Scoring Matrices

25/1/04


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Table of Contents

Scoring Matrices

Scoring matrices

Scoring matrices

Different types of matrices

Different types of matrices

Different types of matrices

PAM Matrices

PPT Slide

Dayhoff estimated mutation rates from substitutions observed in closely related proteins and extrapolated those rates to model distant relationships.

When used for protein comparison, the mutation probability (odds) matrix is normalized and the logarithm is taken. (this lets us add the scores along a protein instead of multiplying the probabilities)

PAM#=Point Accepted Mutations / 100 bases

PAM250

PPT Slide

Pet91 - an updated Dayhoff matrix

BLOSUM Matrices

BLOSUM Matrices

BLOSUM# - where # is the threshold identity percentage of the sequences clustered in those blocks.

PPT Slide

So which observed matrix to use???

Tips...

Tips�.

Matrices used in GCG

To view a list of available matrices for GCG:

PPT Slide

Author: weizmann

Email: shifra.ben-dor@weizmann.ac.il