Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 5774122

Input and runtime details for job 5774122 (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 5774122 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:30:38 CET 2018
?CopraRNA Started@ Fri Feb 16 20:16:08 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 23:32:42 CET 2018
?Post-Processing Finished@ Fri Feb 16 23:32:50 CET 2018
?Job Completed@ Fri Feb 16 23:33:10 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5774122&toolName=CopraRNA ( 30 days expiry )

Description of the job

FsrA

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_000964 Bacillus subtilis subsp. subtilis str. 168

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
125 0.01105 0.2883 bsu27350 yrrN -18.26 0.005831 285 -- 299 16 -- 30 protease YrrN  
162 0.01461 0.3008 bsu28700 ysfE -18.20 0.006050 31 -- 59 26 -- 51 Evidence 5: No homology to any previously reported sequences bsu26940
14 0.0002247 0.05257 bsu30160 ytcQ -17.33 0.009670 159 -- 223 10 -- 51 peptide ABC transporter substrate-binding protein  
200 0.01989 0.3269 bsu30150 ytdP -13.03 0.070310 188 -- 210 28 -- 52 AraC family transcriptional regulator  
160 0.01451 0.3008 bsu30080 yteV -11.71 0.117611 279 -- 298 34 -- 53 sporulation protein cse60  
114 0.009837 0.2871 bsu30580 ytmA -11.73 0.116519 193 -- 212 33 -- 52 peptidase YtmA  
19 0.0003652 0.06216 bsu29920 ytmP -16.30 0.016289 3 -- 31 25 -- 51 phosphotransferase YtmP  
173 0.01667 0.3152 bsu28970 ytxB -13.17 0.066474 182 -- 201 13 -- 34 tvp38/tmem64 family membrane protein YtxB  
184 0.01795 0.3254 bsu30470 ytzC -13.40 0.060457 189 -- 197 28 -- 36 Evidence 4: Homologs of previously reported genes of unknown function  
67 0.004159 0.2071 bsu31830 yueE -13.48 0.058566 169 -- 197 28 -- 51 phosphohydrolase YueE  

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

Use the following button if you want to resubmit the job with altered input or parameterization:
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