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IntaRNA 8403881

Input and runtime details for job 8403881 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_000913
? All repliconsyes
? Extract sequences aroundstart codon
? nt upstream (1-300)75
? nt downstream (1-300)75
? Index first target position-75

Output Parameters

? Number of interactions per RNA pair1
? Suboptimal interaction overlap can overlap in query
? Max. interaction lengthnot provided
? Max. absolute energy of an interaction0
? Max. delta energy above mfe of an interaction100
? No lonely base pairsyes
? No GU at helix endsyes

Seed Parameters

? Min. number of basepairs in seed7
? Max. Number of mismatches in seed0
? Maximal energy0
? Minimal unpaired probability (per RNA)0
? Seed position (query)not provided
? Seed position (target)not provided
? Ignore seeds with GU base pairsno
? Ignore seeds with GU endsyes

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 8403881 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:15:25 CET 2020
?IntaRNA Started@ Mon Jan 27 14:18:18 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:19:13 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:20:45 CET 2020
?Job Completed@ Mon Jan 27 14:20:57 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8403881&toolName=IntaRNA ( 30 days expiry )

Description of the job

RyhB - E. coli

? Output [zip]

Downloadable files

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


heatmap

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

Sort by selecting a column name.
Target Start(T) End(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
b1683 8 33 RyhB 38 66 -21.41 4.71e-05 0.1636725 sufB component of SufBCD Fe-S cluster assembly scaffold
b0894 -38 -18 RyhB 43 62 -19.93 0.0001337 0.1837117 dmsA dimethyl sulfoxide reductase anaerobic subunit A
b3743 40 66 RyhB 34 60 -19.68 0.0001586 0.1837117 asnC transcriptional activator of asnA autorepressor
b4255 -63 -43 RyhB 39 59 -18.09 0.0004554 0.3956288 rraB protein inhibitor of RNase E
b2170 -33 -7 RyhB 2 24 -17.18 0.0008131 0.5651045 setB lactose/glucose efflux system
b4019 -10 7 RyhB 43 58 -16.82 0.001018 0.5895917 metH homocysteine-N5-methyltetrahydrofolate transmethylase B12-dependent
b1181 49 69 RyhB 37 60 -16.27 0.0014284 0.7090986 ycgN UPF0153 family cysteine cluster protein
b4348 -73 -53 RyhB 40 66 -15.87 0.0018209 0.7909534 hsdS specificity determinant for hsdM and hsdR
b3885 56 75 RyhB 41 62 -15.48 0.0023007 0.8637808 yihX alpha-D-glucose-1-phosphate phosphatase anomer-specific
b0313 54 75 RyhB 40 61 -15.35 0.0024857 0.8637808 betI choline-inducible betIBA-betT divergent operon transcriptional repressor
Rows: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 all

Details of Selected Interaction Download Interaction Details

Target

Query

		

		

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When using IntaRNA please cite :

Results are computed with IntaRNA version 3.1.3 linking Vienna RNA package 2.4.14