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]
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[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
11 0.0001804 0.05681 stm0959 lrp -12.80 0.257711 163 -- 181 139 -- 159 leucine-responsive transcriptional regulator  
12 0.0002098 0.05681 stm3344 rpsI -21.57 0.009451 131 -- 172 57 -- 102 30S ribosomal protein S9  
13 0.0002148 0.05681 stm4275 acs -17.09 0.053801 176 -- 229 31 -- 87 acetate--CoA ligase  
14 0.0002233 0.05681 stm3843 trmE -16.53 0.066478 207 -- 249 37 -- 85 tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE  
15 0.000269 0.06194 stm3630 dppA -21.81 0.008578 158 -- 199 51 -- 92 ABC transporter substrate-binding protein  
16 0.0002876 0.06194 stm1378 pykF -16.63 0.064116 5 -- 66 31 -- 91 pyruvate kinase  
17 0.0003055 0.06194 stm2694 N/A -22.95 0.005498 261 -- 295 52 -- 90 Fels-2 prophage protein  
18 0.0003131 0.06194 stm0112 leuB -16.29 0.072835 153 -- 217 44 -- 93 3-isopropylmalate dehydrogenase  
19 0.0004167 0.0781 stm0475 acrB -19.12 0.024591 69 -- 114 139 -- 185 aminoglycoside/multidrug transporter permease  
20 0.0004512 0.08034 stm2384 aroC -21.00 0.011794 171 -- 223 39 -- 90 chorismate synthase  

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

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Feeds the job parameters to the input page to resubmit the job.

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Results are computed with CopraRNA version 2.1.2