Analysis of amino acid substitution during divergent evolution: the 400 by 400 dipeptide substitution matrix.

@article{Gonnet1994AnalysisOA,
  title={Analysis of amino acid substitution during divergent evolution: the 400 by 400 dipeptide substitution matrix.},
  author={G H Gonnet and Michael A. Cohen and S. A. Benner},
  journal={Biochemical and biophysical research communications},
  year={1994},
  volume={199 2},
  pages={489-96}
}
Most formal methods for analyzing the divergent evolution of protein sequences assume a Markov model where position i in a polypeptide chain undergoes amino acid substitution independently from position i + 1. The large number of aligned homologous sequence pairs available from the exhaustive matching of the protein sequence database makes it possible to examine this assumption empirically. We have constructed a 400 by 400 matrix that reports empirical probabilities for the interconversion of… CONTINUE READING

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