Use the following button if you want to resubmit the job with
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Input and runtime details for job 2588722 (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
Heuristics for speed/accuracy tradeoff
Minimal Pair Probability | 5.0E-4 | ||
Minimal Probability for Guide Tree Construction | 0.005 | ||
Maximal Difference for Sizes of Matched Arcs | 30 | ||
Maximal Difference for Alignment Edges | 60 |
Other Parameters
Ignore Constraints | no | ||
Disallow Lonely Pairs | yes | ||
Use alifold consensus dot plots | no | ||
Consistency Transformation (LocARNA-P only) | no | ||
Keep Sequence Input Order | no | ||
Stockholm alignment output | yes |
Job ID 2588722 (server version 4.4.4)
Job Submitted & Queued | @ Thu Jun 08 13:25:35 CEST 2017 | ||
LocARNA Started | @ Thu Jun 08 13:25:48 CEST 2017 | ||
LocARNA Finished & Post-Processing | @ Thu Jun 08 13:25:53 CEST 2017 | ||
Post-Processing Finished | @ Thu Jun 08 13:25:58 CEST 2017 | ||
Job Completed | @ Thu Jun 08 13:25:58 CEST 2017 |
DIRECT ACCESS: https://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2588722&toolName=LocARNA ( 30 days expiry )
Description of the job
snoRNAs with constraints
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 = ACA7 ACA5 #A1 #A2
- intermediates/intermediate2.aln = ACA7 ACA5 ACA30 #A1 #A2
- intermediates/intermediate3.aln = ACA7 ACA5 ACA30 ACA59 #A1 #A2
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