Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 5344133

Input and runtime details for job 5344133 (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 5344133 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:28:43 CET 2018
?CopraRNA Started@ Fri Feb 16 20:36:11 CET 2018
?CopraRNA Finished & Post-Processing@ Sat Feb 17 02:15:51 CET 2018
?Post-Processing Finished@ Sat Feb 17 02:15:58 CET 2018
?Job Completed@ Sat Feb 17 02:16:29 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
103 0.006657 0.2268 b3617 kbl -13.19 0.071337 258 -- 276 7 -- 25 glycine C-acetyltransferase  
177 0.01288 0.2504 b3455 livG -10.61 0.218983 178 -- 198 5 -- 24 branched-chain amino acid ABC transporter ATPase  
48 0.002302 0.1648 b3460 livJ -15.11 0.026091 183 -- 229 1 -- 30 branched-chain amino acid ABC transporter periplasmic binding protein  
30 0.001442 0.1635 b3458 livK -12.84 0.084462 180 -- 215 6 -- 33 leucine transporter subunit  
69 0.003755 0.191 b0889 lrp -14.02 0.046951 165 -- 212 1 -- 32 leucine-responsive global transcriptional regulator  
196 0.01416 0.2529 b0870 ltaE -12.27 0.109556 23 -- 39 7 -- 23 L-allo-threonine aldolase PLP-dependent  
115 0.007886 0.2401 b2890 lysS -11.64 0.144658 161 -- 186 1 -- 20 lysine tRNA synthetase constitutive b4129
28 0.001242 0.1512 b0879 macB -8.34 0.466885 135 -- 159 1 -- 22 macrolide ABC transporter peremase/ATPase  
105 0.007004 0.2333 b4034 malE -12.62 0.093531 92 -- 123 2 -- 32 maltose transporter subunit  
127 0.009277 0.2491 b2781 mazG -12.70 0.090074 53 -- 69 8 -- 24 nucleoside triphosphate pyrophosphohydrolase  

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