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
41 0.001426 0.1215 stm3718 rfaI -15.09 0.114319 193 -- 209 157 -- 173 lipopolysaccharide 1 3-galactosyltransferase stm3717
42 0.001433 0.1215 stm1318 katE -13.62 0.194137 191 -- 230 43 -- 82 catalase HPII  
43 0.001574 0.1267 stm4453 treC -17.28 0.050040 221 -- 269 37 -- 81 trehalose- 6-P hydrolase  
44 0.001631 0.1267 stm1318 katE -13.62 0.194137 191 -- 230 43 -- 82 catalase HPII  
45 0.001635 0.1267 stm2351 hisP -13.82 0.180688 258 -- 282 115 -- 140 histidine and lysine/arginine/ornithine transport protein  
46 0.001637 0.1267 stm2313 elaC -17.21 0.051329 250 -- 300 51 -- 90 ribonuclease Z stm1109
47 0.001676 0.127 stm0637 dacA -17.91 0.039191 14 -- 64 37 -- 92 serine-type D-Ala-D-Ala carboxypeptidase  
48 0.001762 0.1291 stm4523 yjiW -20.55 0.014078 157 -- 299 40 -- 186 endoribonuclease SymE  
49 0.001802 0.1291 stm1787 N/A -18.29 0.033902 137 -- 202 34 -- 90 [Ni/Fe] hydrogenase large subunit  
50 0.001812 0.1291 stm3207 ygiH -15.41 0.101358 70 -- 101 63 -- 93 acyl-phosphate--glycerol-3-phosphate O-acyltransferase  

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)

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Results are computed with CopraRNA version 2.1.2