Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 5882223

Input and runtime details for job 5882223 (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 5882223 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:29:59 CET 2018
?CopraRNA Started@ Fri Feb 16 20:39:56 CET 2018
?CopraRNA Finished & Post-Processing@ Sat Feb 17 03:02:39 CET 2018
?Post-Processing Finished@ Sat Feb 17 03:02:47 CET 2018
?Job Completed@ Sat Feb 17 03:03:15 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
13 4.485e-05 0.01183 b0511 ybbW -13.60 0.002717 173 -- 210 18 -- 58 putative allantoin transporter  
110 0.003442 0.1101 b0528 ybcJ -8.36 0.126664 258 -- 272 21 -- 34 ribosome-associated protein; putative RNA-binding protein  
182 0.007896 0.1519 b0686 ybfF -7.34 0.221050 164 -- 170 2 -- 8 acyl-CoA esterase  
150 0.00611 0.1406 b0735 ybgE -10.35 0.035619 38 -- 71 5 -- 31 putative inner membrane protein in cydABX-ybgE operon  
98 0.002849 0.1023 b0772 ybhC -6.17 0.383539 27 -- 33 49 -- 55 acyl-CoA thioesterase lipoprotein  
2 0 0 b0796 ybiH -7.52 0.201543 119 -- 140 54 -- 76 DUF1956 domain-containing tetR family putative transcriptional regulator b1013
191 0.008587 0.1558 b0823 ybiW -9.49 0.063221 47 -- 54 1 -- 8 putative pyruvate formate lyase b3951
104 0.003257 0.1101 b0858 ybjO -8.07 0.149394 228 -- 257 2 -- 30 DUF2593 family inner membrane protein  
106 0.003365 0.1101 b0955 ycbZ -10.52 0.031644 269 -- 288 48 -- 66 putative peptidase  
96 0.002764 0.1002 b1034 ycdX -5.77 0.451964 102 -- 115 32 -- 46 alkaline phosphatase  

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

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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