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Define PAM Matrices

PAM Matrices: PAM matrices is Percentage of Acceptable point Mutations, developed by Dayhoff mutation data matrix. He developed this method along with his co-workers during analysis of the evolution of proteins. This gives the probability of one amino acid mutating to the other amino acid within a particular evolutionary time. The scoring schemes are denoted by a number following. Examples are PAM40 and PAM250.Lower PAM matrices would determine short alignments of highly similar sequences and higher PAM matrix would determine longer, weaker and lower alignments. For using PAM250, 20% of the amino acids should remain uncharged for the sequences to be considered to be related.

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