Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 4894743

Input and runtime details for job 4894743 (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 4894743 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:35:26 CET 2018
?CopraRNA Started@ Fri Feb 16 21:36:09 CET 2018
?CopraRNA Finished & Post-Processing@ Sat Feb 17 05:38:38 CET 2018
?Post-Processing Finished@ Sat Feb 17 05:38:45 CET 2018
?Job Completed@ Sat Feb 17 05:39:16 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4894743&toolName=CopraRNA ( 30 days expiry )

Description of the job

SR1

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
30 0.0008394 0.1059 bsu25600 comER -17.70 0.008924 72 -- 169 82 -- 187 ComE operon protein 4  
112 0.00483 0.1671 bsu26010 yqbQ -18.75 0.005285 180 -- 239 82 -- 139 Evidence 4: Homologs of previously reported genes of unknown function bsu12700
131 0.006003 0.1741 bsu37510 pbpG -10.90 0.216982 70 -- 106 84 -- 108 penicillin-binding protein 2D  
173 0.008072 0.1751 bsu38150 qoxC -9.07 0.441891 44 -- 68 85 -- 107 quinol oxidase subunit 3  
68 0.002291 0.1242 bsu02600 cwlJ -9.38 0.396883 135 -- 166 88 -- 116 cell wall hydrolase CwlJ  
138 0.00639 0.1741 bsu24900 rpmG -18.16 0.007101 92 -- 175 92 -- 166 50S ribosomal protein L33  
72 0.002326 0.1242 bsu10730 yisI -10.35 0.272902 44 -- 108 96 -- 182 aspartyl-phosphate phosphatase YisI  
87 0.003215 0.1423 bsu04140 pbpC -8.12 0.599206 128 -- 139 96 -- 107 penicillin-binding protein 3  
11 0.0003253 0.1011 bsu31319 yuzI -20.00 0.002830 16 -- 82 99 -- 165 Evidence 4: Homologs of previously reported genes of unknown function; PubMedId: 16704729; Product type f : factor  
19 0.0005622 0.1011 bsu33310 fhuB -20.25 0.002499 30 -- 116 99 -- 184 iron(3+)-hydroxamate import system permease protein FhuB bsu01620

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