Using PAM Matrices in Sequence Alignments.

  title={Using PAM Matrices in Sequence Alignments.},
  author={David W. Mount},
  journal={CSH protocols},
INTRODUCTIONCertain amino acid substitutions commonly occur in related proteins from different species. Because a protein still functions with these substitutions, the substituted amino acids are compatible with protein structure and function. Knowing the types of changes that are most and least common in a large number of proteins can assist with predicting alignments for any set of protein sequences. If related protein sequences are quite similar, they are easy to align, and one can readily… CONTINUE READING