Freiburg RNA Tools
IntaRNA - Results
BIF
IFF
IntaRNA 7119295

Input and runtime details for job 7119295 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_005072
? 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 7119295 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:23:26 CET 2020
?Processing Started@ Mon Jan 27 14:25:03 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:25:25 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:26:09 CET 2020
?Job Completed@ Mon Jan 27 14:26:17 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=7119295&toolName=IntaRNA ( 30 days expiry )

The job description you specified

Yfr1 - Prochlorococcus marinus


? Output download complete results [zip]

Downloadable files

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


heatmap

? Identified Interactions for NC_005072 Prochlorococcus marinus subsp. pastoris str. CCMP1986

Sort by selecting a column name
Target Start(T) End(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
PMM1405 68 75 Yfr1 12 19 -4.34 0.3928103 0.8909401
PMM0135 52 58 Yfr1 31 37 -4.27 0.403326 0.8909401 plsX glycerol-3-phosphate acyltransferase PlsX
PMM1647 17 23 Yfr1 14 20 -4.25 0.4063526 0.8909401 DNA polymerase III subunit delta
PMM0484 -13 -7 Yfr1 31 37 -4.22 0.4109104 0.8909401 xthA exodeoxyribonuclease III
PMM0913 -47 -41 Yfr1 14 20 -4.18 0.4170203 0.8909401 ABC transporter
PMM1264 38 44 Yfr1 32 38 -4.16 0.420089 0.8909401 ftsH3 cell division protein FtsH3
PMM1030 10 17 Yfr1 49 56 -4.09 0.4308989 0.8909401 ferric uptake regulator family protein
PMM1423 36 42 Yfr1 31 37 -4.08 0.4324518 0.8909401
PMM0951 69 75 Yfr1 31 37 -4.03 0.4402471 0.8909401 carA carbamoyl phosphate synthase small subunit
PMM1144 -58 -52 Yfr1 30 36 -4 0.4449483 0.8909401 hydrolase of the alpha/beta-hydrolase fold
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