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
12 0.0002098 0.05681 stm3344 rpsI -21.57 0.009451 131 -- 172 57 -- 102 30S ribosomal protein S9  
87 0.004009 0.1596 stm2067 sbcB -11.70 0.367652 220 -- 292 35 -- 90 exodeoxyribonuclease I  
28 0.0007333 0.08814 stm0376 sbmA -15.26 0.107034 68 -- 102 55 -- 90 peptide transporter  
93 0.004254 0.1596 stm0408 secF -18.22 0.034847 7 -- 64 39 -- 91 protein-export membrane protein SecF  
40 0.001409 0.1215 stm4578 serB -16.00 0.081343 27 -- 78 37 -- 87 phosphoserine phosphatase SerB  
69 0.003278 0.1596 stm3675 sgbH -16.55 0.065932 154 -- 200 33 -- 93 3-keto-L-gulonate-6-phosphate decarboxylase  
70 0.003306 0.1596 stm2688 smpB -12.25 0.308628 191 -- 230 36 -- 77 SsrA-binding protein  
135 0.006796 0.1774 stm1044 sodC -14.39 0.147293 208 -- 244 43 -- 78 Gifsy-2 prophage superoxide dismutase precursor (Cu-Zn) stm1440 stm0924
180 0.009911 0.1961 stm0199 stfF -15.44 0.100302 89 -- 133 44 -- 87 fimbrial protein  
64 0.003108 0.1596 stm4162 thiF -13.53 0.200092 247 -- 294 34 -- 76 molybdopterin/thiamine biosynthesis adenylyltransferase  

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