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
15 0.000269 0.06194 stm3630 dppA -21.81 0.008578 158 -- 199 51 -- 92 ABC transporter substrate-binding protein  
133 0.006689 0.1774 stm0831 dps -13.05 0.236755 141 -- 176 159 -- 184 DNA starvation/stationary phase protection protein Dps  
46 0.001637 0.1267 stm2313 elaC -17.21 0.051329 250 -- 300 51 -- 90 ribonuclease Z stm1109
163 0.008532 0.1864 stm3093 endA -16.58 0.065141 135 -- 160 72 -- 101 deoxyribonuclease I  
84 0.003893 0.1596 stm2015 erfK -27.15 0.001054 109 -- 172 35 -- 90 L D-transpeptidase  
185 0.01043 0.1967 stm1700 fabI -13.03 0.238331 75 -- 107 38 -- 76 enoyl-[acyl-carrier-protein] reductase  
132 0.006673 0.1774 stm2677 ffh -17.54 0.045291 232 -- 275 38 -- 86 4.5S-RNP protein  
134 0.006725 0.1774 stm0546 fimD -17.45 0.046766 176 -- 200 37 -- 60 outer membrane usher protein stm0301 stm0175 stm4593 stm3638 stm0023
195 0.01085 0.197 stm0549 fimZ -13.17 0.226725 219 -- 235 155 -- 171 DNA-binding response regulator  
166 0.009028 0.1932 stm1173 flgA -14.00 0.169768 53 -- 102 33 -- 85 flagella basal body P-ring formation protein FlgA  

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