Difference between PAM and BLOSUM Matrix

Substitution matrices are used to score aligned positions in a sequence alignment procedure, usually of amino acids or nucleotide sequences.

Two commonly used matrices: PAM and BLOSUM
  • PAM = Percent Accepted Mutations (Margaret Dayhoff)
  • BLOSUM = Blocks Substitution Matrix (Steven and Henikoff)
BLOSUM matrix
PAM matrices are used to score alignments between closely related protein sequences. BLOSUM matrices are used to score alignments between evolutionarily divergent protein sequences.
Based on global alignments Based on local alignments
Alignments have high similarity than BLOSUM alignments Alignments have low similarity than PAM alignments
Mutations in global alignments are vey significant based on highly conserved stretches of alignments
Higher numbers in the PAM matrix naming denotes greater evolutionary distance Higher numbers in the BLOSUM matrix naming denotes higher sequence similarity and smaller evolutionary distance
Example: PAM 250 is used for more distant sequences than PAM 120 Example: BLOSUM 80is used for closely related sequences than BLOSUM 62

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