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
1 0 0 stm2982 gcvA -98.53 0.000000 1 -- 73 1 -- 73 transcriptional regulator GcvA  
86 0.004005 0.1596 stm1961 fliS -19.11 0.024619 1 -- 77 23 -- 90 flagellar export chaperone FliS  
124 0.006123 0.1758 stm0794 bioB -18.46 0.031660 1 -- 37 38 -- 79 biotin synthase  
127 0.006343 0.1774 stm1751 hns -12.42 0.292757 1 -- 14 147 -- 162 transcriptional regulator  
183 0.01015 0.1966 stm0813 ybhP -18.40 0.032407 2 -- 54 36 -- 90 similar to E. coli orf hypothetical protein (AAC73877.1); Blastp hit to AAC73877.1 (253 aa) 86% identity in aa 1 - 253  
54 0.002071 0.1363 stm1429 ydhB -17.23 0.050879 3 -- 45 36 -- 79 putative LysR family transcriptional regulator  
16 0.0002876 0.06194 stm1378 pykF -16.63 0.064116 5 -- 66 31 -- 91 pyruvate kinase  
32 0.001017 0.1132 stm1874 N/A -30.35 0.000300 5 -- 53 36 -- 83 putative inner membrane protein  
91 0.004202 0.1596 stm0387 yaiI -16.26 0.073758 5 -- 45 23 -- 58 similar to E. coli orf hypothetical protein (AAC73490.1); Blastp hit to AAC73490.1 (192 aa) 89% identity in aa 41 - 191  
107 0.00529 0.1728 stm0994 mukB -11.10 0.440174 5 -- 20 154 -- 167 cell division protein MukB  

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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Results are computed with CopraRNA version 2.1.2