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INFORNA 7154744

Input and runtime details for job 7154744 (precomputed example)

Constraints

? RNA Secondary Structure(((((...(((((......))))).)))))
? Sequence Constraints and Allowed Violations6 U + 7 G + 8 C - 14 C - 15 A - 16 G - 17 U - 18 G - 19 H + 25 C -
? Maximal number of violations999

Parameters for the Stochastic Local Search

? Objective function mfe (default)
? Probability for accepting bad mutations0.1
? Pre-sort candidates for mutation yes (default)

Result Parameters

? Number of Designed Sequences1

Job ID 7154744 (server version 4.0.0)

?Job Submitted & Queued@ Thu Jun 18 18:36:30 CEST 2015
?Processing Started@ Thu Jun 18 18:36:37 CEST 2015
?INFORNA Finished & Post-Processing@ Thu Jun 18 18:36:38 CEST 2015
?Job Completed@ Thu Jun 18 18:36:39 CEST 2015
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=7154744&toolName=INFORNA ( 30 days expiry )

The job description you specified

Hairpin loop design

Output

Result files for download

download full results [zip]

INFO-RNA Results

Input:

General Parameters:
    RNA secondary structure:
5'-(((((...(((((......))))).)))))-3'
    Sequence constraints:
5'-NNNNNUGCNNNNNCAGUGHNNNNNCNNNNN-3'
    Allowed constraint violations:
5'-000001100000000000100000000000-3'
    Maximal number of violations: 999
Parameters for the Stochastic Local Search:
    Objective function: mfe
    Probability for accepting bad mutations: 0.1
    Pre-sort candidates for mutation: yes

Results:

1. Designed Sequence:

Designed sequence:
5'-GGGCCUACGCCCCCAGUGAGGGGCCGGCCC-3'
Target structure:
5'-(((((...(((((......))))).)))))-3'
Constraint violations: 1
Free energy (target structure): -19.50 kcal/mol
Folding probability (target structure): 0.851084
Base pair distance of the mfe structure
to the target structure:
0
mfe structure: (.svg figure)
5'-(((((...(((((......))))).)))))-3'

Direct output for copy and paste:
designed sequence →  
target structure →  
mfe structure →  
Downloadable File Formats (designed sequence + its mfe structure):

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When using INFORNA please cite :

Results are computed with INFORNA version 2.2.0 linking Vienna RNA package 1.8.4