Difference between revisions of "HMM and alignment"
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==From HHpred original ''Bioinformatics'' paper== | ==From HHpred original ''Bioinformatics'' paper== | ||
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| + | * 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). | ||
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[[Category:Bioinfo notes]] | [[Category:Bioinfo notes]] | ||
Revision as of 17:37, 11 February 2013
From HHpred original Bioinformatics paper
- 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).