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) Query Start(Q) End(Q) Energy p-value fdr gene annotation
lmo1883 -5 28 LhrA2 139 173 -25.95 9.7e-06 0.0277905 chitinase
lmo1187 -62 -29 LhrA2 153 183 -19.53 0.0010984 0.863511 ethanolamine utilization protein EutQ
lmo1835 -25 28 LhrA2 154 207 -18.61 0.0019491 0.863511 carB carbamoyl-phosphate synthetase
lmo0397 -23 37 LhrA2 160 211 -18.55 0.0020219 0.863511
lmo0383 24 64 LhrA2 151 186 -18.44 0.002162 0.863511 methylmalonate-semialdehyde dehydrogenase
lmo2074 -69 -43 LhrA2 147 173 -18.23 0.0024551 0.863511
lmo0835 -20 29 LhrA2 146 186 -18.17 0.0025454 0.863511 peptidoglycan binding protein
lmo1147 -65 10 LhrA2 158 211 -18.08 0.0026867 0.863511 cobalamin biosynthesis protein CopB
lmo0851 -12 20 LhrA2 172 200 -17.88 0.0030274 0.863511 lmo0851
lmo2446 -22 16 LhrA2 154 187 -17.3 0.0042577 0.863511 glycosidase
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