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
1 0 0 stm2982 gcvA -98.53 0.000000 1 -- 73 1 -- 73 transcriptional regulator GcvA  
2 2.663e-05 0.04123 stm2355 argT -17.69 0.042680 144 -- 202 34 -- 91 histidine ABC transporter substrate-binding protein HisJ  
3 3.698e-05 0.04123 stm4398 cycA -21.36 0.010235 127 -- 178 38 -- 82 D-serine/D-alanine/glycine transporter  
4 5.758e-05 0.04123 stm3564 livK -17.90 0.039430 157 -- 215 37 -- 90 leucine ABC transporter subunit substrate-binding protein LivK  
5 6.363e-05 0.04123 stm0399 brnQ -24.27 0.003272 169 -- 224 36 -- 81 branched-chain amino acid transport system II carrier protein  
6 7.515e-05 0.04123 stm0665 gltI -17.87 0.039793 157 -- 199 35 -- 81 glutamate/aspartate transporter  
7 8.283e-05 0.04123 stm1953 yedO -23.64 0.004188 172 -- 228 31 -- 88 D-cysteine desulfhydrase  
8 9.263e-05 0.04123 stm0369 prpC -29.42 0.000431 202 -- 269 31 -- 91 2-methylcitrate synthase  
9 0.0001316 0.05206 stm1221 cobB -19.79 0.018892 28 -- 73 51 -- 101 NAD-dependent protein deacylase  
10 0.0001468 0.05229 stm0680 asnB -17.15 0.052408 158 -- 224 32 -- 90 asparagine synthetase B  

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

		

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