Figure 6
From: XRate: a fast prototyping, training and annotation tool for phylo-grammars
Example Stockholm-format output using the protein secondary structure grammar (see figure 4) and the pancreatic hormone alignment (see figure 5). Line numbers have been added for reference; note the embedded New Hampshire-format tree at line 2, the Viterbi bit-score at line 3 and the Viterbi secondary structure annotation at line 7.