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]
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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
51 0.001912 0.1324 stm2692 N/A -10.31 0.546971 162 -- 173 130 -- 141 putative HlyD family secretion protein  
52 0.001934 0.1324 stm0653 ybeL -17.18 0.051878 262 -- 299 155 -- 188 similar to E. coli putative alpha helical protein (AAC73744.1); Blastp hit to AAC73744.1 (160 aa) 91% identity in aa 1 - 160  
53 0.002045 0.1363 stm1876 holE -16.46 0.068295 21 -- 75 31 -- 90 DNA polymerase III subunit theta  
54 0.002071 0.1363 stm1429 ydhB -17.23 0.050879 3 -- 45 36 -- 79 putative LysR family transcriptional regulator  
55 0.002114 0.1363 stm0887 artJ -12.89 0.249853 160 -- 177 72 -- 90 arginine ABC transporter substrate-binding protein  
56 0.002144 0.1363 pslt006 repA -15.36 0.103288 219 -- 279 36 -- 87 DNA replication  
57 0.002298 0.14 stm3921 wecC -19.39 0.022107 89 -- 132 46 -- 91 UDP-N-acetyl-D-mannosamine dehydrogenase  
58 0.002307 0.14 stm2234 N/A -13.92 0.174542 131 -- 196 38 -- 89 phage tail protein stm2705 stm2233
59 0.00232 0.14 stm4105 metF -16.51 0.066936 223 -- 245 40 -- 59 methylenetetrahydrofolate reductase [NAD(P)H]  
60 0.002585 0.1534 stm0758 ybgR -11.90 0.345594 235 -- 293 32 -- 91 cation transporter  

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