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
101 0.005112 0.1728 stm0113 leuA -13.72 0.187230 187 -- 230 37 -- 84 2-isopropylmalate synthase  
102 0.005164 0.1728 stm0668 ybeY -18.23 0.034693 146 -- 193 37 -- 81 rRNA maturation RNase YbeY  
103 0.005167 0.1728 stm2670 aroF -17.31 0.049328 173 -- 242 25 -- 90 3-deoxy-7-phosphoheptulonate synthase  
104 0.005232 0.1728 stm0744 ybgC -16.85 0.058772 132 -- 175 54 -- 90 tol-pal system-associated acyl-CoA thioesterase  
105 0.005236 0.1728 stm4566 yjjI -12.28 0.305832 96 -- 137 40 -- 77 YjjI family glycine radical enzyme  
106 0.005253 0.1728 stm1172 flgM -15.84 0.086212 196 -- 254 36 -- 82 anti-sigma-28 factor FlgM  
107 0.00529 0.1728 stm0994 mukB -11.10 0.440174 5 -- 20 154 -- 167 cell division protein MukB  
108 0.005311 0.1728 stm2183 cdd -16.35 0.071230 31 -- 68 151 -- 187 cytidine deaminase  
109 0.005328 0.1728 stm3082 N/A -12.60 0.275269 106 -- 154 38 -- 90 galactonate oxidoreductase  
110 0.005337 0.1728 stm1920 cheW -12.58 0.277263 149 -- 192 51 -- 90 chemotaxis protein CheW  

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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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2