Freiburg RNA Tools
IntaRNA - Results
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IntaRNA 2080734

Input and runtime details for job 2080734 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_003210
? 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 2080734 (server version 4.4.2)

?Job Submitted & Queued@ Mon Mar 06 14:23:33 CET 2017
?Processing Started@ Mon Mar 06 14:23:37 CET 2017
?IntaRNA Finished & Post-Processing@ Mon Mar 06 16:12:02 CET 2017
?Post-Processing Finished@ Mon Mar 06 16:12:02 CET 2017
?Job Completed@ Mon Mar 06 16:12:04 CET 2017
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=2080734&toolName=IntaRNA ( 30 days expiry )

The job description you specified

LhrA2 - example

? Output download complete results [zip]

Downloadable files

[csv]
[txt]
[png] [pdf] [ps]
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[html] [pdf]


heatmap

? Identified Interactions for NC_003210 Listeria monocytogenes EGD-e

Sort by selecting a column name:
p-value fdr value Target Position Query Position Energy Gene Annotation
5.45e-05 0.15615 lmo1883 72 -- 103 LhrA2 139 -- 170 -26.66860   chitinase
0.0011717 0.85054 lmo1835 51 -- 103 LhrA2 154 -- 207 -21.89190 carB carbamoyl-phosphate synthetase
0.0012911 0.85054 lmo0851 63 -- 95 LhrA2 172 -- 201 -21.72400   lmo0851
0.0015538 0.85054 lmo1258 99 -- 150 LhrA2 156 -- 207 -21.40020   lmo1258
0.0015555 0.85054 lmo0397 53 -- 107 LhrA2 160 -- 211 -21.39820    
0.0033468 0.85054 lmo2078 63 -- 115 LhrA2 154 -- 207 -20.01370    
0.0036045 0.85054 lmo2286 51 -- 114 LhrA2 155 -- 211 -19.87570   protein gp17
0.0036906 0.85054 lmo0383 99 -- 146 LhrA2 147 -- 186 -19.83160   methylmalonate-semialdehyde dehydrogenase
0.003716 0.85054 lmo0233 113 -- 150 LhrA2 157 -- 198 -19.81880   DNA repair protein RadA
0.0041358 0.85054 lmo1572 41 -- 101 LhrA2 157 -- 229 -19.61800 accA acetyl-CoA carboxylase carboxyltransferase subunit alpha

Details of Selected Interaction Download Interaction Details

Target

Query

		

		

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Results are computed with IntaRNA version 2.0.1 (wrapper 1.1.2) linking Vienna RNA package 2.3.1