Freiburg RNA Tools
AntaRNA - Results
BIF
IFF
AntaRNA 5955684

Input and runtime details for job 5955684 (precomputed example)

Constraints

? Structure constraint(((((((..((((......)))).(((((.......)))))....(((((.......))))))))))))
? Sequence constraintNNNNNNNNAGNNNNNNGGANNNNNNNNGNCNNNNAANCNNNNNNNNNNGGNNNNANNCCNNNNNNNNNN
? Targeted GC-content [0..1]0.8
? Maximum for uniform distribution samplingnot provided
? Variance for normal distribution samplingnot provided

Constraint

? Allow GU base pairsyes
? Allow pseudoknotsno

Energy

? Folding temperature37.0

AntaRNA

? Max. terrain resets5
? Convergence counts130
? Ant termination criterion50
? Probability weight alpha1.0
? Probability weight beta1.0
? Pheromone evaporation rate0.2
? Constraint weight structure0.5
? Constraint weight sequence1.0
? Constraint weight GC-value5.0
? Random seednot provided

Output

? Number of sequences10

Job ID 5955684 (server version 4.0.0)

?Job Submitted & Queued@ Fri Jun 19 13:30:28 CEST 2015
?Processing Started@ Fri Jun 19 13:30:37 CEST 2015
?AntaRNA Finished & Post-Processing@ Fri Jun 19 13:30:54 CEST 2015
?Post-Processing Finished@ Fri Jun 19 13:30:54 CEST 2015
?Job Completed@ Fri Jun 19 13:30:54 CEST 2015
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=5955684&toolName=AntaRNA ( 30 days expiry )

The job description you specified

Design sequences for the clover leaf form of a tRNA with high GC-content.

? Output download complete results [zip]

Designed sequences

Name Sequence & mfe GC% dStr% dSeq% dGC%
Target NNNNNNNNAGNNNNNNGGANNNNNNNNGNCNNNNAANCNNNNNNNNNNGGNNNNANNCCNNNNNNNNNN
(((((((..((((......)))).(((((.......)))))....(((((.......))))))))))))
80.0
antaRNA_0 GCCGCGGGAGCCCGCGGGAGGGCAGCCGCCACCUAAGCGGCCCGCCGCGGAAAUAGGCCGCGCUGCGGC
(((((((..((((......)))).(((((.......)))))....(((((.......))))))))))))
81.1 0.0 0.0 0.0
antaRNA_1 CCCGCGCGAGCCGGGAGGACGGCGCGAGCCCAUCAAGCUCGACGGCGCGGCCGGAAACCGCGGCGCGGG
(((((((..((((......)))).(((((.......)))))....(((((.......))))))))))))
81.1 0.0 0.0 0.0
antaRNA_2 GCGGCCGUAGCCCGCGGGAGGGCGGCCGCCGACGAAGCGGUAACACGGGGACCCAAGCCUCGCGGCCGC
(((((((..((((......)))).(((((.......)))))....(((((.......))))))))))))
79.7 0.0 0.0 0.0
antaRNA_3 GGCCCCCGAGACCAGGGGAGGUCGGCGGGCCCGCAACCCGCGUCUGCAGGAGCAACGCCUGCGGGGGCC
(((((((..((((......)))).(((((.......)))))....(((((.......))))))))))))
79.7 0.0 0.0 0.0
antaRNA_4 CGGCCCCGAGCCCCGCGGAGGGCGACCGCCCCGCAAGCGGUACUGCACGGAAGGAACCCGUGGGGGCCG
(((((((..((((......)))).(((((.......)))))....(((((.......))))))))))))
79.7 0.0 0.0 0.0
antaRNA_5 CGCCCGCGAGCUCGUGGGAGAGCGGGCGGCAGGGAACCGCCGGGGGCCGGAAACAGACCGGCGCGGGCG
(((((((..((((......)))).(((((.......)))))....(((((.......))))))))))))
81.1 0.0 0.0 0.0
antaRNA_6 CCCCGCCGAGCCUGACGGAGGGUGGCGGCCGGAAAAGCCGCACGAGCCGGGCACACGCCGGCGGCGGGG
(((((((..((((......)))).(((((.......)))))....(((((.......))))))))))))
81.1 0.0 0.0 0.0
antaRNA_7 CCGCGGCAAGCCCGCCGGAGGGCGUCCGCCGAGGAAGCGGAGAUGCCGGGAGGGAGACCCGGGCUGCGG
(((((((..((((......)))).(((((.......)))))....(((((.......))))))))))))
79.7 0.0 0.0 0.0
antaRNA_8 GCCGCCUGAGGACCUCGGAGUCCCCCCGCCAAAGAAGCGGGACCGCCCGGCGCGAUCCCGGGGGGCGGC
(((((((..((((......)))).(((((.......)))))....(((((.......))))))))))))
79.7 0.0 0.0 0.0
antaRNA_9 GCCGCCGCAGCGAGGCGGAUCGCAGGGGCCCCCUAAGCCCCCGGAGGCGGCUGAAGACCGCCCGGCGGC
(((((((..((((......)))).(((((.......)))))....(((((.......))))))))))))
81.1 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)