Freiburg RNA Tools
CARNA - Results
CARNA 8880963

Input and runtime details for job 8880963 (precomputed example)

Input Parameter

? Sequence Input in FASTA Format[.fa]
? Upload dot plotsnot provided
? Predict dot plots without pseudoknots (RNAfold)

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 8880963 (server version trunk)

?Job Submitted & Queued@ Fri Jul 22 11:56:40 CEST 2016
?CARNA Started@ Fri Jul 22 11:56:56 CEST 2016
?CARNA Finished & Post-Processing@ Fri Jul 22 11:56:59 CEST 2016
?Post-Processing Finished@ Fri Jul 22 11:58:35 CEST 2016
?Job Completed@ Fri Jul 22 11:58:46 CEST 2016
 DIRECT ACCESS: ( 30 days expiry )

Description of the job

multiple conserved structures

In this small example, we align the RNA xbix to three designed variants that fold into the same two conserved structures. xbix was introduced as an example for multiple metastable structures by Wolfinger et al. (/J.Phys.A: Math.Gen./, 2004). It is instructive to compare the alignments of these sequences by CARNA and LocARNA. Whereas CARNA's alignment preserves both conserved structures in the consensus ensemble, LocARNA aligns only one of the two structures correctly and misaligns the other. The example works with the default settings of the server, i.e. dot plots of the ensembles are predicted without pseudoknots by RNAfold. For further illustration, we list the sequences with their conserved structures. xbixA is the original example from Wolfinger et al.


Multiple Conserved Structures Conservation dot plots for xbix variants A-D, the consensus conservation dot plot of CARNA's alignment and the consensus conservation dot plot of the alignment by LocARNA. The LocARNA consensus dot plot shows a misalignment of the inner stem of one of the two conserved structures. Only CARNA can simultaneously align both structures and aligns this stem and all other base pairs correctly. The misalignment by LocARNA is also seen by annotating LocARNA's alignment with the two conserved structures:


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