BLOSUM Matrices: Blosum is Blocks Substitution matrices, derived based on substitution frequencies for all pairs of amino acids within a group. This is also developed by Dayhoff and his co-workers based on substitution frequencies from global alignments of very similar sequences. Later this is extended by Henikoff and Henikoff by developing substitution matrices using local alignments of distantly related sequences. Multiple alignments (without gaps) of short regions of related sequences, assembled to a database.Theese sequences were clustered into groups (blocks) on the basis of similarity at threshold value of percentage identity. Based on threshold value there are different BLOSUM matrices. The present interest is developing the scoring matrices based on three dimensional structures. Johnson and Overington matrices (JO matrices) are example for this. These investigators aligned the three-dimensional structures in 65 homologous sets of proteins. From such structures, 207,795 amino acid substitutions were tabulated. The proteins in each and every homologous set had 15-40% sequence identity, therefore this substitution matrix must provide a sensitive basis for scoring sequence alignments. They explained that their substitution matrix performed well relative to the other matrices.