Journal
GENOME BIOLOGY AND EVOLUTION
Volume 4, Issue 4, Pages 501-512Publisher
OXFORD UNIV PRESS
DOI: 10.1093/gbe/evs026
Keywords
GCD; oligonucleotide frequency; alignment-free sequence comparison
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Funding
- Ministry of Education, Culture, Sports, Science and Technology, Japan
- Human Genome Network
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Eukaryote genomes contain many noncoding regions, and they are quite complex. To understand these complexities, we constructed a database, Genome Composition Database, for the whole genome composition statistics for 101 eukaryote genome data, as well as more than 1,000 prokaryote genomes. Frequencies of all possible one to ten oligonucleotides were counted for each genome, and these observed values were compared with expected values computed under observed oligonucleotide frequencies of length 1-4. Deviations from expected values were much larger for eukaryotes than prokaryotes, except for fungal genomes. Mammalian genomes showed the largest deviation among animals. The results of comparison are available online at http://esper.lab.nig.ac.jp/genome-composition-database/.
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