PAM Vs BLOSUM

Difference Between PAM & BLOSUM

1. PAM matrices are based on an explicit evolutionary model (i.e. replacements are counted on the branches of a phylogenetic tree), whereas the BLOSUM matrices are based on an implicit model of evolution.
2. The PAM matrices are based on mutations observed throughout a global alignment, this includes both highly conserved and highly mutable regions. The BLOSUM matrices are based only on highly conserved regions in series of alignments forbidden to contain gaps.
3. The method used to count the replacements is different: unlike the PAM matrix, the BLOSUM procedure uses groups of sequences within which not all mutations are counted the same.
4. Higher numbers in the PAM matrix naming scheme denote larger evolutionary distance, while larger numbers in the BLOSUM matrix naming scheme denote higher sequence similarity and therefore smaller evolutionary distance. Example: PAM150 is used for more distant sequences than PAM100; BLOSUM62 is used for closer sequences than Blosum50.

PAM & BLOSUM Equivalents

PAM 100 => BLOSUM 90
PAM 120 => BLOSUM 80
PAM 160 => BLOSUM 60
PAM 200 => BLOSUM 52
PAM 250 => BLOSUM 40