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]
[txt]
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[txt] [svg]


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
111 0.005938 0.1855 b0962 helD -11.18 0.082726 7 -- 19 71 -- 82 DNA helicase IV  
58 0.002925 0.1727 b0427 yajR -11.14 0.084219 218 -- 238 54 -- 78 putative transporter  
135 0.007679 0.1993 b0096 lpxC -11.14 0.084212 289 -- 298 76 -- 85 UDP-3-O-acyl N-acetylglucosamine deacetylase  
130 0.007275 0.1966 b1638 pdxH -11.04 0.087983 237 -- 249 47 -- 59 pyridoxine 5'-phosphate oxidase  
174 0.01024 0.2071 b0889 lrp -11.01 0.089440 79 -- 112 38 -- 78 leucine-responsive global transcriptional regulator  
28 0.001577 0.1727 b0598 cstA -11.00 0.089647 31 -- 48 28 -- 45 carbon starvation protein involved in peptide utilization; APC peptide transporter family protein  
5 5.466e-05 0.03849 b0713 ybgL -10.83 0.096857 234 -- 242 53 -- 61 UPF0271 family protein  
41 0.002142 0.1727 b2153 folE -10.82 0.097170 217 -- 276 53 -- 121 GTP cyclohydrolase I  
73 0.003782 0.1804 b3560 glyQ -10.80 0.098141 7 -- 31 51 -- 74 glycine tRNA synthetase alpha subunit  
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