Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 1786318

Input and runtime details for job 1786318 (precomputed example)

Sequence input

? sRNA sequences[.fa]
? Putative target sequences (organism of interest)[.fa]
? Extract sequences aroundstart codon
? nt up (1-300)200
? nt down (1-300)100

CopraRNA parameters

? Consensus prediction off
? p-value combinationno
? p-value filtering (0=off)0

IntaRNA parameters

? Target folding window size150
? Target max. basepair distance100

Job ID 1786318 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:20:27 CET 2018
?Processing Started@ Fri Feb 16 15:20:56 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 22:01:46 CET 2018
?Post-Processing Finished@ Fri Feb 16 22:01:53 CET 2018
?Job Completed@ Fri Feb 16 22:02:22 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

The job description you specified

ArcZ


Output download complete results [zip]

Downloadable files

[csv]
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heatmap

? Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Sort by selecting a column name:
Rank CopraRNA p-value CopraRNA fdr value Locus Tag Gene Name Energy [kcal/mol] IntaRNA p-value Position mRNA Position sRNA Annotation Additional homologs
1 0 0 b3209 elbB -118.30 0.000000 1 -- 83 1 -- 83 isoprenoid biosynthesis protein with amidotransferase-like domain  
20 0.001165 0.1727 b1763 topB -8.06 0.310309 3 -- 10 34 -- 41 DNA topoisomerase III  
18 0.001002 0.1727 b2284 nuoF -9.91 0.144715 4 -- 28 1 -- 36 NADH:ubiquinone oxidoreductase chain F  
3 3.071e-06 0.003055 b2100 yegV -9.35 0.183884 5 -- 14 51 -- 60 putative kinase  
184 0.01102 0.2089 b1033 ghrA -10.56 0.108938 6 -- 15 64 -- 73 glyoxylate/hydroxypyruvate reductase A  
73 0.003782 0.1804 b3560 glyQ -10.80 0.098141 7 -- 31 51 -- 74 glycine tRNA synthetase alpha subunit  
111 0.005938 0.1855 b0962 helD -11.18 0.082726 7 -- 19 71 -- 82 DNA helicase IV  
52 0.002619 0.1727 b2720 hycF -12.75 0.040951 8 -- 55 44 -- 94 formate hydrogenlyase complex iron-sulfur protein  
93 0.005014 0.1855 b0091 murC -15.25 0.013117 8 -- 30 73 -- 94 UDP-N-acetylmuramate:L-alanine ligase  
100 0.00547 0.1855 b2451 eutA -10.77 0.099200 8 -- 32 56 -- 86 reactivating factor for ethanolamine ammonia lyase  

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

		

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2