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
1 0 0 b3752 rbsK -20.54 0.000534 137 -- 155 1 -- 21 ribokinase  
2 5.107e-11 8.961e-08 b2314 dedD -25.37 0.000001 176 -- 205 1 -- 30 membrane-anchored periplasmic protein involved in septation  
3 3.973e-07 0.0004647 b0081 mraZ -16.47 0.011640 172 -- 200 1 -- 32 RsmH methytransferase inhibitor  
4 1.99e-05 0.01653 b4255 rraB -17.36 0.006479 180 -- 205 1 -- 23 protein inhibitor of RNase E  
5 2.356e-05 0.01653 b1123 potD -19.53 0.001282 190 -- 207 9 -- 25 spermidine/putrescine ABC transporter periplasmic binding protein  
6 9.344e-05 0.05465 b2215 ompC -14.72 0.032428 133 -- 159 1 -- 28 outer membrane porin protein C b0929 b0241 b1377
7 0.0001218 0.05555 b1811 yoaH -21.30 0.000256 259 -- 293 1 -- 35 UPF0181 family protein  
8 0.0001267 0.05555 b2697 alaS -16.66 0.010303 247 -- 274 1 -- 35 alanyl-tRNA synthetase  
9 0.0002541 0.09908 b4000 hupA -15.77 0.017828 82 -- 110 1 -- 35 HU DNA-binding transcriptional regulator alpha subunit  
10 0.0003274 0.1087 b1020 phoH -9.93 0.281763 74 -- 85 48 -- 59 ATP-binding protein; putative PhoH family P-loop ATPase  

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