With the introduction of the dynamic programming algorithm for comparing protein sequences in 1970s, a need arose for scoring amino acid substitutions. Since then, the construction of scoring matrices has become one key issue in sequence comparison. A variety of considerations such as the physicochemical and three-dimensional structure properties have been used for deriving amino acid scoring (or substitution) matrices.
The chapter is divided into eight sections. The PAM matrices are introduced in Section 8.1. We first define the PAM evolutionary distance. We then describe the Dayhoff’s method of constructing the PAMmatrices. Frequently used PAMmatrices are listed at the end of this section.
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© 2009 Springer-Verlag Berlin Heidelberg
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(2009). Scoring Matrices. In: Sequence Comparison. Computational Biology, vol 7. Springer, London. https://doi.org/10.1007/978-1-84800-320-0_8
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DOI: https://doi.org/10.1007/978-1-84800-320-0_8
Publisher Name: Springer, London
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