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
?Processing 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:80/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

The job description you specified

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
61 0.002902 0.1596 stm3567 livJ -18.03 0.037474 150 -- 196 40 -- 87 high-affinity branched-chain amino acid transporter  
62 0.003015 0.1596 stm1299 gdhA -15.31 0.105026 136 -- 171 63 -- 91 glutamate dehydrogenase  
63 0.003024 0.1596 stm3563 livH -16.49 0.067433 27 -- 175 36 -- 184 branched-chain amino acid ABC transporter permease LivH  
64 0.003108 0.1596 stm4162 thiF -13.53 0.200092 247 -- 294 34 -- 76 molybdopterin/thiamine biosynthesis adenylyltransferase  
65 0.003171 0.1596 stm0830 glnH -11.06 0.446113 180 -- 193 153 -- 165 glutamine ABC transporter substrate-binding protein GlnH  
66 0.003179 0.1596 stm0264 dnaQ -14.69 0.132400 209 -- 271 35 -- 91 DNA polymerase III epsilon subunit  
67 0.003193 0.1596 stm0122 ftsI -11.87 0.349270 199 -- 241 52 -- 90 peptidoglycan glycosyltransferase FtsI  
68 0.003225 0.1596 stm3930 yifK -15.10 0.113746 177 -- 247 44 -- 93 amino acid permease  
69 0.003278 0.1596 stm3675 sgbH -16.55 0.065932 154 -- 200 33 -- 93 3-keto-L-gulonate-6-phosphate decarboxylase  
70 0.003306 0.1596 stm2688 smpB -12.25 0.308628 191 -- 230 36 -- 77 SsrA-binding protein  

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.

de.NBI usability assessment

Please support us by filling this short quality survey for evaluating this de.NBI service.

When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2