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
?Processing 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:80/RetrieveResults.jsp?jobID=4935127&toolName=IntaRNA ( 30 days expiry )

The job description you specified

GcvB - E. coli


? Output download complete results [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
STM3909 -34 -14 GcvB 67 88 -21.24 6.85e-05 0.2036716 ilvC ketol-acid reductoisomerase
STM3630 -43 -2 GcvB 51 92 -20.93 9.35e-05 0.2036716 dppA ABC transporter substrate-binding protein
STM1107 4 61 GcvB 36 82 -20.55 0.0001353 0.2036716 hpaX 4-hydroxyphenylacetate permease
STM3251 -5 39 GcvB 45 87 -20.16 0.0001949 0.2200421 sugar kinase
STM4398 -30 6 GcvB 125 169 -19.27 0.000428 0.3847632 cycA D-serine/D-alanine/glycine transporter
STM0369 2 69 GcvB 31 91 -18.82 0.0006231 0.3847632 prpC 2-methylcitrate synthase
STM1953 -28 28 GcvB 31 87 -18.8 0.0006334 0.3847632 yedO D-cysteine desulfhydrase
STM0001 -71 -15 GcvB 141 186 -18.71 0.0006816 0.3847632 thrL thr operon leader peptide
STM3344 -70 -27 GcvB 48 102 -18.35 0.0009093 0.4343002 rpsI 30S ribosomal protein S9
STM1098 -69 -36 GcvB 62 90 -18.25 0.0009836 0.4343002 hpaC 4-hydroxyphenylacetate 3-monooxygenase reductase component
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