Amino acid substitution matrices from an information theoretic perspective.

  title={Amino acid substitution matrices from an information theoretic perspective.},
  author={Stephen F. Altschul},
  journal={Journal of molecular biology},
  volume={219 3},
Protein sequence alignments have become an important tool for molecular biologists. Local alignments are frequently constructed with the aid of a "substitution score matrix" that specifies a score for aligning each pair of amino acid residues. Over the years, many different substitution matrices have been proposed, based on a wide variety of rationales. Statistical results, however, demonstrate that any such matrix is implicitly a "log-odds" matrix, with a specific target distribution for… CONTINUE READING
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