Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 1786318

Input and runtime details for job 1786318 (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 1786318 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:20:27 CET 2018
?Processing Started@ Fri Feb 16 15:20:56 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 22:01:46 CET 2018
?Post-Processing Finished@ Fri Feb 16 22:01:53 CET 2018
?Job Completed@ Fri Feb 16 22:02:22 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

The job description you specified

ArcZ


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
89 0.004811 0.1855 b4336 yjiN -13.14 0.034257 120 -- 134 70 -- 84 zinc-type alcohol dehydrogenase-like protein  
96 0.005105 0.1855 b0870 ltaE -12.99 0.036706 93 -- 116 68 -- 88 L-allo-threonine aldolase PLP-dependent  
33 0.001709 0.1727 b0023 rpsT -12.95 0.037339 65 -- 78 72 -- 85 30S ribosomal subunit protein S20  
31 0.001682 0.1727 b1887 cheW -12.93 0.037697 13 -- 28 70 -- 86 purine-binding chemotaxis protein  
166 0.009748 0.2068 b1261 trpB -12.89 0.038353 88 -- 97 52 -- 61 tryptophan synthase beta subunit  
8 0.000265 0.1166 b1244 oppB -12.83 0.039495 280 -- 295 70 -- 84 oligopeptide ABC transporter permease  
13 0.0004745 0.1198 b1688 ydiK -12.82 0.039628 213 -- 226 68 -- 82 UPF0118 family inner membrane protein  
52 0.002619 0.1727 b2720 hycF -12.75 0.040951 8 -- 55 44 -- 94 formate hydrogenlyase complex iron-sulfur protein  
187 0.01114 0.2089 b0801 ybiC -12.72 0.041489 266 -- 279 27 -- 40 putative dehydrogenase b0517
6 0.0001378 0.08054 b3860 dsbA -12.69 0.042007 89 -- 111 55 -- 75 periplasmic protein disulfide isomerase I  

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