Table 1 Overview of methods
From: Strategies for measuring evolutionary conservation of RNA secondary structures
Category | Methods | Description | References |
|---|---|---|---|
Methods based on folding energies | SCI | RNAalifold consensus energy normalized by dividing by the average energy of the single sequences folded independently. | [7] |
| Â | SCI RN Aeval | Evaluation of energies of sequences under the constraint of being forced to fold into the structures of the other sequences in comparison to the unconstrained energies. | this work |
Methods based on single structures | Base-pair distance | Number of base-pairs not shared by two structures. | [64] |
| Â | Mountain metric | Distance as the difference of two mountain functions, which give the number of base-pairs enclosing a position. | [40] |
| Â | Tree editing | Based on the representation of RNA secondary structures as trees. A distance is deined as the cost of transforming one tree into the other. | [41-43] |
Methods considering the entire folding space | Ensemble distance | Base-pair distance extended to compare ensembles of structures. | this work |
| Â | Ensemble mountain metric | Distance as the difference of two mountain functions, which give the number of base-pairs that are, on average, expected to enclose a position. | [47] |
| Â | RNApdist like distance | Distance measure based on the comparison of vectors of probabilities of being paired upstream, paired downstream, and unpaired. | [33,48] |
| Â | RNAshapes | Similarity measure based on probabilities of abstract shapes. | [49] |
Other Methods | ddbRNA | Evaluates compensatory mutations in all possible stem loops in all sequences of an alignment. | [9] |
| Â | MSARi | Evaluation of the statistical significance of short, contiguous potential base-pair regions under different distribution models. | [8] |