Question

WHY IT'S BETTER TO USE BLOSUM MATRIX , THAN PAM MATRIX IN BIOINFORMATIC'S ???

Answer 1

BLOSUM is far more robust than PAM because its alignment algorithm works in small blocks rather than on the whole global sequence like PAM does. BLOSUM is able to find regions of similarity while PAM looks at global similarity. For this reason BLOSUM allows for gaps of missing residues when comparing evolutionarily distant sequences and if you have a pair of protein sequences where certain regions are conserved while others are lost entirely or replaced with something else (paralogs), BLOSUM will be able to identify those similar regions. PAM will look at the whole length of the paralog sequences and decide they have little in common overall.