Figure 1
From: Generalizations of Markov model to characterize biological sequences
The figure illustrates the six configurable parameters. There are three parameter associated with the prior – model unit size L 1 , order (number of units) 0, and spacing between units g 1 . There are two parameter associated with the posterior – model unit size L 2 , and spacing between bases g 2 . And there is a gap parameter G. Although not as general as arbitrary graphical models, this implementation is highly configurable with respect to model unit sizes and the dependence structures in terms of gap lengths.