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: http://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
160 0.008331 0.1845 stm0002 thrA -15.10 0.113872 18 -- 81 44 -- 90 bifunctional aspartate kinase/homoserine dehydrogenase I  
43 0.001574 0.1267 stm4453 treC -17.28 0.050040 221 -- 269 37 -- 81 trehalose- 6-P hydrolase  
14 0.0002233 0.05681 stm3843 trmE -16.53 0.066478 207 -- 249 37 -- 85 tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE  
186 0.01044 0.1967 stm1725 trpC -12.00 0.335236 146 -- 174 55 -- 86 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase  
79 0.003723 0.1596 stm1723 trpE -16.56 0.065817 202 -- 256 41 -- 91 anthranilate synthase subunit I  
143 0.007336 0.182 stm2276 ubiG -14.65 0.134291 225 -- 278 36 -- 81 2-octaprenyl-6-hydroxy phenol methylase  
119 0.005831 0.1745 stm1998 umuD -19.31 0.022806 33 -- 72 46 -- 81 DNA polymerase V subunit UmuD  
57 0.002298 0.14 stm3921 wecC -19.39 0.022107 89 -- 132 46 -- 91 UDP-N-acetyl-D-mannosamine dehydrogenase  
153 0.008123 0.1845 stm2512 xseA -14.57 0.138273 215 -- 252 42 -- 82 exodeoxyribonuclease VII large subunit  
177 0.009665 0.1945 stm0079 yaaU -14.30 0.152587 187 -- 218 40 -- 79 MFS transporter  

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