Use of Artificial Genomes in Assessing Methods for Atypical Gene Detection
Figure 7
The oval represents a hidden state, and the square represents observation sequence. Each state emits a string of nucleotides and then makes a transition to another state. The transitions that are allowed between hidden states are shown by line arrows, and the emission of observation sequence is shown by block arrows. This HMM generates one strand of a genome; by including models of reverse complement of protein-coding sequence (“Shadow”), the HMM encapsulates the information of sequences on both strands of DNA helix. The “Reverse Start” and “Reverse Stop” states correspond to the reverse complement of start codons and stop codons, respectively.