BLAST

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Chapter 4: Sequence Similarity

PAM and BLOSUM Matrices

Two different kinds of amino acid scoring matrices, PAM (Percent Accepted Muta-

tion) and BLOSUM (BLOcks SUbstitution Matrix), are in wide use. The PAM matri-

ces were created by Margaret Dayhoff and coworkers and are thus sometimes

referred to as the Dayhoff matrices. These scoring matrices have a strong theoretical

component and make a few evolutionary assumptions. The BLOSUM matrices, on

the other hand, are more empirical and derive from a larger data set. Most research-

ers today prefer to use BLOSUM matrices because in silico experiments indicate that

searches employing BLOSUM matrices have higher sensitivity.

There are several PAM matrices, each one with a numeric suffix. The PAM1 matrix

was constructed with a set of proteins that were all 85 percent or more identical to

one another. The other matrices in the PAM set were then constructed by multiply-

ing the PAM1 matrix by itself: 100 times for the PAM100; 160 times for the

PAM160; and so on, in an attempt to model the course of sequence evolution.

Though highly theoretical (and somewhat suspect), it is certainly a reasonable

approach. There was little protein sequence data in the 1970s when these matrices

were created, so this approach was a good way to extrapolate to larger ...