Dayhoff-like matrices derive their initial substitution frequencies from global alignments of very similar sequences. An alternative approach has been developed by Henikoff and Henikoff using local multiple alignments of more distantly related sequences [9]. First a database of multiple alignments without gaps for short regions of related sequences was derived. Within each alignment in the database, the sequences were clustered into groups where the sequences are similar at some threshold value of percentage identity. Substitution frequencies for all pairs of amino acids were then calculated between the groups and this used to calculate a log odds BLOSUM (blocks substitution matrix) matrix. Different matrices are obtained by varying the clustering threshold. For example, the BLOSUM 80 matrix was derived using a threshold of 80%identity.

geoff.barton@ox.ac.uk