Nucleic Acid Structure Prediction - Comparative Secondary Structure Prediction

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:

  1. Folding of alignment
  2. Simultaneous sequence alignment and folding
  3. Alignment of predicted structures

Read more about this topic:  Nucleic Acid Structure Prediction

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