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]
[csv]
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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
138 0.007086 0.182 stm0624 citC -16.00 0.081371 136 -- 192 38 -- 93 [citrate (pro-3S)-lyase] ligase stm0058
134 0.006725 0.1774 stm0546 fimD -17.45 0.046766 176 -- 200 37 -- 60 outer membrane usher protein stm0301 stm0175 stm4593 stm3638 stm0023
190 0.01053 0.1967 stm4032 N/A -12.98 0.242168 37 -- 92 31 -- 85 lipase stm0490
75 0.003517 0.1596 stm1214 ycfR -14.36 0.148951 168 -- 212 35 -- 81 multiple stress resistance protein BhsA stm0823
95 0.004301 0.1596 stm4114 pflD -11.77 0.360092 46 -- 100 34 -- 88 formate C-acetyltransferase stm0843
46 0.001637 0.1267 stm2313 elaC -17.21 0.051329 250 -- 300 51 -- 90 ribonuclease Z stm1109
135 0.006796 0.1774 stm1044 sodC -14.39 0.147293 208 -- 244 43 -- 78 Gifsy-2 prophage superoxide dismutase precursor (Cu-Zn) stm1440 stm0924
58 0.002307 0.14 stm2234 N/A -13.92 0.174542 131 -- 196 38 -- 89 phage tail protein stm2705 stm2233
74 0.003449 0.1596 stm1129 N/A -19.64 0.020096 190 -- 238 139 -- 186 N-acetylmannosamine-6-phosphate 2-epimerase stm3337
41 0.001426 0.1215 stm3718 rfaI -15.09 0.114319 193 -- 209 157 -- 173 lipopolysaccharide 1 3-galactosyltransferase stm3717

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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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2