Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 6756176

Input and runtime details for job 6756176 (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 6756176 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:22:58 CET 2018
?Processing Started@ Fri Feb 16 15:23:17 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 20:01:55 CET 2018
?Post-Processing Finished@ Fri Feb 16 20:02:03 CET 2018
?Job Completed@ Fri Feb 16 20:02:30 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

The job description you specified

DsrA

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
1 4.307e-10 1.387e-06 b2741 rpoS -17.23 0.000044 75 -- 104 10 -- 40 RNA polymerase sigma S (sigma 38) factor  
2 4.936e-07 0.0007949 b1237 hns -13.24 0.001473 195 -- 222 26 -- 57 global DNA-binding transcriptional dual regulator H-NS  
3 4.385e-06 0.004708 b3749 rbsA -11.98 0.003917 29 -- 86 17 -- 57 D-ribose ABC transporter ATPase  
4 1.769e-05 0.01424 b2105 rcnR -7.88 0.065143 12 -- 26 36 -- 49 transcriptional repressor of rcnA  
5 2.271e-05 0.01463 b0476 aes -9.47 0.023317 2 -- 45 10 -- 53 acetyl esterase  
6 4.032e-05 0.02042 b0889 lrp -10.51 0.011361 210 -- 221 37 -- 48 leucine-responsive global transcriptional regulator  
7 4.438e-05 0.02042 b0794 ybhF -10.77 0.009494 150 -- 165 11 -- 26 putative ABC transporter ATPase  
8 5.642e-05 0.02272 b2282 nuoH -5.33 0.272754 189 -- 221 13 -- 44 NADH:ubiquinone oxidoreductase membrane subunit H  
9 7.531e-05 0.02695 b0491 fetB -11.86 0.004271 187 -- 209 25 -- 47 iron export ABC transporter permease; peroxide resistance protein  
10 0.0001005 0.03239 b1260 trpA -10.26 0.013526 184 -- 203 5 -- 22 tryptophan synthase alpha subunit  

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

		

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.

de.NBI usability assessment

Please support us by filling this short quality survey for evaluating this de.NBI service.

When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2