Freiburg RNA Tools
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IntaRNA 4935127

Input and runtime details for job 4935127 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_003197
? 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 4935127 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:12:23 CET 2020
?IntaRNA Started@ Mon Jan 27 14:14:40 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:16:11 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:17:25 CET 2020
?Job Completed@ Mon Jan 27 14:17:35 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4935127&toolName=IntaRNA ( 30 days expiry )

Description of the job

GcvB - E. coli

? Output [zip]

Downloadable files

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


heatmap

? Identified Interactions for NC_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Sort by selecting a column name.
Target Start(T) End(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
PSLT042 2 70 GcvB 37 91 -14.17 0.0156913 0.7979576 putative integrase protein
STM0001 -71 -15 GcvB 141 186 -18.71 0.0006816 0.3847632 thrL thr operon leader peptide
STM0022 -74 -55 GcvB 127 147 -14.36 0.0140165 0.7904009 bcfB fimbrial chaperone protein
STM0069 -71 -52 GcvB 60 81 -14.87 0.0102821 0.7883581 caiE phenylacetic acid degradation protein PaaY
STM0085 63 75 GcvB 152 164 -14.92 0.009969 0.7883581 yabF glutathione-regulated potassium-efflux system ancillary protein KefF
STM0283 41 60 GcvB 152 169 -16.47 0.0036267 0.6975035
STM0330 -25 -8 GcvB 152 170 -14.16 0.0157842 0.7979576 3-isopropylmalate dehydratase small subunit
STM0369 2 69 GcvB 31 91 -18.82 0.0006231 0.3847632 prpC 2-methylcitrate synthase
STM0399 -32 12 GcvB 43 76 -15.64 0.006314 0.7419678 brnQ branched-chain amino acid transport system II carrier protein
STM0412 27 72 GcvB 35 73 -14.92 0.009969 0.7883581 putative inner membrane protein
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