Freiburg RNA Tools
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IntaRNA 9449895

Input and runtime details for job 9449895 (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 9449895 (server version trunk)

?Job Submitted & Queued@ Wed Sep 27 16:44:55 CEST 2017
?Processing Started@ Wed Sep 27 16:45:06 CEST 2017
?IntaRNA Finished & Post-Processing@ Wed Sep 27 17:16:57 CEST 2017
?Post-Processing Finished@ Wed Sep 27 17:16:57 CEST 2017
?Job Completed@ Wed Sep 27 17:17:01 CEST 2017
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=9449895&toolName=IntaRNA ( 30 days expiry )

The job description you specified

ChiX - 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
0.0003068 0.86698 b1737 9 -- 27 ChiX 38 -- 56 -19.20380 chbC NN'-diacetylchitobiose-specific enzyme IIC component of PTS
0.001143 0.86698 b0619 39 -- 50 ChiX 46 -- 57 -16.11310 citA sensory histidine kinase in two-component regulatory system with CitB
0.0013067 0.86698 b0681 57 -- 68 ChiX 45 -- 56 -15.80670 chiP chitoporin uptake of chitosugars
0.0044362 0.86698 b1363 2 -- 18 ChiX 35 -- 51 -13.07290 trkG Rac prophage potassium transporter subunit
0.0054332 0.86698 b1561 112 -- 148 ChiX 44 -- 82 -12.63050 rem Qin prophage uncharacterized protein
0.0054975 0.86698 b0847 99 -- 128 ChiX 26 -- 55 -12.60490 ybjL putative transporter
0.0058555 0.86698 b3133 60 -- 69 ChiX 44 -- 53 -12.46790 agaV N-acetylgalactosamine-specific enzyme IIB component of PTS
0.0061629 0.86698 b4199 59 -- 70 ChiX 46 -- 57 -12.35700 yjfY YhcN family protein periplasmic
0.0072594 0.86698 b2688 129 -- 139 ChiX 45 -- 55 -12.00330 gshA glutamate-cysteine ligase
0.0072881 0.86698 b0549 64 -- 74 ChiX 43 -- 53 -11.99480 ybcO DLP12 prophage uncharacterized protein

Details of Selected Interaction Download Interaction Details

Target

Query

		

		

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Results are computed with IntaRNA version 2.0.5 (wrapper 1.1.2) linking Vienna RNA package 2.3.1