Use the following button if you want to resubmit the job with
altered input or parameterization:
Input and runtime details for job 7154744 (precomputed example)
Constraints
RNA Secondary Structure | (((((...(((((......))))).))))) | ||
Sequence Constraints and Allowed Violations | 6 U +
7 G +
8 C -
14 C -
15 A -
16 G -
17 U -
18 G -
19 H +
25 C - | ||
Maximal number of violations | 999 |
Parameters for the Stochastic Local Search
Objective function | mfe (default) | ||
Probability for accepting bad mutations | 0.1 | ||
Pre-sort candidates for mutation | yes (default) |
Result Parameters
Number of Designed Sequences | 1 |
Job ID 7154744 (server version 4.0.0)
Job Submitted & Queued | @ Thu Jun 18 18:36:30 CEST 2015 | ||
INFORNA 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: https://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7154744&toolName=INFORNA ( 30 days expiry )
Description of the job
Hairpin loop design
Design of a long hairpin loop with soft and hard sequence constraints
Output
Result files for download
download full results [zip]
INFO-RNA Results
Input:
General Parameters: | |||
RNA secondary structure: |
| ||
Sequence constraints: |
| ||
Allowed constraint violations: |
| ||
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: |
| |||
Target structure: |
| |||
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) |
| |||
Direct output for copy and paste:
designed sequence → target structure → mfe structure → |
Downloadable File Formats (designed sequence + its mfe structure):
Job resubmission
usability assessment
When using INFORNA please cite :
- Anke Busch and Rolf Backofen
INFO-RNA - A Server for Fast Inverse RNA Folding Satisfying Sequence Constraints
Nucleic Acid Research, 35 (Web Server Issue) W310-3, 2007 - Anke Busch and Rolf Backofen
INFO-RNA - a fast approach to inverse RNA folding
Bioinformatics, 22 no. 15 pp. 1823-31, 2006 - Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.
Results are computed with INFORNA version 2.2.0 linking Vienna RNA package 1.8.4