The 1978 family of Dayhoff matrices was derived from a comparatively small set of sequences. Many of the 190 possible substitutions were not observed at all and so suitable weights were determined indirectly. Recently, Jones et al. [7] have derived an updated substitution matrix by examining 2,621 families of of sequences in the SWISSPROT database release 15.0. The principal differences between the Jones et al. matrix (PET91) and the Dayhoff matrix are for substitutions that were poorly represented in the 1978 study. However, the overall character of the matrices is similar. Both reflect substitutions that conserve size and hydrophobicity, which are the principle properties of the amino aids [8]