Freiburg RNA Tools
IntaRNA - Results
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IFF
IntaRNA 6234649

Input and runtime details for job 6234649 (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 6234649 (server version trunk)

?Job Submitted & Queued@ Sat Feb 17 12:30:33 CET 2018
?Processing Started@ Sat Feb 17 12:30:42 CET 2018
?IntaRNA Finished & Post-Processing@ Sat Feb 17 12:35:10 CET 2018
?Post-Processing Finished@ Sat Feb 17 12:35:10 CET 2018
?Job Completed@ Sat Feb 17 12:35:13 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=6234649&toolName=IntaRNA ( 30 days expiry )

The job description you specified

Yfr1 - example

? Output download complete results [zip]

Downloadable files

[csv]
[txt]
[png] [pdf] [ps]
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[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
0.0017789 0.31664 PMM1119 73 -- 82 Yfr1 22 -- 31 -11.27540 som porin
0.0107314 0.7503 PMM0417 5 -- 13 Yfr1 28 -- 36 -9.93274    
0.0234111 0.7503 PMM1634 80 -- 86 Yfr1 22 -- 28 -9.17196 gyrB DNA gyrase subunit B
0.0234416 0.7503 PMM0173 116 -- 131 Yfr1 25 -- 38 -9.17058    
0.0238093 0.7503 PMM0494 40 -- 48 Yfr1 22 -- 30 -9.15405 ppa inorganic pyrophosphatase
0.025291 0.7503 PMM1278 135 -- 145 Yfr1 28 -- 38 -9.08939   circadian phase modifier CpmA-like protein
0.0377503 0.85018 PMM1121 73 -- 81 Yfr1 23 -- 31 -8.63764 som porin
0.0412091 0.85018 PMM0384 28 -- 34 Yfr1 22 -- 28 -8.53318 spnII-interrupted-C  
0.043834 0.85018 PMM1021 87 -- 93 Yfr1 21 -- 27 -8.45832   pili assembly chaperone
0.0501507 0.85018 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 2.1.0 (wrapper 1.1.3) linking Vienna RNA package 2.4.3