Difference between revisions of "HMM and alignment"
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* The logarithms of these probabilities are in fact equivalent to position-specific gap penalties (Durbin et al., 1998). | * The logarithms of these probabilities are in fact equivalent to position-specific gap penalties (Durbin et al., 1998). | ||
| − | [[File:HMM 1998 review.png]] | + | [[File:HMM 1998 review.png|400px]] |
* '''The alignment algorithm maximizes a weighted form of coemission probability, the probability that the two HMMs will emit the same sequence of residues. ''' | * '''The alignment algorithm maximizes a weighted form of coemission probability, the probability that the two HMMs will emit the same sequence of residues. ''' | ||
Revision as of 18:19, 11 February 2013
- 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).
- 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.
- Secondary structure can be included in the HMM-HMM comparison.
- We score pairs of aligned secondary structure states in a way analogous to the classical amino acids substitution matrices.
- We use ten different substitution matrices that we derived from a statistical analysis of the structure database, one for each confidence value given by PSIPRED.