Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties
A. Schematic of a hypothetical GISMO phase 1 block based alignment, which is initialized to consist of many short, ungapped aligned blocks. B. Architecture for the GISMO phase 2 HMM. Red transition arrows between states emit residues. Transition probabilities are inferred from the sequence data. Note that the HMM is local with respect to each sequence but global with respect to the model.