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
1 0 0 pa3775 N/A -6.65 0.627514 32 -- 38 50 -- 56 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
2 9.847e-10 2.263e-06 pa5490 cc4 -23.49 0.000003 181 -- 254 56 -- 120 cytochrome C4  
3 1.464e-07 0.0002243 pa3814 iscS -11.38 0.090161 182 -- 237 39 -- 110 cysteine desulfurase  
4 5.154e-07 0.0005922 pa1581 sdhC -15.05 0.009907 206 -- 221 108 -- 123 succinate dehydrogenase subunit C  
5 7.253e-07 0.0006667 pa5351 rubA1 -17.51 0.001615 172 -- 222 71 -- 121 rubredoxin  
6 4.972e-06 0.003808 pa1336 N/A -12.31 0.054230 242 -- 253 107 -- 120 two-component sensor  
7 9.272e-06 0.004211 pa1571 N/A -18.24 0.000884 168 -- 194 96 -- 121 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
8 1.007e-05 0.004211 pa3621 fdxA -18.47 0.000724 244 -- 255 71 -- 82 ferredoxin I  
9 1.098e-05 0.004211 pa0119 N/A -18.72 0.000584 256 -- 296 78 -- 118 C4-dicarboxylate transporter DctA pa5479 pa1183
10 1.1e-05 0.004211 pa5300 cycB -16.80 0.002828 155 -- 174 99 -- 117 cytochrome C5  

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