Freiburg RNA Tools
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IntaRNA 4627738

Input and runtime details for job 4627738 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_003210
? 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 4627738 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:20:43 CET 2020
?IntaRNA Started@ Mon Jan 27 14:22:37 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:24:00 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:24:55 CET 2020
?Job Completed@ Mon Jan 27 14:25:04 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4627738&toolName=IntaRNA ( 30 days expiry )

Description of the job

LhrA2 - Listeria monocytogenes

? Output [zip]

Downloadable files

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


heatmap

? Identified Interactions for NC_003210 Listeria monocytogenes EGD-e

Sort by selecting a column name.
Target Start(T) End(T) End(seed-T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
lmo1584 -2 11 LhrA2 169 181 -15.55 0.0113911 0.863511
lmo2654 -5 11 LhrA2 167 184 -14.34 0.0216662 0.9474659 fus elongation factor G
lmo0022 -2 42 LhrA2 160 208 -14.13 0.02415 0.9474659 PTS fructose transporter subunit IIB
lmo2793 -2 47 LhrA2 115 174 -13.69 0.0302275 0.9493467 lmo2793
lmo2282 -21 35 LhrA2 157 205 -15.26 0.0133252 0.8878302 protein gp21
lmo1689 -16 16 LhrA2 157 186 -15.11 0.0144414 0.9011628 A/G-specific adenine glycosylase
lmo1401 -52 9 LhrA2 155 204 -13.43 0.0344502 0.9493467
lmo1883 -5 28 LhrA2 139 173 -25.95 9.7e-06 0.0277905 chitinase
lmo2308 -14 7 LhrA2 147 170 -16.63 0.0062544 0.863511 single-stranded DNA-binding protein
lmo1147 -65 10 LhrA2 158 211 -18.08 0.0026867 0.863511 cobalamin biosynthesis protein CopB
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