By G Dunn; Brian Everitt

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3. For each possible alignment one counts the number of unit characters that match in the two aligned fragments. So, for the three alignments given above, the number of matches are one, three and twelve, respectively. 4. One selects the alignment that maximizes the match between sequences. If the number of matches is greater than a preassigned value one decides that the sequences are homologous. 5. Homologous unit characters (nucleotide bases) are those opposing each other during optimum alignment.

2) In words, it is the ratio of the number of positive matches to the total number of characters minus the number of negative matches. The decision to include or exclude the number of matched Os, that is d, is a difficult and, at times, a contentious one. In some situations it would be improper to neglect conjoint absences when estimating similarity, in others it would seem rid,iculous to regard two taxa as similar largely on the basis of their both lacking some feature. ) The following example from Sokal & Sneath (1963) illustrates some of the difficulties over the appropriate way to deal with negative matches when estimating similarity.

3) between differing homologous amino acids Man Dog Chicken 1 4 Man o Dog 1 o 5 4 5 Chicken o (c) Euclidean distance, based on the simple matching coefficient Man Dog Chicken Man Dog Chicken o Jt Ji Ji o Ji Ji Ji o Note that (c) is jointly monotonic with (a~ and that it would be with (b) if one were comparing nucleotide, rather than amino acid, sequences. 4(b). 3 which gives the minimum number of nucleotide changes required to convert the coding from one amino acid to the other. So, for example, if one wishes to determine the mutation value for glutamic acid and lysine, one notes that the codons for glutamic acid are GAA and GAG and those for lysine are AAA and AAG.

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