Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 1786318

Input and runtime details for job 1786318 (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 1786318 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:20:27 CET 2018
?CopraRNA Started@ Fri Feb 16 15:20:56 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 22:01:46 CET 2018
?Post-Processing Finished@ Fri Feb 16 22:01:53 CET 2018
?Job Completed@ Fri Feb 16 22:02:22 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
46 0.002359 0.1727 b4139 aspA -15.43 0.012067 239 -- 273 37 -- 76 aspartate ammonia-lyase  
82 0.004565 0.1855 b4144 yjeI -10.12 0.132253 163 -- 240 1 -- 93 DUF4156 family lipoprotein  
162 0.009519 0.2068 b4167 nnr -8.70 0.240671 167 -- 176 76 -- 85 bifunctional NAD(P)H-hydrate repair enzyme; C-terminal domain ADP-dependent (S)-NAD(P)H-hydrate dehydratase and N-terminal domain NAD(P)H-hydrate epimerase  
98 0.005208 0.1855 b4174 hflK -10.42 0.116019 265 -- 284 65 -- 83 modulator for HflB protease specific for phage lambda cII repressor  
191 0.01171 0.2159 b4221 tamB -9.06 0.207346 81 -- 101 52 -- 76 translocation and assembly module for autotransporter export inner membrane subunit  
89 0.004811 0.1855 b4336 yjiN -13.14 0.034257 120 -- 134 70 -- 84 zinc-type alcohol dehydrogenase-like protein  
29 0.001588 0.1727 b4371 rsmC -11.43 0.073969 145 -- 160 74 -- 89 16S rRNA m(2)G1207 methyltransferase SAM-dependent  
188 0.01115 0.2089 b4377 yjjU -9.16 0.198952 213 -- 243 51 -- 77 putative patatin-like family phospholipase  
34 0.001871 0.1727 b4485 ytfR -15.36 0.012458 204 -- 227 64 -- 86 putative sugar ABC transporter ATPase  
180 0.01069 0.2089 b4529 ydbJ -7.20 0.426635 222 -- 243 41 -- 61 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)

Job resubmission

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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2