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
151 0.00796 0.1845 stm2365 folC -10.71 0.491716 269 -- 300 50 -- 78 bifunctional tetrahydrofolate synthase/dihydrofolate synthase  
124 0.006123 0.1758 stm0794 bioB -18.46 0.031660 1 -- 37 38 -- 79 biotin synthase  
121 0.006021 0.1758 stm3903 ilvE -13.34 0.214101 130 -- 170 39 -- 78 branched chain amino acid aminotransferase  
63 0.003024 0.1596 stm3563 livH -16.49 0.067433 27 -- 175 36 -- 184 branched-chain amino acid ABC transporter permease LivH  
5 6.363e-05 0.04123 stm0399 brnQ -24.27 0.003272 169 -- 224 36 -- 81 branched-chain amino acid transport system II carrier protein  
42 0.001433 0.1215 stm1318 katE -13.62 0.194137 191 -- 230 43 -- 82 catalase HPII  
44 0.001631 0.1267 stm1318 katE -13.62 0.194137 191 -- 230 43 -- 82 catalase HPII  
60 0.002585 0.1534 stm0758 ybgR -11.90 0.345594 235 -- 293 32 -- 91 cation transporter  
80 0.003756 0.1596 stm0132 ftsA -17.45 0.046754 189 -- 236 139 -- 186 cell division protein FtsA  
81 0.003764 0.1596 stm0121 ftsL -18.45 0.031843 91 -- 225 48 -- 186 cell division protein FtsL  

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