Doublet frequencies in evolutionary distinct groups

We analyze the dinucleotide frequencies of occurrence and preferences separately within the vertebrates, nonvertebrates, DNA viruses, mitochondria, RNA viruses, bacteria and phage sequences. Over half a million nucleotides from more than 400 sequences were used in this study. Distinct patterns are observed. Some of the patterns are common to all sequences, some to either eukaryotes or prokaryotes and others to the subgroups within them. Doublets are the most basic ingredient of order in nucleotide sequences. We suggest that their preferences and the arrangement of nucleotides in the DNA in general is determined to a large extent by the conformational and packaging considerations of the double helix. Some principles of DNA conformation are viewed in light of our results.