Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 1654565

Input and runtime details for job 1654565 (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 1654565 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:23:36 CET 2018
?CopraRNA Started@ Fri Feb 16 15:24:05 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 22:25:53 CET 2018
?Post-Processing Finished@ Fri Feb 16 22:26:01 CET 2018
?Job Completed@ Fri Feb 16 22:26:34 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
124 0.004441 0.1258 b1656 sodB -12.34 0.027802 164 -- 220 1 -- 93 superoxide dismutase Fe  
133 0.004969 0.1313 b0148 hrpB -12.31 0.028366 190 -- 234 2 -- 40 putative ATP-dependent helicase  
79 0.001882 0.08273 b2219 atoS -12.26 0.029240 6 -- 44 51 -- 94 sensory histidine kinase in two-component regulatory system with AtoC  
14 2.236e-05 0.005627 b3306 rpsH -12.22 0.029933 187 -- 206 35 -- 55 30S ribosomal subunit protein S8  
24 0.0001125 0.01591 b3212 gltB -12.14 0.031409 27 -- 43 59 -- 75 glutamate synthase large subunit  
105 0.003386 0.1114 b0517 allD -12.14 0.031589 151 -- 204 43 -- 92 ureidoglycolate dehydrogenase b0801
149 0.005854 0.1368 b2166 psuK -12.08 0.032688 265 -- 298 54 -- 89 pseudouridine kinase  
8 8.903e-06 0.003921 b1654 grxD -12.06 0.033180 187 -- 203 41 -- 57 glutaredoxin-4  
138 0.00525 0.1336 b0031 dapB -12.01 0.034078 16 -- 66 61 -- 114 dihydrodipicolinate reductase  
44 0.0004181 0.03347 b3429 glgA -12.00 0.034422 173 -- 196 35 -- 55 glycogen synthase  

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)

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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2