Mutation probability matrices

The PAM250 scoring matrix in the log-odds form [Dayhoff 1978], Each element is given by S,j — 10(/og2o My/fi), where M j is the appropriate element of the mutation probability matrix (Appendix 10.4) and f is the frequency cf occurrence of amino acid i (i e the probability that i will occur in a sequence by chance). 

Each element of matrix corresponds to the probability that the amino acid in coiumn wiii mutate to the jmino acid in row j after a period of 1 PAM. The vaiues have been multipiied by 10000. (Based on Dayhoff M O 1978. Atlas of Protein Sequence and Structure Voiume 5 Suppiement 3. Dayhoff M O (Editor) Georgetown Jniversity Medicai Center, National Biomedical Research Foundation Figure 82.)... 

The PAM matrices, ° which were developed by Dayhoff et ah, are based on the probability of an amino acid residue mutating to another amino acid residue. The original PAM matrix was derived using a small group of closely related sequences and tracking the amino acid residue substitutions. Each evolutionary PAM matrix is determined by multiplying the original PAM matrix by itself n — 1 times, where n is the number of desired evolutionary... 

By examining the PAM20 matrix we see that there is a small probability (1) that a mutation to or from tyrosine (Y) to a phenylalanine (F) will happen, but almost no chance (—19) of tryptophan (W) mutating to glutamic acid (E). It is reasonable to expect that a conversion between a tyrosine and phenylala-... 

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