Transition probabilities

Transition probabilities are also known to vary quite a bit with the C+G content (although not as much as the initial probabilities). Thus, transition probabilities are also separately computed for each of the categories. Of course, while estimating these probabilities, it is ensured that the transitions are biologically permissible. For example, some transitions are obligatory (like $P^+\rightarrow F^+$ ). Such transitions are assigned probability one.