Difference between revisions of "HMM and alignment"
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| − | + | * '''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 | * 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 | ||
Revision as of 17:48, 11 February 2013
- 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).