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Point Accepted Mutation (PAM) or Percent Accepted Mutation, is a set of matrices used to score sequence alignments. The PAM matrices were introduced by Margaret Dayhoff in 1978 based on 1572 observed mutations in 71 families of closely related proteins.1 Each matrix is twenty-by-twenty (for the twenty standard amino acids); the value in a given cell represents the probability of a substitution of one amino acid for another. This type of matrix is commonly known as a substitution matrix.
The PAM matrices imply a Markov chain model of protein mutation.2 The PAM matrices are normalized so that the PAM1 matrix has one point mutation per hundred amino acids, and is appropriate for scoring sequences which are very similar. PAM matrices for comparing sequences of lower similarity are calculated from repeated multiplication of the PAM1 matrix by itself. PAM250 is equivalent to 250 substitutions per hundred amino acids.
See also
References
- ^ Dayhoff, M.O., Schwartz, R. and Orcutt, B.C. (1978), "A model of Evolutionary Change in Proteins", Atlas of protein sequence and structure (volume 5, supplement 3 ed.), Nat. Biomed. Res. Found., p. 345-358, ISBN 0912466073
- ^ Baldi P, Chauvin Y, Hunkapiller T, McClure MA. (1994). "Hidden Markov models of biological primary sequence information". Proc Natl Acad Sci U S A 91 (3): 1059-63. doi:. PMID 8302831, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8302831.
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- This page was last modified on 5 October 2008, at 06:09.
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