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
117 0.003878 0.1165 b3078 ygjI -10.25 0.038289 174 -- 181 1 -- 8 putative transporter b0899
133 0.004686 0.1239 b3081 fadH -11.00 0.022420 2 -- 21 1 -- 24 2 4-dienoyl-CoA reductase NADH and FMN-linked  
38 0.0004278 0.03766 b3092 uxaC -12.53 0.006845 206 -- 269 1 -- 57 uronate isomerase  
170 0.007042 0.1457 b3110 yhaO -10.02 0.044877 174 -- 180 1 -- 7 putative transporter  
74 0.001232 0.05856 b3139 agaC -9.25 0.073815 213 -- 219 1 -- 7 N-acetylgalactosamine-specific enzyme IIC component of PTS  
51 0.0006491 0.04477 b3224 nanT -16.25 0.000177 140 -- 151 1 -- 12 sialic acid transporter b4279
55 0.0008105 0.05184 b3262 yhdJ -10.49 0.032282 53 -- 83 1 -- 34 DNA adenine methyltransferase SAM-dependent  
81 0.001761 0.07647 b3311 rpsQ -9.62 0.058411 217 -- 225 1 -- 9 30S ribosomal subunit protein S17  
200 0.009019 0.1567 b3343 tusB -6.18 0.382258 145 -- 152 1 -- 8 mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein  
141 0.00519 0.1284 b3550 yiaC -7.29 0.227336 55 -- 76 1 -- 22 GNAT family putative N-acetyltransferase  

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