Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 3202356

Input and runtime details for job 3202356 (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 3202356 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:24:02 CET 2018
?CopraRNA Started@ Fri Feb 16 15:24:35 CET 2018
?CopraRNA Finished & Post-Processing@ Sat Feb 17 02:03:47 CET 2018
?Post-Processing Finished@ Sat Feb 17 02:03:55 CET 2018
?Job Completed@ Sat Feb 17 02:04:28 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
176 0.009613 0.1945 stm3378 N/A -14.56 0.138793 155 -- 243 45 -- 125 sulfoxide reductase heme-binding subunit YedZ  
4 5.758e-05 0.04123 stm3564 livK -17.90 0.039430 157 -- 215 37 -- 90 leucine ABC transporter subunit substrate-binding protein LivK  
6 7.515e-05 0.04123 stm0665 gltI -17.87 0.039793 157 -- 199 35 -- 81 glutamate/aspartate transporter  
48 0.001762 0.1291 stm4523 yjiW -20.55 0.014078 157 -- 299 40 -- 186 endoribonuclease SymE  
10 0.0001468 0.05229 stm0680 asnB -17.15 0.052408 158 -- 224 32 -- 90 asparagine synthetase B  
15 0.000269 0.06194 stm3630 dppA -21.81 0.008578 158 -- 199 51 -- 92 ABC transporter substrate-binding protein  
89 0.004143 0.1596 stm2957 ygcA -15.40 0.101796 159 -- 208 35 -- 82 23S rRNA (uracil(1939)-C(5))-methyltransferase  
90 0.004161 0.1596 stm1124 putA -17.89 0.039481 159 -- 201 125 -- 168 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase  
112 0.005549 0.1728 stm0602 ybdH -14.01 0.169356 159 -- 193 39 -- 79 oxidoreductase  
141 0.007251 0.182 stm2325 nuoE -19.46 0.021521 159 -- 233 56 -- 129 NADH-quinone oxidoreductase subunit E  

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