Detour: PAM Scoring Matrices

What is the PAM scoring matrix?

Mutations of a gene’s nucleotide sequence often change the amino acid sequence of the translated protein. Some of these mutations impair the protein’s ability to function, making them rare events in molecular evolution. Asn, Asp, Glu, and Ser are the most “mutable” amino acids, whereas Cys and Trp are the least mutable. Knowledge of the likelihood of each possible mutation allows biologists to construct amino acid scoring matrices for biologically sound sequence alignments in which different substitutions are penalized differently. The ( ...