Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 6793193

Input and runtime details for job 6793193 (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 6793193 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:27:03 CET 2018
?CopraRNA Started@ Fri Feb 16 15:27:32 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 21:26:02 CET 2018
?Post-Processing Finished@ Fri Feb 16 21:26:10 CET 2018
?Job Completed@ Fri Feb 16 21:26:45 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
5 9.512e-06 0.006694 b4006 purH -17.40 0.004319 188 -- 204 31 -- 46 IMP cyclohydrolase and phosphoribosylaminoimidazolecarboxamide formyltransferase  
6 1.32e-05 0.00774 b0475 hemH -21.46 0.000115 123 -- 162 34 -- 75 ferrochelatase  
7 1.819e-05 0.009142 b1849 purT -22.68 0.000026 168 -- 199 33 -- 74 phosphoribosylglycinamide formyltransferase 2  
8 3.984e-05 0.01752 b2752 cysD -11.53 0.128779 103 -- 132 45 -- 74 sulfate adenylyltransferase subunit 2  
9 4.743e-05 0.01855 b1204 pth -17.38 0.004387 162 -- 190 43 -- 74 peptidyl-tRNA hydrolase  
10 6.564e-05 0.0231 b3458 livK -17.14 0.005196 153 -- 196 35 -- 71 leucine transporter subunit  
11 9.086e-05 0.0245 b3337 bfd -12.11 0.098410 247 -- 280 34 -- 76 bacterioferritin-associated ferredoxin  
12 9.939e-05 0.0245 b2308 hisQ -13.21 0.056865 186 -- 218 34 -- 75 histidine ABC transporter permease  
13 0.0001005 0.0245 b1921 fliZ -13.92 0.038869 246 -- 263 63 -- 78 RpoS antagonist; putative regulator of FliA activity  
14 0.0001025 0.0245 b4051 qorA -14.73 0.024599 192 -- 224 48 -- 76 quinone oxidoreductase NADPH-dependent  

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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Results are computed with CopraRNA version 2.1.2