Freiburg RNA Tools
ExpaRNA - Exact Matching
BIF
IFF
ExpaRNA

ExpaRNA - Exact Matching

ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Instead of computing a full sequence-structure alignment, it computes the best arrangement of sequence-structure motifs common to two RNAs. A motif is a local (or isolated) substructure which is identical to both RNAs. ExpaRNA requires a given nested secondary structure for both RNAs. If no structure is available, RNAfold from Vienna RNA Package is used for a structure prediction. The accuracy of the algorithm is mainly controlled by the minimal size of the included sequence-structure motifs. ExpaRNA is especially useful for comparative structural RNA analysis and to speed-up complex sequence-structure alignment methods. For this purpose, the predicted common substructures by ExpaRNA are used as anchor constraints for a full structural alignment.

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 ExpaRNA with these examples:

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Output Parameter

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When using ExpaRNA please cite :

Results are computed with ExpaRNA version 1.0.0 linking Vienna RNA package 1.8.5