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
151 0.03043 0.6177 b3081 fadH -8.56 0.080347 290 -- 297 43 -- 50 2 4-dienoyl-CoA reductase NADH and FMN-linked  
155 0.03087 0.6177 b1003 yccJ -9.03 0.064630 130 -- 145 43 -- 56 uncharacterized protein  
156 0.03128 0.6177 b4512 ybdD -7.87 0.110479 26 -- 38 43 -- 55 DUF466 family protein  
173 0.03478 0.6177 b1234 rssA -4.70 0.418234 181 -- 188 43 -- 50 putative patatin-like family phospholipase  
181 0.03769 0.6177 b0912 ihfB -7.34 0.140491 192 -- 199 43 -- 50 integration host factor (IHF) DNA-binding protein beta subunit  
197 0.04129 0.6177 b1205 ychH -8.72 0.074776 153 -- 162 43 -- 52 DUF2583 family putative inner membrane protein  
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  
11 0.002274 0.593 b1476 fdnI -10.73 0.029150 152 -- 175 44 -- 69 formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible  
13 0.003065 0.593 b4529 ydbJ -10.82 0.027981 161 -- 194 44 -- 78 DUF333 family putative lipoprotein  

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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Feeds the job parameters to the input page to resubmit the job.

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Results are computed with CopraRNA version 2.1.2