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]
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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
161 0.008343 0.1845 stm3321 yhbH -14.15 0.160801 194 -- 246 48 -- 88 ribosomal subunit interface protein  
162 0.00849 0.1864 stm4221 pgi -15.16 0.111294 249 -- 289 56 -- 88 glucose-6-phosphate isomerase  
163 0.008532 0.1864 stm3093 endA -16.58 0.065141 135 -- 160 72 -- 101 deoxyribonuclease I  
164 0.008796 0.191 stm2932 ygbE -13.54 0.199482 240 -- 279 44 -- 82 putative inner membrane protein  
165 0.008886 0.1918 stm0281 N/A -13.47 0.204933 267 -- 289 36 -- 56 type VI secretion system-associated protein  
166 0.009028 0.1932 stm1173 flgA -14.00 0.169768 53 -- 102 33 -- 85 flagella basal body P-ring formation protein FlgA  
167 0.009062 0.1932 stm2673 rplS -14.99 0.118272 119 -- 180 38 -- 88 50S ribosomal protein L19  
168 0.009144 0.1938 stm3609 yhjE -18.08 0.036777 202 -- 261 35 -- 91 MFS transporter  
169 0.009276 0.1945 stm0495 ybaK -13.73 0.186840 16 -- 30 44 -- 58 aminoacyl-tRNA deacylase  
170 0.009347 0.1945 stm0477 acrR -17.70 0.042454 229 -- 246 74 -- 91 DNA-binding transcriptional repressor AcrR  

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