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
181 0.0171 0.3152 bsu32040 yuiF -15.17 0.027943 179 -- 194 29 -- 51 amino acid transporter YuiF  
182 0.01724 0.3161 bsu22340 nth -14.82 0.032761 30 -- 59 25 -- 52 endonuclease III  
183 0.01776 0.3237 bsu08550 sspK -13.38 0.060997 172 -- 193 31 -- 48 small acid-soluble spore protein K  
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  
185 0.01858 0.3269 bsu27560 hisS -8.40 0.345340 122 -- 132 25 -- 38 histidine--tRNA ligase  
186 0.01872 0.3269 bsu09880 yhaR -10.74 0.166509 137 -- 152 16 -- 29 enoyl-CoA hydratase/isomerase YhaR  
187 0.01872 0.3269 bsu10530 ntdC -12.62 0.082941 177 -- 192 32 -- 53 NTD biosynthesis operon putative oxidoreductase NtdC  
188 0.01873 0.3269 bsu10750 yisK -12.58 0.084103 165 -- 222 21 -- 51 'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type pe: enzyme'  
189 0.01911 0.3269 bsu24290 xseB -12.91 0.073825 187 -- 193 30 -- 36 exodeoxyribonuclease 7 small subunit  
190 0.01911 0.3269 bsu05370 ydfD -12.16 0.099313 269 -- 294 11 -- 36 GntR family transcriptional regulator bsu10880

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