Figure 3

Simplified topology of a jumping profile HMM (jpHMM). The sequence family $\mathcal{S}$ is partitioned into k subtypes $\mathcal{S}$₁,...,$\mathcal{S}$ _k . Each subtype is modeled by a profile HMM here pictured as a dashed box. Arrows indicate possible transitions between states within the same subtypes and transitions between different subtypes, so-called jumps. For clarity we omit insert and delete states of the profile HMMs and sketch a case where the first three columns are consensus columns.