Figure 2

A Plan7 profile-HMM. This is the Plan7 profile-HMM employed in the HMMER package for scans of nucleotide or polypeptide sequences [13]. Most transitions are assigned scores (not shown). Additionally, each match state (M) and each insertion state (I) emits a character, as does each of the self-loop transitions for the prefix (N), suffx (C), and joining (J) states. Typically, the emission scores vary among the match states; they can vary among the insertion states as well. A score of zero is employed for each possible emission from the N, C, and J self-loop transitions. The D1 and D4 states are shaded, to indicate that, unlike the other positions, the first and last positions of a profile-HMM do not have delete states (D).