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
PMM0285 -70 -64 Yfr1 22 28 -5.21 0.2739089 0.8751146 phr DNA photolyase
PMM0387 -68 -62 Yfr1 25 31 -5.21 0.2739089 0.8751146 aroD 3-dehydroquinate dehydratase
PMM1151 15 21 Yfr1 28 34 -5.12 0.285094 0.8751146 infA translation initiation factor IF-1
PMM0131 37 43 Yfr1 23 29 -5.11 0.2863537 0.8751146 P-type ATPase transporter for copper
PMM0487 67 73 Yfr1 32 38 -4.95 0.3069599 0.8751146
PMM0668 -30 -23 Yfr1 31 38 -4.94 0.3082757 0.8751146 16S ribosomal RNA methyltransferase RsmE
PMM1174 21 36 Yfr1 22 38 -4.93 0.3095948 0.8751146
PMM1485 49 58 Yfr1 28 38 -4.87 0.3175766 0.8751146 rpoB DNA-directed RNA polymerase subunit beta
PMM0396 -40 -34 Yfr1 21 27 -4.84 0.3216106 0.8751146 proC Delta 1-pyrroline-5-carboxylate reductase
PMM0483 68 74 Yfr1 20 26 -4.77 0.3311335 0.8751146 hemL glutamate-1-semialdehyde aminotransferase
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