Dayhoff matrix

Each element of matrix corresponds to the probability that the amino acid in coiumn wiii mutate to the jmino acid in row j after a period of 1 PAM. The vaiues have been multipiied by 10000. (Based on Dayhoff M O 1978. Atlas of Protein Sequence and Structure Voiume 5 Suppiement 3. Dayhoff M O (Editor) Georgetown Jniversity Medicai Center, National Biomedical Research Foundation Figure 82.)... 

Retrieve the amino acid sequences of liver alcohol dehydrogenase from six organisms to perform phylogenetic analysis. Compare phylogenetic results from Fitch-Margoliash methods without (Fitch) versus with (Kisch) molecular clock using the Dayhoff PAM 001 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. 

Identity was determined using Pairwise alignment in Homology. Dayhoff mutation matrix, gap penalty and gap length penalty of 6 and 1.65, respectively, were used. 

The work by Cronet et al. [136] made clear that general rales for residue exchanges in membrane helices are hard to derive because residue preferences are very position specific. A good Dayhoff-type matrix can therefore not be derived for the transmembrane helices, which makes it difficult to use standard sequence-alignment techniques. 

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-... 

The PAM250 scoring matrix in the log-odds form [Dayhoff 1978], Each element is given by S,j — 10(/og2o My/fi), where M j is the appropriate element of the mutation probability matrix (Appendix 10.4) and f is the frequency cf occurrence of amino acid i (i e the probability that i will occur in a sequence by chance). 

The most widely used models of amino acid substitution include distance-based methods, which are based on matrixes such as PAM and BLOSUM. Again, such matrices are described fiuther in other chapters in this book. Briefly, Dayhoff s PAM 001 matrix (Dayhoff, 1979) is an empirical model that scales probabilities of change from one amino acid to another in terms of an expected 1% change between two amino acid sequences. This matrix is used to make a transition probability matrix that allows prediction of the probability of changing from one amino acid to another and also predicts equilibriiun amino acid composition. Phylogenetic distances are calculated with the assumption that the probabilities in the matrix are correct. The... 

The third (default) method uses a table of empirically observed transitions between amino acids (the Dayhoff PAM 001 matrix). The character-based analysis of sequence data can be initiated via the appropriate executable file (e.g. DnaPars, DnaML or ProtPars). PHYLIP comprises DnaPars and DnaML to estimate phylogenetic relationships by the parsimony method and the maximum likelihood methods from nucleotide sequences respectively. ProtPars is the parsimony program for protein sequences. 

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