Remote homology search with hidden Potts models
Fig 1
Hidden Potts model architecture.
Squares are conserved match states and diamonds are insert states. No delete states exist. Silent begin and end states are represented by circles. An HPM is a hybrid between a Potts model and a pHMM: correlated character generation (including deletion “characters” rather than delete states) in match columns (consensus sites in an MSA) comes from a Potts distribution (dotted orange arrows), while transition probabilities linking states and site-independent character emissions in unaligned insert columns come from a pHMM (solid and dashed black arrows, respectively).