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
181 0.01001 0.1966 stm2266 apbE -12.19 0.314808 267 -- 297 62 -- 90 FAD:protein FMN transferase ApbE  
182 0.01014 0.1966 stm3011 galR -12.96 0.243649 22 -- 54 60 -- 90 transcriptional regulator GalR  
183 0.01015 0.1966 stm0813 ybhP -18.40 0.032407 2 -- 54 36 -- 90 similar to E. coli orf hypothetical protein (AAC73877.1); Blastp hit to AAC73877.1 (253 aa) 86% identity in aa 1 - 253  
184 0.01016 0.1966 stm1690 pspA -15.34 0.103900 116 -- 183 38 -- 113 phage shock protein PspA  
185 0.01043 0.1967 stm1700 fabI -13.03 0.238331 75 -- 107 38 -- 76 enoyl-[acyl-carrier-protein] reductase  
186 0.01044 0.1967 stm1725 trpC -12.00 0.335236 146 -- 174 55 -- 86 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase  
187 0.01045 0.1967 stm4558 rimI -18.19 0.035171 194 -- 252 42 -- 91 ribosomal-protein-alanine N-acetyltransferase  
188 0.01049 0.1967 stm0290 N/A -13.50 0.202376 129 -- 157 48 -- 69    
189 0.01049 0.1967 stm0871 ybjM -13.57 0.197684 34 -- 53 71 -- 89 similar to E. coli orf hypothetical protein (AAC73935.1); Blastp hit to AAC73935.1 (125 aa) 72% identity in aa 1 - 125  
190 0.01053 0.1967 stm4032 N/A -12.98 0.242168 37 -- 92 31 -- 85 lipase stm0490

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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Results are computed with CopraRNA version 2.1.2