Comparative Secondary Structure Prediction
Sequence covariation methods rely on the existence of a data set composed of multiple homologous RNA sequences with related but dissimilar sequences. These methods analyze the covariation of individual base sites in evolution; maintenance at two widely separated sites of a pair of base-pairing nucleotides indicates the presence of a structurally required hydrogen bond between those positions. The general problem of pseudoknot prediction has been shown to be NP-complete.
In general, the problem of alignment and consensus structure prediction are closely related. Three different approaches to the prediction of consensus structures can be distinguished:
- Folding of alignment
- Simultaneous sequence alignment and folding
- Alignment of predicted structures
Read more about this topic: Nucleic Acid Structure Prediction
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