PAM vs BLOSUM

http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/Scoring2.html

The relationship between BLOSUM and PAM substitution matrices. BLOSUM matrices with higher numbers and PAM matrices with low numbers are both designed for comparisons of closely related sequences. BLOSUM matrices with low numbers and PAM matrices with high numbers are designed for comparisons of distantly related proteins. If distant relatives of the query sequence are specifically being sought, the matrix can be tailored to that type of search.

The PAM family


PAM matrices are based on global alignments of closely related proteins.

The PAM1 is the matrix calculated from comparisons of sequences with no more than 1% divergence.

BLOSUM matrices are based on local alignments.


BLOSUM 62 is a matrix calculated from comparisons of sequences with no less than 62% divergence.

All BLOSUM matrices are based on observed alignments; they are not extrapolated from comparisons of closely related proteins.

BLOSUM 62 is the default matrix in BLAST 2.0.