Dayhoff similarity matrix

As an example, we consider a comparison between the two sequences discussed in the FASTA alignment, and we use the Dayhoff similarity matrix in Table 8-3. As a first step we set up the matrix as shown below and enter the similarity scores from Table 8-3. 

The concept of using a substitution matrix, i.e. a knowledge-derived table for judging amino acid similarities, was introduced by Dayhoff et al. in 19781171. Most types of currently used substitution matrices are derived from the analysis of well established alignments, by counting which types of residues are frequently substi-... 

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