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
72 0.001216 0.05856 b3699 gyrB -10.53 0.031588 1 -- 17 9 -- 25 DNA gyrase subunit B  
166 0.006804 0.1439 b0475 hemH -7.56 0.197603 220 -- 228 1 -- 9 ferrochelatase  
28 0.0002139 0.02687 b4174 hflK -10.82 0.025576 125 -- 140 42 -- 58 modulator for HflB protease specific for phage lambda cII repressor  
151 0.006118 0.1406 b1103 hinT -6.52 0.328434 216 -- 241 45 -- 70 purine nucleoside phosphoramidase dadA activator protein  
186 0.008252 0.1556 b2026 hisI -8.65 0.106637 17 -- 26 42 -- 51 phosphoribosyl-AMP cyclohydrolase and phosphoribosyl-ATP pyrophosphatase  
177 0.007672 0.1511 b2307 hisM -10.48 0.032509 175 -- 237 1 -- 57 histidine ABC transporter permease  
142 0.005204 0.1284 b3931 hslU -6.88 0.277791 3 -- 17 52 -- 65 molecular chaperone and ATPase component of HslUV protease  
174 0.007262 0.1466 b0473 htpG -8.02 0.153160 10 -- 17 50 -- 57 protein refolding molecular co-chaperone Hsp90 Hsp70-dependent; heat-shock protein; ATPase  
108 0.003398 0.1101 b0973 hyaB -11.40 0.016694 267 -- 275 48 -- 56 hydrogenase 1 large subunit  
183 0.007903 0.1519 b2725 hycA -8.51 0.115738 229 -- 236 49 -- 56 regulator of the transcriptional regulator FhlA  

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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Results are computed with CopraRNA version 2.1.2