Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 3202356

Input and runtime details for job 3202356 (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 3202356 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:24:02 CET 2018
?Processing Started@ Fri Feb 16 15:24:35 CET 2018
?CopraRNA Finished & Post-Processing@ Sat Feb 17 02:03:47 CET 2018
?Post-Processing Finished@ Sat Feb 17 02:03:55 CET 2018
?Job Completed@ Sat Feb 17 02:04:28 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

The job description you specified

GcvB


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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
78 0.003685 0.1596 stm0423 ispA -20.49 0.014403 269 -- 289 38 -- 58 (2E 6E)-farnesyl diphosphate synthase  
152 0.008087 0.1845 stm0213 dapD -12.65 0.271269 222 -- 289 49 -- 104 2 3 4 5-tetrahydropyridine-2 6-dicarboxylate N-succinyltransferase  
101 0.005112 0.1728 stm0113 leuA -13.72 0.187230 187 -- 230 37 -- 84 2-isopropylmalate synthase  
8 9.263e-05 0.04123 stm0369 prpC -29.42 0.000431 202 -- 269 31 -- 91 2-methylcitrate synthase  
143 0.007336 0.182 stm2276 ubiG -14.65 0.134291 225 -- 278 36 -- 81 2-octaprenyl-6-hydroxy phenol methylase  
139 0.007115 0.182 stm0826 ybiN -18.61 0.029895 232 -- 282 36 -- 90 23S rRNA (adenine(1618)-N(6))-methyltransferase  
89 0.004143 0.1596 stm2957 ygcA -15.40 0.101796 159 -- 208 35 -- 82 23S rRNA (uracil(1939)-C(5))-methyltransferase  
116 0.005629 0.1728 stm2662 rluD -17.46 0.046576 204 -- 257 36 -- 86 23S rRNA pseudouridine(1911/1915/1917) synthase  
103 0.005167 0.1728 stm2670 aroF -17.31 0.049328 173 -- 242 25 -- 90 3-deoxy-7-phosphoheptulonate synthase  
18 0.0003131 0.06194 stm0112 leuB -16.29 0.072835 153 -- 217 44 -- 93 3-isopropylmalate dehydrogenase  

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