Use the following button if you want to resubmit the job with
altered input or parameterization:
Input and runtime details for job 8334265 (precomputed example)
Sequence and Structure
 Sequence Input in FASTA Format | [.fa] |
Alignment
| Alignment Type | Global | ||
| Alignment Mode | no |
Alignment Scoring
| Structure Weight | 200 | ||
| Indel Opening Score | -800 | ||
| Indel Score | -50 | ||
| Use RIBOSUM | yes | ||
| Match Score | 50 | ||
| Mismatch Score | 0 |
RNA Folding
| Local folding: max. base pair span | 150 | ||
| Temperature in °C | 37.0 | ||
| Energy parameter set (Vienna package) | /scratch/rna/bisge001/Software/locarna/1.9.1_largepf/bin/rna_turner2004.par | ||
| Upload dot plots | not provided |
Heuristics for speed/accuracy tradeoff
| Minimal Pair Probability | 0.01 | ||
| Minimal Probability for Guide Tree Construction | 0.01 | ||
| Maximal Difference for Sizes of Matched Arcs | 30 | ||
| Maximal Difference for Alignment Edges | 40 |
Other Parameters
| Ignore Constraints | yes | ||
| Disallow Lonely Pairs | yes | ||
| Use alifold consensus dot plots | no | ||
| Consistency Transformation (LocARNA-P only) | yes | ||
| Keep Sequence Input Order | no | ||
| Stockholm alignment output | yes |
Job ID 8334265 (server version 4.4.4)
 | Job Submitted & Queued | @ Thu Jun 08 13:24:38 CEST 2017 | |
| LocARNA Started | @ Thu Jun 08 13:24:48 CEST 2017 | |
| LocARNA Finished & Post-Processing | @ Thu Jun 08 13:25:35 CEST 2017 | |
| Post-Processing Finished | @ Thu Jun 08 13:25:44 CEST 2017 | |
| Job Completed | @ Thu Jun 08 13:25:46 CEST 2017 |
DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8334265&toolName=LocARNA ( 30 days expiry )
Description of the job
RNA Boundaries with LocARNA-P
Output download complete results [zip]
Alignment annotated with RNAalifold consensus structure
download alignment
[ClustalW]
[Stockholm]
[FASTA]
[structure]
[structure-pairs]
download alignment figure
[.pdf]
[.ps]
[.png]
Bases are encoded by IUPAC codes. For interpretation of the colors see this legend. For a detailed description of the output, please see the help page.
Guide tree and Intermediate Alignments
download guide tree
[NEWICK format]
[.svg]
download
[similarity matrix]
Intermediate Alignments
- intermediates/intermediate1.aln = DroMel_CAF1 DroYak_CAF1
- intermediates/intermediate2.aln = DroMel_CAF1 DroYak_CAF1 DroSec_CAF1
- intermediates/intermediate3.aln = DroMel_CAF1 DroYak_CAF1 DroSec_CAF1 DroPer_CAF1
LocARNA-P Reliability Profile (STAR Profile Plot)
RNAalifold consensus structure
For interpretation of the colors see this legend. 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
usability assessment
When using LocARNA please cite :
- Sebastian Will, Tejal Joshi, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen.
LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs
RNA, 18 no. 5, pp. 900-14, 2012 - Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen.
Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering
PLoS Computational Biology, 3 no. 4, pp. e65, 2007 - 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 LocARNA version 1.9.1 linking Vienna RNA package 2.3.2
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