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
81 0.003764 0.1596 stm0121 ftsL -18.45 0.031843 91 -- 225 48 -- 186 cell division protein FtsL  
82 0.003783 0.1596 stm0710 ybgH -19.90 0.018103 103 -- 151 33 -- 90 MFS transporter  
83 0.003855 0.1596 stm1680 ycjI -14.22 0.156552 151 -- 200 34 -- 86 murein peptide amidase A  
84 0.003893 0.1596 stm2015 erfK -27.15 0.001054 109 -- 172 35 -- 90 L D-transpeptidase  
85 0.003998 0.1596 stm1098 hpaC -22.15 0.007534 132 -- 187 37 -- 90 4-hydroxyphenylacetate 3-monooxygenase reductase component  
86 0.004005 0.1596 stm1961 fliS -19.11 0.024619 1 -- 77 23 -- 90 flagellar export chaperone FliS  
87 0.004009 0.1596 stm2067 sbcB -11.70 0.367652 220 -- 292 35 -- 90 exodeoxyribonuclease I  
88 0.00402 0.1596 stm2651 yfiQ -16.02 0.080775 116 -- 159 50 -- 88 protein acetyltransferase  
89 0.004143 0.1596 stm2957 ygcA -15.40 0.101796 159 -- 208 35 -- 82 23S rRNA (uracil(1939)-C(5))-methyltransferase  
90 0.004161 0.1596 stm1124 putA -17.89 0.039481 159 -- 201 125 -- 168 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase  

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