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
111 0.005436 0.1728 stm2683 yfjB -15.36 0.103307 255 -- 299 43 -- 90 NAD(+) kinase  
112 0.005549 0.1728 stm0602 ybdH -14.01 0.169356 159 -- 193 39 -- 79 oxidoreductase  
113 0.005549 0.1728 stm2948 cysJ -13.61 0.194760 269 -- 298 56 -- 85 sulfite reductase [NADPH] flavoprotein subunit alpha  
114 0.005594 0.1728 stm4557 holD -13.75 0.185681 35 -- 94 141 -- 186 DNA polymerase III subunit psi  
115 0.005604 0.1728 stm0982 himD -16.93 0.057154 154 -- 192 37 -- 75 integration host factor subunit beta  
116 0.005629 0.1728 stm2662 rluD -17.46 0.046576 204 -- 257 36 -- 86 23S rRNA pseudouridine(1911/1915/1917) synthase  
117 0.005749 0.1738 stm2562 yfhA -19.31 0.022783 16 -- 66 47 -- 100 two-component system response regulator GlrR  
118 0.005761 0.1738 stm1840 yobG -17.14 0.052758 234 -- 267 153 -- 188 PhoP regulon feedback inhibition protein MgrB  
119 0.005831 0.1745 stm1998 umuD -19.31 0.022806 33 -- 72 46 -- 81 DNA polymerase V subunit UmuD  
120 0.006002 0.1758 stm2925 nlpD -17.26 0.050371 258 -- 274 153 -- 170 lipoprotein NlpD  

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