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]
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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
191 0.01055 0.1967 stm0634 ybeF -18.83 0.027435 210 -- 262 35 -- 82 putative LysR family transcriptional regulator  
192 0.01067 0.197 stm2650 yfiP -13.22 0.223534 188 -- 232 36 -- 90 DTW domain-containing protein  
193 0.01075 0.197 stm3734 rph -15.48 0.098722 165 -- 206 34 -- 78 ribonuclease PH  
194 0.01081 0.197 stm1954 fliY -13.82 0.181182 183 -- 228 153 -- 193 cystine ABC transporter substrate-binding protein  
195 0.01085 0.197 stm0549 fimZ -13.17 0.226725 219 -- 235 155 -- 171 DNA-binding response regulator  
196 0.01089 0.197 stm3904 ilvD -14.14 0.161583 237 -- 253 179 -- 194 dihydroxy-acid dehydratase  
197 0.01093 0.197 stm2924 rpoS -16.80 0.060020 191 -- 216 36 -- 60 RNA polymerase sigma factor RpoS  
198 0.01098 0.197 stm2803 N/A -14.51 0.140962 192 -- 262 36 -- 101 DNA-binding transcriptional regulator  
199 0.01101 0.197 stm3346 yhcM -12.83 0.254909 186 -- 228 33 -- 82 cell division protein ZapE  
200 0.01112 0.198 stm2809 proV -15.77 0.088450 57 -- 94 50 -- 85 glycine betaine/L-proline ABC transporter ATP-binding protein  

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)

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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