ApA dinucleotide periodicity in prokaryote, eukaryote, and organelle genomes

Masaru Tomita, Masahiko Wada, Yukihiro Kawashima

Research output: Contribution to journalArticlepeer-review

23 Citations (Scopus)


Computer analyses of various genome sequences revealed the existence of certain periodical patterns of adenine-adenine dinucleotides (ApA). For each genome sequence of 13 eubacteria, 3 archaebacteria, 10 eukaryotes, 60 mitochondria, and 9 chloroplasts, we counted frequencies of ApA dinucleotides at each downstream position within 50 bp from every ApA. We found that the complete genomes of all three archaebacteria have clear ApA periodicities of about 10 bps. On the other hand, all of the 13 eubacteria we analyzed were found to have an ApA periodicity of about 11 bp. Similar periodicities exist in the 10 eukaryotes, although higher organisms such as primates tend to have weaker periodic patterns. None of the mitochondria and chroloplasts we analyzed showed an evident periodic pattern.

Original languageEnglish
Pages (from-to)182-192
Number of pages11
JournalJournal of Molecular Evolution
Issue number2
Publication statusPublished - 1999 Aug 9


  • Chroloplast
  • Complete genome
  • Dinucleotide
  • Eukaryote
  • Mitochondria
  • Prokaryote
  • Sequence periodicity

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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