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
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  
72 0.003348 0.1596 stm0849 yliB -19.23 0.023527 175 -- 193 139 -- 162 glutathione ABC transporter substrate-binding protein GsiB  
73 0.003444 0.1596 stm1437 ydhM -18.33 0.033340 6 -- 47 35 -- 81 TetR family transcriptional regulator  
74 0.003449 0.1596 stm1129 N/A -19.64 0.020096 190 -- 238 139 -- 186 N-acetylmannosamine-6-phosphate 2-epimerase stm3337
75 0.003517 0.1596 stm1214 ycfR -14.36 0.148951 168 -- 212 35 -- 81 multiple stress resistance protein BhsA stm0823
76 0.003538 0.1596 stm3058 pepP -14.75 0.129287 129 -- 167 36 -- 78 Xaa-Pro aminopeptidase  
77 0.003608 0.1596 stm4473 yjgM -11.12 0.437983 252 -- 285 42 -- 82 GNAT family N-acetyltransferase  
78 0.003685 0.1596 stm0423 ispA -20.49 0.014403 269 -- 289 38 -- 58 (2E 6E)-farnesyl diphosphate synthase  
79 0.003723 0.1596 stm1723 trpE -16.56 0.065817 202 -- 256 41 -- 91 anthranilate synthase subunit I  
80 0.003756 0.1596 stm0132 ftsA -17.45 0.046754 189 -- 236 139 -- 186 cell division protein FtsA  

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