Freiburg RNA Tools
CARNA - Results
CARNA 3326122

Input and runtime details for job 3326122 (precomputed example)

Input Parameter

? Sequence Input in FASTA Format[.fa]
? Upload dot plotsnot provided
? Predict dot plots with pseudoknots (NUPACK)

Scoring Parameters

? Structure Weight200
? Indel Opening Score-500
? Indel Score-350
? Use RIBOSUMyes
? Match Score50
? Mismatch Score0

Heuristics for speed/accuracy tradeoff

? Minimal Pair Probability0.01
? Maximal Difference for Sizes of Matched Arcs30
? Maximal Difference for Alignment Edges60

Other Parameter

? Ignore Constraintsno
? Search Time Limit (in milliseconds)300000
? Disallow Lonely Pairsyes

Job ID 3326122 (server version trunk)

?Job Submitted & Queued@ Fri Jul 22 11:59:54 CEST 2016
?CARNA Started@ Fri Jul 22 11:59:56 CEST 2016
?CARNA Finished & Post-Processing@ Fri Jul 22 12:00:01 CEST 2016
?Post-Processing Finished@ Fri Jul 22 12:02:00 CEST 2016
?Job Completed@ Fri Jul 22 12:02:15 CEST 2016
 DIRECT ACCESS: ( 30 days expiry )

Description of the job


This example demonstrates CARNA's capability to align RNA with pseudoknots. In this example, we provide fixed input structures with pseudoknots. Thereby, we demonstrate the syntax of constraint annotation in the fasta file. In the output of this example correct alignment of the pseudoknots is best seen from our conservation consensus dot plot representation. Please note that the consensus structure in the shown alignment (Alignment annotated with pseudoknot-free consensus structure) does not show the pseudoknot because this consensus structure is generated by RNAalifold from the CARNA alignment. RNAalifold was not designed to predict pseudoknots. Since we provide fixed structures in this example, it runs with default settings. To predict pseudoknots from ensembles, one has to explicitly predict the ensemble dot plots with pseudoknots. This is supported via a tool from NUPACK. Due to the hardness of pseudoknot folding, this will work for only comparably simple pseudoknots as described by Dirks and Pierce (J Comput Chem, 2004).

Outputdownload complete results [zip]

Conservation Dot Plots

Loading image Plot View

Plot View
Base Pairs
magnifier Click on the dot plot to enlarge it.

Dot plot modifier

highlight average probabilities ≥ off

Probability Threshold

0.10 [ps] [png] [pdf]
0.25 [ps] [png] [pdf]
0.50 [ps] [png] [pdf]

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).

Rainbow color legend

Alignment annotated with pseudoknot-free consensus structure

download [ps] [png] [pdf]
download [alignment] [FASTA] [structure] [matrix] [tree]
Aligned 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

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:
Feeds the job parameters to the input page to resubmit the job.

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When using CARNA please cite :

Results are computed with CARNA version 1.3.2 linking LocARNA 1.8.10, Gecode 4.4.0, using Vienna RNA package 2.2.5