lect 12 matrices

lect 12 matrices - Bioc 2808 Lecture 12 Substitution...

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Click to edit Master subtitle style 7/29/10 Bioc 2808 Lecture 12 Substitution Matrices Instructor Dr. Junwen Wang
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7/29/10
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7/29/10 Two Main Styles of Matrix One based on an evolutionary model – on observed changes from one sequence to another in a phylogenetic tree – count the changes observed in the tree. One based on observed substitutions – on what we see in the equivalent position in a family of sequences – count the changes observed in the
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7/29/10 Dayhoff’s PAM Matrices Based on a model of evolutionary change in proteins. Counts accepted point mutations in proteins – a mutation occurs and then is accepted (fixed). Need to consider the frequency of change of one amino acid to another as seen in a phylogenetic tree of related sequences.
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7/29/10 Dayhoff’s PAM Matrices Take a set sequences (34 super families; 71 groups) Sequences chosen to be ≥ 85% identical (minimise multiple substitutions) Construct an evolutionary tree Reconstruct ancestral sequences at interior nodes Ambiguities distributed
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7/29/10 Counting Changes Following a Tree
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7/29/10 Number of Mutations in Tree (*10)
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This note was uploaded on 07/29/2010 for the course BIOC BIOC2808 taught by Professor Dr.jjwang during the Fall '09 term at HKU.

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lect 12 matrices - Bioc 2808 Lecture 12 Substitution...

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