Input and runtime details for job 4329548 (precomputed example)
Input Parameter
 Sequence Input in FASTA Format | [.fa] | ||
| Upload dot plots | not provided | ||
| Predict dot plots | with pseudoknots (NUPACK) |
Scoring Parameters
| Structure Weight | 200 | ||
| Indel Opening Score | -500 | ||
| Indel Score | -350 | ||
| Use RIBOSUM | yes | ||
| Match Score | 50 | ||
| Mismatch Score | 0 |
Heuristics for speed/accuracy tradeoff
| Minimal Pair Probability | 0.01 | ||
| Maximal Difference for Sizes of Matched Arcs | 30 | ||
| Maximal Difference for Alignment Edges | 60 |
Other Parameter
| Ignore Constraints | no | ||
| Search Time Limit (in milliseconds) | 300000 | ||
| Disallow Lonely Pairs | yes |
Job ID 4329548 (server version trunk)
 | Job Submitted & Queued | @ Tue Jan 24 17:32:34 CET 2017 | |
| CARNA Started | @ Tue Jan 24 17:37:01 CET 2017 | |
| CARNA Finished & Post-Processing | @ Tue Jan 24 17:37:05 CET 2017 | |
| Post-Processing Finished | @ Tue Jan 24 17:38:23 CET 2017 | |
| Job Completed | @ Tue Jan 24 17:38:25 CET 2017 |
DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4329548&toolName=CARNA ( 30 days expiry )
Description of the job
alignment of pseudoknots from familiy HDV RF00094
HDV RF00094 pseudoknots
Outputdownload complete results [zip]
Conservation Dot Plots
Loading image 
Consensus(average)
Click on the dot plot to enlarge it.
![[png]](/DownloadFile.jsp?jobID=4329548&toolName=CARNA&fileNameOrType=input.out/plots/average_dlin_025.png){kind=link}
![[png]](/DownloadFile.jsp?jobID=4329548&toolName=CARNA&fileNameOrType=input.out/plots/average_dlin_05.png){kind=link}
For interpretation of the colors see the legend below. For a detailed description of the output, please see the help page.
Color Legend
The lower left triangle of the dot plots contains the average dot plot colored with variance information. Pure green means maximum variance (e.g. in half of the sequences the dot has probability 0 and in the other half it has probability 1); pure red means no variance at all (the dot has the same probability in all sequences).
Alignment annotated with pseudoknot-free consensus structure
Bases are encoded by IUPAC codes. For interpretation of the colors see the legend below. For a detailed description of the output, please see the help page.
Color Legend
Compatible base pairs are colored, where the hue shows the number of different types C-G, G-C, A-U, U-A, G-U or U-G of compatible base pairs in the corresponding columns. In this way the hue shows sequence conservation of the base pair. The saturation decreases with the number of incompatible base pairs. Thus, it indicates the structural conservation of the base pair.
Job resubmission
Use the following button if you want to resubmit the job with
altered input or parameterization:
usability assessment
When using CARNA please cite :
- Dragos A. Sorescu, Mathias Moehl, Martin Mann, Rolf Backofen, and Sebastian Will
CARNA - alignment of RNA structure ensembles
Nucleic Acids Reseach, 2012, 40 no. W1 pp. W49-W53 - Alessandro Dal Palu, Mathias Moehl, Sebastian Will
A Propagator for Maximum Weight String Alignment with Arbitrary Pairwise Dependencies
Proceedings of the 16th International Conference on Principles and Practice of Constraint Programming (CP-2010), 2010, 8 - 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 CARNA version 1.3.3 linking LocARNA 1.9.1, Gecode 5.0.0, using Vienna RNA package 2.3.2
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