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
76 0.003538 0.1596 stm3058 pepP -14.75 0.129287 129 -- 167 36 -- 78 Xaa-Pro aminopeptidase  
66 0.003179 0.1596 stm0264 dnaQ -14.69 0.132400 209 -- 271 35 -- 91 DNA polymerase III epsilon subunit  
173 0.009489 0.1945 stm3985 yigZ -14.68 0.132642 77 -- 135 33 -- 90 YigZ family protein  
122 0.00604 0.1758 stm2353 hisQ -14.65 0.134227 190 -- 212 140 -- 163 amino acid ABC transporter permease  
143 0.007336 0.182 stm2276 ubiG -14.65 0.134291 225 -- 278 36 -- 81 2-octaprenyl-6-hydroxy phenol methylase  
153 0.008123 0.1845 stm2512 xseA -14.57 0.138273 215 -- 252 42 -- 82 exodeoxyribonuclease VII large subunit  
176 0.009613 0.1945 stm3378 N/A -14.56 0.138793 155 -- 243 45 -- 125 sulfoxide reductase heme-binding subunit YedZ  
198 0.01098 0.197 stm2803 N/A -14.51 0.140962 192 -- 262 36 -- 101 DNA-binding transcriptional regulator  
130 0.00652 0.1774 stm4228 malF -14.47 0.143021 162 -- 175 1 -- 15 maltose ABC transporter permease MalF  
158 0.00827 0.1845 stm1712 acnA -14.47 0.143385 236 -- 294 48 -- 104 aconitate hydratase 1  

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