Scoring Matrices
Scoring 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
Pet91 - an updated Dayhoff matrix
BLOSUM Matrices
BLOSUM# - where # is the threshold identity percentage of the sequences clustered in those blocks.
So which observed matrix to use???
Tips...
Tips�.
Matrices used in GCG
To view a list of available matrices for GCG:
Email: shifra.ben-dor@weizmann.ac.il