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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[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
56 0.002144 0.1363 pslt006 repA -15.36 0.103288 219 -- 279 36 -- 87 DNA replication  
160 0.008331 0.1845 stm0002 thrA -15.10 0.113872 18 -- 81 44 -- 90 bifunctional aspartate kinase/homoserine dehydrogenase I  
177 0.009665 0.1945 stm0079 yaaU -14.30 0.152587 187 -- 218 40 -- 79 MFS transporter  
71 0.003339 0.1596 stm0105 yabI -14.10 0.163814 151 -- 168 141 -- 162 similar to E. coli orf hypothetical protein (AAC73176.1); Blastp hit to AAC73176.1 (254 aa) 89% identity in aa 1 - 253  
18 0.0003131 0.06194 stm0112 leuB -16.29 0.072835 153 -- 217 44 -- 93 3-isopropylmalate dehydrogenase  
101 0.005112 0.1728 stm0113 leuA -13.72 0.187230 187 -- 230 37 -- 84 2-isopropylmalate synthase  
81 0.003764 0.1596 stm0121 ftsL -18.45 0.031843 91 -- 225 48 -- 186 cell division protein FtsL  
67 0.003193 0.1596 stm0122 ftsI -11.87 0.349270 199 -- 241 52 -- 90 peptidoglycan glycosyltransferase FtsI  
80 0.003756 0.1596 stm0132 ftsA -17.45 0.046754 189 -- 236 139 -- 186 cell division protein FtsA  
38 0.001379 0.1215 stm0150 aroP -12.21 0.313123 213 -- 232 63 -- 83 APC family aromatic amino acid 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)

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Results are computed with CopraRNA version 2.1.2