Next: Identity scoring
Up: No Title
Previous: Introduction
All algorithms to compare protein sequences rely on some scheme to
score the equivalencing of each of the 210 possible pairs of amino
acids. (i.e. 190 pairs of different amino acids + 20 pairs of
identical amino acids). Most scoring schemes represent the 210 pairs
of scores as a 
matrix of similarities where identical amino
acids and those of similar character (e.g. I, L) give higher scores
compared to those of different character (e.g. I, D). Since the first
protein sequences were obtained, many different types of scoring
scheme have been devised. The most commonly used are those
based on observed substitution and of these, the 1976 Dayhoff matrix
for 250 PAMS [1] has until recently dominanted. This and other
schemes are discussed in the following sections.