[PPT模板]ch 2 pair-align.ppt

* Percent Accepted Mutation (PAM or Dayhoff) Matrices Because changes observed in closely related proteins represent amino acid substitutions that do not significantly change the function of protein. Hence they are called “accepted mutations” defined as amino acid changes “accepted” by natural selection. * Percent Accepted Mutation (PAM or Dayhoff) Matrices Studied by Margaret Dayhoff Amino acid substitutions Alignment of common protein sequences 1572 amino acid substitutions 71 groups of protein, 85% similar * Percent Accepted Mutation (PAM or Dayhoff) Matrices Similar sequences organized into phylogenetic trees Number of amino acid changes into every other amino acid were counted Relative mutabilities were by counting the number of changes of each amino acid divided by a normalization factor. * Percent Accepted Mutation (PAM or Dayhoff) Matrices The factor which means exposure to mutation of the amino acid, is defined as F= fi *N fi is the frequency of occurrence of the amino acid in that group, and N is the total number of all amino acid changes that occurred in that group per 100 sites. * Percent Accepted Mutation (PAM or Dayhoff) Matrices This normalized the data for variations in amino acid composition, mutation rate, and sequence length. The normalized frequencies were then averaged for sequence groups * Percent Accepted Mutation (PAM or Dayhoff) Matrices The amino acid exchange counts and mutability values were used to generate a 20 × 20 mutation probability matrix representing all possible amino acid changes. A detailed example of calculating the PAM matrix is located in Mount, p82 (table 3.2). * PAM1 matrix (see p80-81) normalized probabilities multiplied by 10000 A l a A r g A s n A s p C y s Gl n G l u G l y H i s Il e L e u L y s M e t P h e P r o S e r T h r T r p T y r V a l A R N D C Q E G H I L K M