What are BLOSUM and PAM scoring matrices used for?

BLOSUM (BLOcks SUbstitution Matrix) and PAM (Point Accepted Mutation) are substitution matrices used to score amino acid alignments in protein sequence comparison. They assign scores based on how frequently amino acid substitutions occur in related proteins. PAM matrices (PAM1, PAM120, PAM250) are based on evolutionary models, with higher numbers for distantly related sequences. BLOSUM matrices (BLOSUM62, BLOSUM80) are derived from conserved blocks in alignments, with higher numbers for closely related sequences. BLOSUM62 is commonly used as default in BLAST. These matrices improve alignment accuracy by weighting biologically meaningful substitutions.