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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) ED(Q) Energy p-value fdr gene annotation
b3084 -35 -25 RyhB 37 47 -13.75 0.0062866 0.9291058 rlmG 23S rRNA m(2)G1835 methyltransferase SAM-dependent
b3991 -75 -66 RyhB 40 49 -13.4 0.0076567 0.9291058 thiG thiamine biosynthesis ThiGH complex subunit
b2820 2 13 RyhB 37 48 -12.36 0.0135901 0.9496255 recB exonuclease V (RecBCD complex) beta subunit
b1224 -50 -41 RyhB 37 46 -12.19 0.0149008 0.9496255 narG nitrate reductase 1 alpha subunit
b2727 -7 4 RyhB 39 49 -12.05 0.0160688 0.9496255 hypB GTP hydrolase involved in nickel liganding into hydrogenases
b2007 -72 -61 RyhB 37 48 -11.62 0.0202189 0.9496255 yeeX UPF0265 family protein
b3645 -7 3 RyhB 40 49 -11.31 0.0238147 0.9496255 dinD DNA damage-inducible protein
b2550 -75 -66 RyhB 39 49 -11.07 0.0270016 0.9496255 yphH putative DNA-binding transcriptional regulator
b2799 -75 -65 RyhB 56 66 -13.09 0.0091019 0.9291058 fucO L-12-propanediol oxidoreductase
b4281 -9 2 RyhB 36 46 -10.82 0.0307429 0.9496255 yjhD pseudogene KpLE2 phage-like element
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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Results are computed with IntaRNA version 3.1.3 linking Vienna RNA package 2.4.14