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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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
121 0.006021 0.1758 stm3903 ilvE -13.34 0.214101 130 -- 170 39 -- 78 branched chain amino acid aminotransferase  
122 0.00604 0.1758 stm2353 hisQ -14.65 0.134227 190 -- 212 140 -- 163 amino acid ABC transporter permease  
123 0.006073 0.1758 stm4355 yjeS -17.69 0.042665 80 -- 140 31 -- 90 putative Fe-S protein  
124 0.006123 0.1758 stm0794 bioB -18.46 0.031660 1 -- 37 38 -- 79 biotin synthase  
125 0.006333 0.1774 stm3094 yggJ -12.37 0.297521 35 -- 55 69 -- 89 putative cytoplasmic protein  
126 0.006333 0.1774 stm1584 ansP -14.21 0.157463 122 -- 184 36 -- 93 amino acid permease  
127 0.006343 0.1774 stm1751 hns -12.42 0.292757 1 -- 14 147 -- 162 transcriptional regulator  
128 0.006467 0.1774 stm3907 N/A -18.55 0.030594 118 -- 173 37 -- 89    
129 0.006472 0.1774 stm0158 acnB -11.80 0.356459 140 -- 172 33 -- 60 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase  
130 0.00652 0.1774 stm4228 malF -14.47 0.143021 162 -- 175 1 -- 15 maltose ABC transporter permease MalF  

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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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2