Freiburg RNA Tools
IntaRNA - Results
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IntaRNA 6338432

Input and runtime details for job 6338432 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_005072
? 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 6338432 (server version trunk)

?Job Submitted & Queued@ Tue Feb 21 13:08:01 CET 2017
?Processing Started@ Tue Feb 21 13:08:06 CET 2017
?IntaRNA Finished & Post-Processing@ Tue Feb 21 13:13:20 CET 2017
?Post-Processing Finished@ Tue Feb 21 13:13:21 CET 2017
?Job Completed@ Tue Feb 21 13:13:21 CET 2017
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=6338432&toolName=IntaRNA ( 30 days expiry )

The job description you specified

ncRNA-NCBI prediction

? Output download complete results [zip]

Downloadable files

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


heatmap

? Identified Interactions for NC_005072 Prochlorococcus marinus subsp. pastoris str. CCMP1986

Sort by selecting a column name:
p-value fdr value Target Position Query Position Energy Gene Annotation
0.0040176 0.87936 PMM1119 73 -- 82 Yfr1 22 -- 31 -11.27540 som porin
0.0129125 0.87936 PMM0417 5 -- 13 Yfr1 28 -- 36 -9.93274    
0.0140311 0.87936 PMM0173 116 -- 144 Yfr1 19 -- 38 -9.82893    
0.0232417 0.87936 PMM1634 80 -- 86 Yfr1 22 -- 28 -9.17196 gyrB DNA gyrase subunit B
0.0235522 0.87936 PMM0494 40 -- 48 Yfr1 22 -- 30 -9.15405 ppa inorganic pyrophosphatase
0.0247028 0.87936 PMM1278 135 -- 145 Yfr1 28 -- 38 -9.08939   circadian phase modifier CpmA-like protein
0.0341669 0.87936 PMM1121 73 -- 81 Yfr1 23 -- 31 -8.63764 som porin
0.0367485 0.87936 PMM0384 28 -- 34 Yfr1 22 -- 28 -8.53318 spnII-interrupted-C  
0.0386989 0.87936 PMM1021 87 -- 93 Yfr1 21 -- 27 -8.45832   pili assembly chaperone
0.0433681 0.87936 PMM1448 137 -- 143 Yfr1 21 -- 27 -8.29132    

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