Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation
Fig 10
A few states in the internal region of a B cell receptor sequence HMM.
On the left is a state representing a position in a gene with a germline G, which usually emits a G, but sometimes emits other bases (i.e. mutates). If this state is near enough to the start or end of the gene, there will likely be transitions from the initial state, or to the end state (upper arrows). On the other hand, if it is in the middle of a gene the path is more likely to simply traverse the states in order (straight horizontal arrows).