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
3 3.698e-05 0.04123 stm4398 cycA -21.36 0.010235 127 -- 178 38 -- 82 D-serine/D-alanine/glycine transporter  
36 0.00125 0.1215 stm3523 glpR -16.55 0.065942 207 -- 266 37 -- 89 DeoR/GlpR family transcriptional regulator  
163 0.008532 0.1864 stm3093 endA -16.58 0.065141 135 -- 160 72 -- 101 deoxyribonuclease I  
196 0.01089 0.197 stm3904 ilvD -14.14 0.161583 237 -- 253 179 -- 194 dihydroxy-acid dehydratase  
66 0.003179 0.1596 stm0264 dnaQ -14.69 0.132400 209 -- 271 35 -- 91 DNA polymerase III epsilon subunit  
114 0.005594 0.1728 stm4557 holD -13.75 0.185681 35 -- 94 141 -- 186 DNA polymerase III subunit psi  
53 0.002045 0.1363 stm1876 holE -16.46 0.068295 21 -- 75 31 -- 90 DNA polymerase III subunit theta  
119 0.005831 0.1745 stm1998 umuD -19.31 0.022806 33 -- 72 46 -- 81 DNA polymerase V subunit UmuD  
56 0.002144 0.1363 pslt006 repA -15.36 0.103288 219 -- 279 36 -- 87 DNA replication  
133 0.006689 0.1774 stm0831 dps -13.05 0.236755 141 -- 176 159 -- 184 DNA starvation/stationary phase protection protein Dps  

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