HMM and alignment

• The alignment algorithm maximizes a weighted form of coemission probability, the probability that the two HMMs will emit the same sequence of residues.
• Amino acids are weighted according to their abundance, rare coemitted amino acids contributing more to the alignment score.
• This weighting is analogous to the use of a null model with amino acid background probabilities in HMM-sequence comparison.

• Profile HMMs are similar to simple sequence profiles, but in addition to the amino acid frequencies in the columns of a multiple sequence alignment they contain the position-specific probabilities for inserts and deletions along the alignment
• The logarithms of these probabilities are in fact equivalent to position-specific gap penalties (Durbin et al., 1998).