Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 6793193

Input and runtime details for job 6793193 (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 6793193 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:27:03 CET 2018
?CopraRNA Started@ Fri Feb 16 15:27:32 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 21:26:02 CET 2018
?Post-Processing Finished@ Fri Feb 16 21:26:10 CET 2018
?Job Completed@ Fri Feb 16 21:26:45 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
172 0.008479 0.1735 b4395 ytjC -10.99 0.163500 244 -- 268 34 -- 71 phosphatase  
62 0.002558 0.1417 b3579 yiaO -11.31 0.142375 245 -- 258 62 -- 75 2 3-diketo-L-gulonate-binding periplasmic protein  
153 0.007486 0.1668 b1732 katE -14.34 0.030774 245 -- 275 42 -- 74 catalase HPII heme d-containing  
13 0.0001005 0.0245 b1921 fliZ -13.92 0.038869 246 -- 263 63 -- 78 RpoS antagonist; putative regulator of FliA activity  
11 9.086e-05 0.0245 b3337 bfd -12.11 0.098410 247 -- 280 34 -- 76 bacterioferritin-associated ferredoxin  
164 0.007775 0.1668 b2097 fbaB -9.67 0.277966 247 -- 265 48 -- 68 fructose-bisphosphate aldolase class I  
190 0.009703 0.1776 b4125 dcuS -9.98 0.246838 251 -- 265 60 -- 75 sensory histidine kinase in two-component regulatory system with DcuR regulator of anaerobic fumarate respiration  
91 0.00412 0.1538 b0931 pncB -13.41 0.051237 255 -- 284 48 -- 77 nicotinate phosphoribosyltransferase  
152 0.007399 0.1668 b0591 entS -13.87 0.039944 258 -- 287 45 -- 70 enterobactin exporter iron-regulated  
161 0.00773 0.1668 b0945 pyrD -11.84 0.111523 258 -- 300 33 -- 77 dihydro-orotate oxidase FMN-linked  

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