A use for principal coordinate analysis in the comparison of protein sequences

Principal Coordinate analysis (PCO) was applied to the comparison of protein sequences. A similarity matrix was derived from a dataset containing 21 c-type cytochrome sequences and this was analysed using PCO to produce a plot of the first three principal axes. The relationships indicated from this plot are considered in conjunction with those derived by cluster analysis using the UPGMA method, and the advantages offered by a nonhierarchical method of sequence comparison discussed.