Cluster analysis of genes in codon space

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Abstract
We construct a “codon space” in which a given DNA sequence can be plotted as a function of its base composition in each of the three codon positions. We demonstrate that the base composition is very highly nonrandom, with sequences from more primitive organisms having the least random compositions. By using cluster analysis on the points plotted in codon space we show that there is a strong correlation between base composition and type of organism, with the most primitive organisms having the highest A or T content in the second and third codon positions. A smooth transition toward lower A+T and higher G+C content is observed in the second and third codon positions as the evolutionary complexity of the organism increases. Besides this general trend, more detailed structure can be observed in the clustering that will become clearer as the data base is increased.

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