Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 5882223

Input and runtime details for job 5882223 (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 5882223 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:29:59 CET 2018
?CopraRNA Started@ Fri Feb 16 20:39:56 CET 2018
?CopraRNA Finished & Post-Processing@ Sat Feb 17 03:02:39 CET 2018
?Post-Processing Finished@ Sat Feb 17 03:02:47 CET 2018
?Job Completed@ Sat Feb 17 03:03:15 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

Output download complete results [zip]

Downloadable files

[csv]
[txt]
[csv]
[png] [pdf] [ps]
[png] [pdf] [ps]
[html] [pdf]
[png] [pdf]
[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
150 0.00611 0.1406 b0735 ybgE -10.35 0.035619 38 -- 71 5 -- 31 putative inner membrane protein in cydABX-ybgE operon  
47 0.0005047 0.03778 b1888 cheA -10.26 0.037926 179 -- 191 53 -- 66 fused chemotactic sensory histidine kinase in two-component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein  
117 0.003878 0.1165 b3078 ygjI -10.25 0.038289 174 -- 181 1 -- 8 putative transporter b0899
58 0.000878 0.0531 b2150 mglB -10.24 0.038484 153 -- 179 1 -- 24 methyl-galactoside transporter subunit  
158 0.00634 0.1412 b3598 yibI -10.19 0.039756 289 -- 298 49 -- 58 DUF3302 family inner membrane protein b3587
146 0.005604 0.1342 b1637 tyrS -10.18 0.040102 30 -- 71 2 -- 50 tyrosyl-tRNA synthetase  
86 0.002239 0.09158 b0434 yajG -10.16 0.040736 167 -- 223 4 -- 56 putative lipoprotein  
29 0.0002348 0.02849 b4015 aceA -10.12 0.041760 186 -- 214 1 -- 27 isocitrate lyase  
170 0.007042 0.1457 b3110 yhaO -10.02 0.044877 174 -- 180 1 -- 7 putative transporter  
5 1.055e-05 0.007422 b1287 yciW -9.98 0.045809 266 -- 289 4 -- 27 putative oxidoreductase  

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)

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.

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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2