Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 7743500

Input and runtime details for job 7743500 (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 7743500 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:35:00 CET 2018
?CopraRNA Started@ Fri Feb 16 21:27:12 CET 2018
?CopraRNA Finished & Post-Processing@ Sat Feb 17 06:56:30 CET 2018
?Post-Processing Finished@ Sat Feb 17 06:56:38 CET 2018
?Job Completed@ Sat Feb 17 06:57:11 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7743500&toolName=CopraRNA ( 30 days expiry )

Description of the job

PrrF1

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_002516 Pseudomonas aeruginosa PAO1

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
68 0.0007335 0.0493 pa0794 N/A -9.72 0.203453 182 -- 194 107 -- 118 aconitate hydratase  
69 0.0007462 0.0493 pa0882 N/A -13.09 0.034380 240 -- 255 104 -- 119 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
70 0.0007568 0.0493 pa3767 N/A -16.77 0.002880 160 -- 178 98 -- 122 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
71 0.000767 0.0493 pa3381 N/A -11.39 0.089379 127 -- 140 103 -- 116 transcriptional regulator  
72 0.0007723 0.0493 pa2659 N/A -15.67 0.006436 157 -- 217 75 -- 121 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
73 0.0008061 0.04991 pa0112 N/A -16.64 0.003170 93 -- 149 38 -- 90 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
76 0.0008254 0.04991 pa0029 N/A -13.54 0.026240 35 -- 51 100 -- 123 sulfate transporter  
79 0.0008761 0.05078 pa2577 N/A -12.88 0.038908 242 -- 256 40 -- 55 transcriptional regulator  
85 0.001072 0.05733 pa4430 N/A -13.41 0.028331 184 -- 204 101 -- 120 cytochrome b  
86 0.001073 0.05733 pa0916 N/A -12.39 0.051807 188 -- 200 107 -- 119 ribosomal protein S12 methylthiotransferase RimO  

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