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
171 0.004404 0.117 pa3327 N/A -14.55 0.013827 159 -- 238 39 -- 118 non-ribosomal peptide synthetase  
172 0.004404 0.117 pa3327 N/A -14.55 0.013827 159 -- 238 39 -- 118 non-ribosomal peptide synthetase  
173 0.004404 0.117 pa3327 N/A -14.55 0.013827 159 -- 238 39 -- 118 non-ribosomal peptide synthetase  
108 0.001802 0.07562 pa0365 N/A -14.54 0.013920 243 -- 252 101 -- 110 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
179 0.004617 0.1185 pa4812 fdnG -14.50 0.014314 180 -- 196 94 -- 109 formate dehydrogenase-O major subunit  
200 0.005522 0.1269 pa1052 N/A -14.49 0.014391 203 -- 224 103 -- 123 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
13 1.26e-05 0.004211 pa3276 N/A -14.47 0.014594 182 -- 242 38 -- 108 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
122 0.002226 0.08331 pa4286 N/A -14.46 0.014621 171 -- 194 98 -- 121 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
155 0.003654 0.1083 pa1551 N/A -14.46 0.014645 185 -- 205 100 -- 119 ferredoxin  
174 0.00444 0.1171 pa4756 carB -14.46 0.014655 252 -- 264 107 -- 119 carbamoyl phosphate synthase large subunit  

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

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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