Enlargement of null model and internal looped codons. LEFT: The state structure of the NULL model. The background state is of third order and models the general composition of the genome. The three shadow states model coding regions on the complementary strand. There are transitions from the background state to the first RBS state and to the first state modelling the start codon. RIGHT: Details of model of internal codons. A codon is modelled by three states with a transition from the last state back to the first and one out of the codon model. By putting several codon models in series, the length distribution of coding regions can be captured. From the last state there is a transition to the first state of the 'BSTOP' model, which models the last codon before the stop codon.
Larsen and Krogh BMC Bioinformatics 2003 4:21 doi:10.1186/1471-2105-4-21