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
PMM0017 23 29 Yfr1 29 35 -4.48 0.3721584 0.8754181 dnaJ molecular chaperone DnaJ
PMM0021 -74 -68 Yfr1 14 20 -6.53 0.141895 0.8751146 murB UDP-N-acetylenolpyruvoylglucosamine reductase
PMM0080 -65 -59 Yfr1 32 38 -4.75 0.3338823 0.8751146
PMM0120 28 40 Yfr1 22 33 -5.7 0.2179004 0.8751146 cell division inhibitor
PMM0131 37 43 Yfr1 23 29 -5.11 0.2863537 0.8751146 P-type ATPase transporter for copper
PMM0135 52 58 Yfr1 31 37 -4.27 0.403326 0.8909401 plsX glycerol-3-phosphate acyltransferase PlsX
PMM0137 -62 -51 Yfr1 24 36 -7.35 0.0882142 0.8607323 fabD malonyl CoA-ACP transacylase
PMM0173 41 68 Yfr1 20 38 -10.31 0.0097181 0.8607323
PMM0224 54 72 Yfr1 12 29 -6.64 0.13353 0.8751146 aroC chorismate synthase
PMM0229 -75 -67 Yfr1 22 31 -7.62 0.0745694 0.8607323 dfp p-pantothenate cysteine ligase and p-pantothenenoylcysteine decarboxylase
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