Scoring Matrices

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Advantages of BLOSUM overPAM• BLOSUM matrices are created only usingblocks– These conserved regions are the most useful areasto give us information about meaningful homologies• BLOSUM incorporates differences betweendistantly related proteins– <strong>Scoring</strong> matrices are often used to compare verydifferent proteins, so this is an appropriate source ofdata.• BLOSUM gathers data using larger proteinfamilies.– Generally, more data more accurate
Summary• The two major sets of scoring matrices:– PAM is based on evolutionary mutation ratesacross entire proteins– BLOSUM is based on differences betweenconserved regions of related proteins– BLOSUM generally works better
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 and 8: Genetic Code Matrix• Looks at the
Page 9 and 10: Making PAM Matrices• To Create a
Page 11 and 12: BLOSUM Matrices• Developed by Ste
Page 13: BLOSUM Matrices - Clustering• Wha

Scoring Matrices

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