A method for evaluating phylogenetic relationship of alpha-satellite DNA suprachromosomal family by nucleotide frequency calculation.

The sequence similarity among chromosome-specific alpha-satellite DNA was quantitatively evaluated by a novel procedure: nucleotide frequency calculation. Tandem-arrayed repetitive DNA segments were aligned with unit length repeat, and the nucleotide frequency at each position was used to estimate the phylogenetic distance between repetitive DNA segments. The calculations for human and chimpanzee X chromosome alpha-satellites showed that the results were consistent with the known relationships of primates, indicating that the nucleotide frequency calculation worked effectively to estimate the distances between satellite arrays. Human chromosome-specific alpha-satellites had been grouped into three suprachromosomal families (I, II, and III), and in the current work the nucleotide frequency analysis has defined the quantitative distances between the chromosome-specific alpha-satellite DNA. Copyright 1999 Academic Press.