Freiburg RNA Tools
CARNA - Ensemble Alignment
BIF
IFF
CARNA

CARNA - Ensemble Alignment

CARNA is a tool for multiple alignment of RNA molecules. CARNA requires only the RNA sequences as input and will compute base pair probability matrices and align the sequences based on their full ensembles of structures. Alternatively, you can also provide base pair probability matrices (dot plots in .ps format) or fixed structures (as annotation in the FASTA alignment) for your sequences. If you provide fixed structures, only those structures and not the entire ensemble of possible structures is aligned. In contrast to LocARNA, CARNA does not pick the most likely consensus structure, but computes the alignment that fits best to all likely structures simultaneously. Hence, CARNA is particularly useful when aligning RNAs like riboswitches, which have more than one stable structure. Also, CARNA is not limited to nested structures, but is able to align arbitrary pseudoknots.

For articles describing the tool refer to the reference section below. Please cite us when using our tools.
For more information check the help page.

Try CARNA with these examples:

Input Parameter

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Note: each dot plot has to correspond to a sequence from the above FASTA input.

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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 2.2.7