Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 1765463

Input and runtime details for job 1765463 (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 1765463 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:41:59 CET 2018
?CopraRNA Started@ Fri Feb 16 15:42:13 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 19:57:45 CET 2018
?Post-Processing Finished@ Fri Feb 16 19:57:53 CET 2018
?Job Completed@ Fri Feb 16 19:58:19 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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_000913 Escherichia coli str. K-12 substr. MG1655

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
1 0 0 b0481 ybaK -91.37 0.000000 1 -- 79 1 -- 79 Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase  
2 6.241e-06 0.01004 b1737 chbC -18.35 0.000789 134 -- 152 38 -- 56 N N'-diacetylchitobiose-specific enzyme IIC component of PTS  
3 9.453e-06 0.01014 b0681 chiP -16.40 0.001982 182 -- 193 45 -- 56 chitoporin uptake of chitosugars  
4 0.0002658 0.2138 b1040 csgD -11.06 0.024985 185 -- 199 38 -- 52 csgBAC operon transcriptional regulator  
5 0.0004437 0.2856 b0847 ybjL -12.50 0.012601 224 -- 253 26 -- 55 putative transporter  
6 0.0006545 0.351 b1857 znuA -11.78 0.017745 58 -- 67 45 -- 54 zinc ABC transporter periplasmic binding protein  
7 0.001184 0.5444 b0817 mntR -11.99 0.016054 285 -- 294 46 -- 55 Mn(2+)-responsive manganese regulon transcriptional regulator  
8 0.001474 0.5928 b1048 opgG -11.67 0.018726 159 -- 168 44 -- 53 OPG biosynthetic periplasmic beta-1 6 branching glycosyltransferase  
9 0.001801 0.593 b1276 acnA -10.22 0.037037 184 -- 198 44 -- 55 aconitate hydratase 1; aconitase A  
10 0.001925 0.593 b2910 zapA -12.97 0.010115 44 -- 65 38 -- 56 FtsZ stabilizer  

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