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Figure 1 | BMC Bioinformatics

Figure 1

From: Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction

Figure 1

Examples of CFG parse trees for an example RNA structure Left: an RNA secondary structure with two stems. Middle: a parse tree for that structure using the grammar S → aS | aS | Sa | SS | ε, with nonterminals in red and terminals in black. Note the correspondence between the RNA structure and the structure of the parse tree; that the individual steps in the grammar correspond to base pairs and single nucleotides (that is, the grammar is used to factor the structure down into individually scored steps); and that the RNA sequence can be read off the parse tree by following the margin of the tree counterclockwise. Right: an alternative parse tree for the same structure, demonstrating that this grammar is structurally ambiguous.

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