Relationships between amino acid sequences determined through optimum alignments, clustering, and specific distance...

Optimum alignment in all pairwise combinations among a group of amino acid sequences generated a distance matrix. These distances were clustered to evaluate relationships among the sequences. The degree of relationship among sequences was also evaluated by calculating specific distances from the distance matrix and examining correlations between patterns of specific distances for pairs of sequences. The sequences examined were a group of 20 amino acid sequences of scorpion toxins originally published and analyzed by M.J. Dufton and H. Rochat in 1984. Alignment gap penalties were constant for all 190 pairwise sequence alignments and were chosen after assessing the impact of changing penalties on resultant distances. The total distances generated by the 190 pairwise sequence alignments were clustered using complete (farthest neighbour) linkage. The square, symmetrical input distance matrix is analogous to diallel cross data where reciprocal and parental values are absent. Diallel analysis methods provided analogues for the distance matrix to genetical specific combining abilities, namely specific distances between all sequence pairs that are independent of the average distances shown by individual sequences. Correlation of specific distance patterns, with transformation to modified z values and a stringent probability level, were used to delineate subgroups of related sequences. These were compared with complete linkage clustering results. Excellent agreement between the two approaches was found. Three originally outlying sequences were placed within the four new subgroups.