Freiburg RNA Tools
IntaRNA - Results
BIF
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) End(seed-T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
lmo2251 -12 5 LhrA2 149 165 -13.92 0.0268942 0.9474659 amino acid ABC transporter ATP-binding protein
lmo0835 -20 29 LhrA2 146 186 -18.17 0.0025454 0.863511 peptidoglycan binding protein
lmo1666 -46 7 LhrA2 157 204 -16.3 0.0075316 0.863511 peptidoglycan-linked protein
lmo2759 -28 4 LhrA2 141 173 -14.73 0.0176689 0.9128702
lmo2765 -13 18 LhrA2 155 199 -15.86 0.0096143 0.863511 PTS cellbiose transporter subunit IIA
lmo2446 -22 16 LhrA2 154 187 -17.3 0.0042577 0.863511 glycosidase
lmo0066 -22 6 LhrA2 158 199 -14.3 0.0221203 0.9474659 toxin
lmo2566 -22 16 LhrA2 155 186 -14.16 0.0237797 0.9474659 lmo2566
lmo1246 -20 5 LhrA2 184 206 -13.51 0.0330966 0.9493467 ATP-dependent RNA helicase
lmo0057 -22 7 LhrA2 157 181 -16.2 0.0079642 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

		

		

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:
Feeds the job parameters to the input page to resubmit the job.

de.NBI usability assessment

Please support us by filling this short quality survey for evaluating this de.NBI service.

When using IntaRNA please cite :

Results are computed with IntaRNA version 3.1.3 linking Vienna RNA package 2.4.14