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Chapter 8: Prediction of RNA Secondary Structure
Chapters 3 and 5 have discussed the alignment of protein and nucleic acid sequences using methods that either align entire sequences or search for common patterns in the sequences. In either case, the objective is to locate a set of sequence characters in the same order in the sequences. Nucleic acid sequences that specify RNA molecules must be compared differently because sequence variations in RNA sequences maintain base-pairing patterns that give rise to double-stranded regions, called secondary structures, and three-dimensional, tertiary structures in the molecule that are necessary for biological function. Sequences of RNA-specifying genes may also have rows of similar sequence characters that reflect the common ancestry of the genes.
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