Freiburg RNA Tools
AntaRNA - Results
BIF
IFF
AntaRNA 7495372

Input and runtime details for job 7495372 (precomputed example)

Constraints

? Structure constraint.(((....[[[[[)))..]]]]]......
? Sequence constraintNGNNGNNNNNNNANGNUNNNNNNUNNNNU
? Targeted GC-content [0..1]0.4
? Maximum for uniform distribution samplingnot provided
? Variance for normal distribution samplingnot provided

Constraint

? Allow GU base pairsyes
? Allow pseudoknotsyes

Energy

? Folding temperature37.0

AntaRNA

? Max. terrain resets5
? Convergence counts130
? Ant termination criterion50
? Probability weight alpha1
? Probability weight beta1
? Pheromone evaporation rate0.2
? Constraint weight structure0.5
? Constraint weight sequence1
? Constraint weight GC-value5
? Random seednot provided

Output

? Number of sequences10

Job ID 7495372 (server version 4.0.0)

?Job Submitted & Queued@ Fri Jun 19 13:30:44 CEST 2015
?AntaRNA Started@ Fri Jun 19 13:30:52 CEST 2015
?AntaRNA Finished & Post-Processing@ Fri Jun 19 13:31:09 CEST 2015
?Post-Processing Finished@ Fri Jun 19 13:31:10 CEST 2015
?Job Completed@ Fri Jun 19 13:31:11 CEST 2015
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7495372&toolName=AntaRNA ( 30 days expiry )

Description of the job

Design sequences for the crossing pseudoknot structures PKB298 with low GC-content.

? Output download complete results [zip]

Designed sequences

Name Sequence & mfe GC% dStr% dSeq% dGC%
Target NGNNGNNNNNNNANGNUNNNNNNUNNNNU
.(((....[[[[[)))..]]]]]......
40.0
antaRNA_0 CGCAGCAUAUAGAUGCUCUCUGUUUUUGU
.[[[....{{{{{]]]..}}}}}......
41.3 0.0 0.0 0.0
antaRNA_1 GGCCGGAUGCUAAGGUUAUUAGUUUAUGU
.[[[....{{{{{]]]..}}}}}......
41.3 0.0 0.0 0.0
antaRNA_2 AGCGGUUUCACAAUGUUCUUGUGUUUGUU
.[[[....{{{{{]]]..}}}}}......
37.9 0.0 0.0 0.0
antaRNA_3 UGUCGUCUACUGAGGCUCUUAGUUGUAAU
.[[[....{{{{{]]]..}}}}}......
41.3 0.0 0.0 0.0
antaRNA_4 CGCCGUAUCUAAAGGCUAUUUGGUAGAAU
.[[[....{{{{{]]]..}}}}}......
41.3 0.0 0.0 0.0
antaRNA_5 GGCCGUACACUAAGGUUAUUGGUUUGUAU
.[[[....{{{{{]]]..}}}}}......
41.3 0.0 0.0 0.0
antaRNA_6 CGUAGUAUGAAGAUGCUCUCUUCUAAAGU
.[[[....{{{{{]]]..}}}}}......
37.9 0.0 0.0 0.0
antaRNA_7 CGUCGUCUAAUGAGGCUGUCAUUUCAAUU
.[[[....{{{{{]]]..}}}}}......
41.3 0.0 0.0 0.0
antaRNA_8 GGUCGACUCAUUAGGCUUUGGUGUAUUAU
.[[[....{{{{{]]]..}}}}}......
41.3 0.0 0.0 0.0
antaRNA_9 CGUCGUCUUGAAAGGCUAUUUCAUUGAUU
.[[[....{{{{{]]]..}}}}}......
37.9 0.0 0.0 0.0


Download:

Visualization of the selected sequence

[save as SVG] Explicit constraint violations are highlighted in red. Visualization done with forna (Kerpedjiev et al., 2015)

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.

de.NBI usability assessment

Please support us by filling this short quality survey for evaluating this de.NBI service.

When using AntaRNA please cite :

Results are computed with AntaRNA version 1.1.2 using Vienna RNA package 2.1.8 or pKiss (2014-03-17)