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
?CopraRNA 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: https://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

Output download complete results [zip]

Downloadable files

[csv]
[txt]
[csv]
[png] [pdf] [ps]
[png] [pdf] [ps]
[html] [pdf]
[png] [pdf]
[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
6 7.515e-05 0.04123 stm0665 gltI -17.87 0.039793 157 -- 199 35 -- 81 glutamate/aspartate transporter  
25 0.0006298 0.08814 stm3161 metC -13.21 0.223681 190 -- 249 35 -- 90 cystathionine beta-lyase  
37 0.001263 0.1215 stm2511 guaB -22.14 0.007548 255 -- 298 35 -- 73 IMP dehydrogenase  
66 0.003179 0.1596 stm0264 dnaQ -14.69 0.132400 209 -- 271 35 -- 91 DNA polymerase III epsilon subunit  
73 0.003444 0.1596 stm1437 ydhM -18.33 0.033340 6 -- 47 35 -- 81 TetR family transcriptional regulator  
75 0.003517 0.1596 stm1214 ycfR -14.36 0.148951 168 -- 212 35 -- 81 multiple stress resistance protein BhsA stm0823
84 0.003893 0.1596 stm2015 erfK -27.15 0.001054 109 -- 172 35 -- 90 L D-transpeptidase  
87 0.004009 0.1596 stm2067 sbcB -11.70 0.367652 220 -- 292 35 -- 90 exodeoxyribonuclease I  
89 0.004143 0.1596 stm2957 ygcA -15.40 0.101796 159 -- 208 35 -- 82 23S rRNA (uracil(1939)-C(5))-methyltransferase  
94 0.0043 0.1596 stm3866 atpG -16.85 0.058909 206 -- 253 35 -- 80 F0F1 ATP synthase subunit gamma  

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

Use the following button if you want to resubmit the job with altered input or parameterization:
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