Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 1786318

Input and runtime details for job 1786318 (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 1786318 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:20:27 CET 2018
?Processing Started@ Fri Feb 16 15:20:56 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 22:01:46 CET 2018
?Post-Processing Finished@ Fri Feb 16 22:01:53 CET 2018
?Job Completed@ Fri Feb 16 22:02:22 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

The job description you specified

ArcZ


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
181 0.0108 0.2089 b1683 sufB -11.33 0.077347 153 -- 175 52 -- 74 component of SufBCD Fe-S cluster assembly scaffold  
182 0.01083 0.2089 b0314 betT -9.44 0.176432 217 -- 228 66 -- 77 choline transporter of high affinity  
183 0.011 0.2089 b0906 ycaP -11.77 0.063722 48 -- 74 48 -- 75 UPF0702 family putative inner membrane protein  
184 0.01102 0.2089 b1033 ghrA -10.56 0.108938 6 -- 15 64 -- 73 glyoxylate/hydroxypyruvate reductase A  
185 0.01108 0.2089 b0662 ubiF -8.33 0.279302 272 -- 292 6 -- 27 2-octaprenyl-3-methyl-6-methoxy-1 4-benzoquinol oxygenase  
186 0.01109 0.2089 b3234 degQ -11.96 0.058310 267 -- 277 3 -- 13 serine endoprotease periplasmic  
187 0.01114 0.2089 b0801 ybiC -12.72 0.041489 266 -- 279 27 -- 40 putative dehydrogenase b0517
188 0.01115 0.2089 b4377 yjjU -9.16 0.198952 213 -- 243 51 -- 77 putative patatin-like family phospholipase  
189 0.01136 0.2116 b3413 gntX -9.78 0.152759 211 -- 235 52 -- 76 DNA catabolic protein  
190 0.01143 0.2119 b3233 yhcB -11.72 0.064941 161 -- 178 66 -- 81 DUF1043 family inner membrane-anchored protein  

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.

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