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
?CopraRNA 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: https://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

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
11 0.0001804 0.05681 stm0959 lrp -12.80 0.257711 163 -- 181 139 -- 159 leucine-responsive transcriptional regulator  
190 0.01053 0.1967 stm4032 N/A -12.98 0.242168 37 -- 92 31 -- 85 lipase stm0490
41 0.001426 0.1215 stm3718 rfaI -15.09 0.114319 193 -- 209 157 -- 173 lipopolysaccharide 1 3-galactosyltransferase stm3717
120 0.006002 0.1758 stm2925 nlpD -17.26 0.050371 258 -- 274 153 -- 170 lipoprotein NlpD  
130 0.00652 0.1774 stm4228 malF -14.47 0.143021 162 -- 175 1 -- 15 maltose ABC transporter permease MalF  
59 0.00232 0.14 stm4105 metF -16.51 0.066936 223 -- 245 40 -- 59 methylenetetrahydrofolate reductase [NAD(P)H]  
82 0.003783 0.1596 stm0710 ybgH -19.90 0.018103 103 -- 151 33 -- 90 MFS transporter  
136 0.006805 0.1774 stm2812 N/A -16.76 0.060981 84 -- 153 36 -- 90 MFS transporter  
168 0.009144 0.1938 stm3609 yhjE -18.08 0.036777 202 -- 261 35 -- 91 MFS transporter  
177 0.009665 0.1945 stm0079 yaaU -14.30 0.152587 187 -- 218 40 -- 79 MFS transporter  

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.

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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2