The general consensus is that matrices derived from observed substitution data (e.g. the Dayhoff or BLOSUM matrices) are superior to identity, genetic code or physical property matrices (e.g. see [3]). However, there are Dayhoff matrices of different PAM values and BLOSUM matrices of different percentage identity and which of these should be used?
Schwartz and Dayhoff [2] recommended a mutation data matrix for the distance of 250 PAMs as a result of a study using a dynamic programming procedure [13] to compare a variety of proteins known to be distantly related. The 250 PAM matrix was selected since in Monte Carlo studies (see Section 4.1) matrices reflecting this evolutionary distance gave a consistently higher significance score than other matrices in the range 0-750 PAM. The matrix also gave better scores when compared to McLachlan's substitution matrix [6], the genetic code matrix and identity scoring. Recently, Altschul [14] has examined Dayhoff style mutation data matrices from an information theoretical perspective. For alignments that do not include gaps he concluded, in broad agreement with Schwarz and Dayhoff, that a matrix of 200 PAMS was most appropriate when the sequences to be compared were thought to be related. However, when comparing sequences that were not known in advance to be related, for example when database scanning, a 120 PAM matrix was the best compromise. When using a local alignment method (Section 6.7) Altschul suggests that three matrices should ideally be used: PAM40, PAM120 and PAM250, the lower PAM matrices will tend to find short alignments of highly similar sequences, while higher PAM matrices will find longer, weaker local alignments. Similar conclusions were reached by Collins and Coulson [15] who advocate using a compromise PAM100 matrix, but also suggest the use of multiple PAM matrices to allow detection of local similarities of all types.
Henikoff and Henikoff [16] have compared the BLOSUM matrices to PAM, PET, Overington, Gonnet [17] and multiple PAM matrices by evaluating how effectively the matrices can detect known members of a protein family from a database when searching with the ungapped local alignment program BLAST [18]. They conclude that overall the BLOSUM 62 matrix is the most effective. However, all the substitution matrices investigated perform better than BLOSUM 62 for a proportion of the families. This suggests that no single matrix is the complete answer for all sequence comparisons. It is probably best to compliment the BLOSUM 62 matrix with comparisons using PET91 at 250 PAMS, and Overington structurally derived matrices. It seems likely that as more protein three dimensional structures are determined, substitution tables derived from structure comparison will give the most reliable data.