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
141 0.008132 0.2031 b3412 bioH -10.51 0.111302 230 -- 255 56 -- 74 pimeloyl-ACP methyl ester carboxylesterase  
142 0.00825 0.2033 b3457 livH -8.25 0.287512 56 -- 64 3 -- 11 branched-chain amino acid ABC transporter permease  
143 0.008308 0.2033 b2049 cpsB -11.81 0.062535 184 -- 242 25 -- 78 mannose-1-phosphate guanyltransferase  
144 0.008344 0.2033 b3159 yhbV -10.12 0.132236 144 -- 228 15 -- 82 U32 peptidase family protein  
145 0.008374 0.2033 b0068 thiB -7.61 0.367750 229 -- 244 73 -- 87 thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein  
146 0.008611 0.2059 b3750 rbsC -8.88 0.223197 137 -- 159 56 -- 77 D-ribose ABC transporter permease  
147 0.008705 0.2059 b0071 leuD -8.42 0.269085 76 -- 114 1 -- 54 3-isopropylmalate dehydratase small subunit  
148 0.008708 0.2059 b1754 ynjB -13.35 0.031185 160 -- 171 50 -- 61 putative ABC transporter periplasmic binding protein  
149 0.008735 0.2059 b3088 alx -8.37 0.274530 278 -- 288 25 -- 35 putative membrane-bound redox modulator  
150 0.008837 0.2059 b0453 ybaY -11.57 0.069675 268 -- 294 71 -- 94 outer membrane lipoprotein  

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