Freiburg RNA Tools
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IFF
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
?Processing 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:80/RetrieveResults.jsp?jobID=4627738&toolName=IntaRNA ( 30 days expiry )

The job description you specified

LhrA2 - Listeria monocytogenes


? Output download complete results [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) Query Start(Q) End(Q) Energy Seq(T) p-value fdr gene annotation
lmo0022 -2 42 LhrA2 160 208 -14.13 0.02415 0.9474659 PTS fructose transporter subunit IIB
lmo0066 -22 6 LhrA2 158 199 -14.3 0.0221203 0.9474659 toxin
lmo0200 -10 14 LhrA2 175 204 -14.21 0.0231743 0.9474659 prfA listeriolysin positive regulatory protein
lmo2282 -21 35 LhrA2 157 205 -15.26 0.0133252 0.8878302 protein gp21
lmo1517 -59 -32 LhrA2 172 198 -14 0.0258166 0.9474659 nitrogen regulatory PII protein
lmo0788 -23 -4 LhrA2 197 212 -14.54 0.0195222 0.9163749 lmo0788
lmo1258 24 74 LhrA2 157 207 -15.61 0.011025 0.863511 lmo1258
lmo0482 44 69 LhrA2 172 210 -15.99 0.008949 0.863511 ribosomal RNA large subunit methyltransferase N
lmo1454 -29 16 LhrA2 154 211 -14.13 0.02415 0.9474659 rpoD RNA polymerase sigma factor RpoD
lmo0131 -8 31 LhrA2 165 204 -15.78 0.0100463 0.863511
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