Freiburg RNA Tools
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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
b2830 62 74 RyhB 44 56 -13.5 0.0072388 0.9291058 rppH RNA pyrophosphohydrolase
b3010 -68 -29 RyhB 38 86 -11.97 0.0167745 0.9496255 yqhC transcriptional activator of yqhD
b3032 -67 -43 RyhB 40 63 -10.86 0.0301134 0.9496255 cpdA 3'5' cAMP phosphodiesterase
b3080 -59 -34 RyhB 1 25 -14.07 0.0052402 0.9291058 ygjK alpha-glucosidase
b3084 -35 -25 RyhB 37 47 -13.75 0.0062866 0.9291058 rlmG 23S rRNA m(2)G1835 methyltransferase SAM-dependent
b3110 57 75 RyhB 44 62 -13.55 0.0070381 0.9291058 yhaO putative transporter
b3219 -10 11 RyhB 39 59 -12.48 0.0127312 0.9496255 yhcF putative transcriptional regulator
b3248 19 35 RyhB 18 35 -12.53 0.0123886 0.9496255 yhdE dTTP/UTP pyrophosphatase m(5)UTP/m(5)CTP/pseudo-UTP pyrophosphatase
b3311 -68 -41 RyhB 37 60 -11.34 0.0234421 0.9496255 rpsQ 30S ribosomal subunit protein S17
b3365 -9 12 RyhB 38 57 -10.98 0.0282964 0.9496255 nirB nitrite reductase large subunit NAD(P)H-binding
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