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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 geneID annotation
PMM0933 32 38 Yfr1 32 38 -5.33 0.2594242 0.8751146 ksgA dimethyladenosine transferase
PMM1466 60 73 Yfr1 21 33 -6.56 0.1395757 0.8751146 fumC fumarate hydratase
PMM1538 29 35 Yfr1 25 31 -7.18 0.0977678 0.8607323 rpmJ 50S ribosomal protein L36
PMM0303 -70 -64 Yfr1 30 36 -4.75 0.3338823 0.8751146 tRNA nucleotidyltransferase/poly(A) polymerase
PMM0137 -62 -51 Yfr1 24 36 -7.35 0.0882142 0.8607323 fabD malonyl CoA-ACP transacylase
PMM0396 -40 -34 Yfr1 21 27 -4.84 0.3216106 0.8751146 proC Delta 1-pyrroline-5-carboxylate reductase
PMM0487 67 73 Yfr1 32 38 -4.95 0.3069599 0.8751146
PMM1430 68 74 Yfr1 29 35 -4.71 0.3394167 0.8751146
PMM1443 61 75 Yfr1 19 31 -5.46 0.2442923 0.8751146
PMM1604 -72 -66 Yfr1 21 27 -6.15 0.1738046 0.8751146
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

		

		

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