Figure 4.

The init_phased() algorithm. Initialization of a single exon array σ, given a sequence S = x₀..x_L-1, a set of three Markov chains P_{0,1,2}, and initial phase (i.e., phase of the first array element) ω. All parameters are assumed to be passed by reference. This procedure is similar to init_nonphased(), except that the conditional probabilities are computed in a phase-specific manner by the appropriate member of the three-periodic Markov chain.