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
89 0.002377 0.09395 b4136 dsbD -10.47 0.032769 211 -- 231 1 -- 22 thiol:disulfide interchange protein and activator of DsbC  
14 5.486e-05 0.01183 b0420 dxs -9.76 0.053178 24 -- 31 1 -- 8 1-deoxyxylulose-5-phosphate synthase thiamine triphosphate-binding FAD-requiring  
70 0.001199 0.05856 b0954 fabA -10.37 0.035200 228 -- 254 4 -- 31 beta-hydroxydecanoyl thioester dehydrase  
133 0.004686 0.1239 b3081 fadH -11.00 0.022420 2 -- 21 1 -- 24 2 4-dienoyl-CoA reductase NADH and FMN-linked  
21 0.0001601 0.02641 b2344 fadL -13.31 0.003531 80 -- 135 1 -- 58 long-chain fatty acid outer membrane transporter  
143 0.005218 0.1284 b1922 fliA -8.86 0.094137 133 -- 141 50 -- 58 RNA polymerase sigma 28 (sigma F) factor  
71 0.001214 0.05856 b1921 fliZ -11.32 0.017729 260 -- 276 48 -- 65 RpoS antagonist; putative regulator of FliA activity  
198 0.008802 0.1558 b1905 ftnA -8.07 0.149574 234 -- 260 3 -- 24 ferritin iron storage protein (cytoplasmic)  
99 0.00311 0.1096 b2801 fucP -13.12 0.004165 162 -- 172 46 -- 56 L-fucose transporter  
26 0.0002109 0.02687 b4122 fumB -13.50 0.002989 276 -- 286 47 -- 57 anaerobic class I fumarate hydratase (fumarase B) b1612

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