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
136 0.004892 0.1265 b2349 intS -8.19 0.139381 273 -- 281 3 -- 11 CPS-53 (KpLE1) prophage; putative prophage CPS-53 integrase  
172 0.007198 0.1466 b2395 yfeA -7.88 0.166321 272 -- 292 49 -- 69 putative diguanylate cyclase  
95 0.002686 0.09947 b2419 yfeK -12.78 0.005552 57 -- 65 1 -- 9 uncharacterized protein  
152 0.006159 0.1406 b2467 nudK -9.74 0.053801 255 -- 261 1 -- 7 GDP-mannose pyrophosphatase  
196 0.008709 0.1558 b2498 upp -7.14 0.244299 249 -- 259 45 -- 56 uracil phosphoribosyltransferase  
87 0.00233 0.09349 b2522 sseB -8.85 0.094489 280 -- 288 1 -- 9 rhodanase-like enzyme sulfur transfer from thiosulfate  
192 0.008619 0.1558 b2561 yfhH -12.96 0.004772 194 -- 222 4 -- 32 putative DNA-binding transcriptional regulator  
3 0 0 b2564 pdxJ -5.03 0.588876 273 -- 283 52 -- 62 pyridoxine 5'-phosphate synthase  
120 0.003999 0.1172 b2582 trxC -9.28 0.072721 206 -- 219 4 -- 16 thioredoxin 2  
139 0.005017 0.127 b2603 yfiR -11.92 0.011246 223 -- 243 1 -- 19 putative periplasmic inhibitor of YfiN activity  

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