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
81 0.004478 0.1855 b3327 gspF -8.77 0.233220 243 -- 251 26 -- 34 general secretory pathway component cryptic  
82 0.004565 0.1855 b4144 yjeI -10.12 0.132253 163 -- 240 1 -- 93 DUF4156 family lipoprotein  
83 0.004611 0.1855 b1593 ynfK -13.15 0.034145 276 -- 295 66 -- 83 putative dethiobiotin synthetase  
84 0.004676 0.1855 b0526 cysS -14.43 0.019007 256 -- 269 64 -- 77 cysteinyl-tRNA synthetase  
85 0.004761 0.1855 b2077 iceT -11.46 0.073016 53 -- 74 64 -- 86 putative citrate/iron-citrate/zinc-citrate efflux transporter  
86 0.004777 0.1855 b3157 yhbT -11.83 0.061936 277 -- 294 70 -- 85 SCP-2 sterol transfer family protein  
87 0.004792 0.1855 b0476 aes -9.71 0.157345 34 -- 55 56 -- 76 acetyl esterase  
88 0.004799 0.1855 b2213 ada -9.32 0.185618 222 -- 245 63 -- 86 fused DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase  
89 0.004811 0.1855 b4336 yjiN -13.14 0.034257 120 -- 134 70 -- 84 zinc-type alcohol dehydrogenase-like protein  
90 0.004828 0.1855 b2149 mglA -7.32 0.409352 216 -- 239 61 -- 86 methyl-galactoside ABC transporter 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