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
?Processing 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:80/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

The job description you specified

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
31 0.0007673 0.08814 stm0403 yajB -17.88 0.039643 23 -- 70 41 -- 90 ACP phosphodiesterase  
32 0.001017 0.1132 stm1874 N/A -30.35 0.000300 5 -- 53 36 -- 83 putative inner membrane protein  
33 0.001058 0.1142 stm0380 ddlA -21.71 0.008945 31 -- 67 39 -- 76 D-alanine--D-alanine ligase A  
34 0.001111 0.1164 stm2746 N/A -14.94 0.120804 53 -- 101 36 -- 90 putative excinuclease ATPase subunit stm4494 stm3753
35 0.001151 0.1171 stm1336 rplT -16.07 0.079235 51 -- 96 49 -- 98 50S ribosomal protein L20  
36 0.00125 0.1215 stm3523 glpR -16.55 0.065942 207 -- 266 37 -- 89 DeoR/GlpR family transcriptional regulator  
37 0.001263 0.1215 stm2511 guaB -22.14 0.007548 255 -- 298 35 -- 73 IMP dehydrogenase  
38 0.001379 0.1215 stm0150 aroP -12.21 0.313123 213 -- 232 63 -- 83 APC family aromatic amino acid transporter  
39 0.001399 0.1215 stm4007 glnA -20.44 0.014679 143 -- 217 36 -- 106 type I glutamate--ammonia ligase  
40 0.001409 0.1215 stm4578 serB -16.00 0.081343 27 -- 78 37 -- 87 phosphoserine phosphatase SerB  

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.

de.NBI usability assessment

Please support us by filling this short quality survey for evaluating this de.NBI service.

When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2