 57 -11.32060 puuE 4-aminobutyrate aminotransferase PLP-dependent
0.0044494 0.89934 b4621 28 -- 35 Spot42 1 -- 8 -11.15090 yjbS uncharacterized protein

Details of Selected Interaction Download Interaction Details

Target

Query

		

		

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Results are computed with IntaRNA version 2.1.0 (wrapper 1.1.3) linking Vienna RNA package 2.4.3