Scoring Matrices

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PAM Matrices• PAM = Percent Accepted Mutation• Based on observed frequencies of evolutionary change insequences of amino acidsPAM250

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PAM Matrices• PAM = Percent Accepted Mutation• Based on observed frequencies of evolutionary change insequences of amino acidsPAM250

Making PAM Matrices• To Create a PAM Matrix:– Arrange a family of closely related proteins(greater than 85% identical) into anphylogenic tree– Observe frequencies of amino acid changesacross individual evolutionary steps– Scores are generated from these frequencies

Page 1 and 2: Scoring MatricesThe Arrays Used to
Page 3 and 4: What are Scoring Matrices?• 20x20
Page 5 and 6: Uses of Scoring Matrices• Used in
Page 7: Genetic Code Matrix• Looks at the
Page 11 and 12: BLOSUM Matrices• Developed by Ste
Page 13 and 14: BLOSUM Matrices - Clustering• Wha
Page 15 and 16: Summary• The two major sets of sc

Scoring Matrices

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