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Input and runtime details for job 7235457 (precomputed example)
Input Parameter
Sequence Input in FASTA Format | [.fa] |
Scoring Parameter
Minimal size of included substructures | 7 | ||
Maximal number of used substructures | all | ||
EPM scoring | just EPM size (default) |
Output Parameter
Write ExpaRNA result as alignment into text file | no | ||
Write ExpaRNA results as list in file | no | ||
Write all EPMs into file | no |
Job ID 7235457 (server version unknown)
Job Submitted & Queued | @ Fri Jan 11 16:14:43 CET 2013 | ||
ExpaRNA Started | @ Fri Jan 11 16:14:57 CET 2013 | ||
ExpaRNA Finished & Post-Processing | @ Fri Jan 11 16:14:58 CET 2013 | ||
Post-Processing Finished | @ Fri Jan 11 16:15:05 CET 2013 | ||
Job Completed | @ Fri Jan 11 16:15:06 CET 2013 |
DIRECT ACCESS: https://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7235457&toolName=ExpaRNA ( 30 days expiry )
Output parameters
Write ExpaRNA result as input for LocARNA with anchor constraints | [.fa] |
Description of the job
small example
Alignment of two relatively small ncRNAs without pre-defined structure. Here, the minimum free energy structure is computed and used for the alignment.
Output download complete results [zip]
Feed the Anchor Constraints" produced by ExpaRNA into the LocARNA tool.
Graphical output
Sequence 1 | Sequence 2 |
download   [.pdf]   [.ps]   [.png]   | download   [.pdf]   [.ps]   [.png]   |
Job resubmission
usability assessment
When using ExpaRNA please cite :
- Steffen Heyne, Sebastian Will, Michael Beckstette, and Rolf Backofen
Lightweight comparison of RNAs based on exact sequence-structure matches
Bioinformatics, 25 no. 16 pp. 2095-2102, 2009 - 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 ExpaRNA version 1.0.0 linking Vienna RNA package 1.8.5