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Figure 4 | BMC Bioinformatics

Figure 4

From: XRate: a fast prototyping, training and annotation tool for phylo-grammars

Figure 4

An excerpt from an xgram-format grammar reproducing the protein secondary structure phylo-HMM of Goldman, Thorne and Jones. This excerpt shows only the transformation rules, and omits the alphabet and chain definitions. Three separate Markov chains for amino acid substitution are used (and are assumed to be defined elsewhere in the file): alpha_col denotes an amino acid in an alpha helix (annotated with character H), beta_col denotes an amino acid in a beta sheet (annotated with character E) and loop_col denotes an amino acid in a loop region (annotated with character L).

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