A new database (GCD) on genome composition for eukaryote and prokaryote genome sequences and their initial analyses

Kirill Kryukov; Kenta Sumiyama; Kazuho Ikeo; Takashi Gojobori; Naruya Saitou

doi:10.1093/gbe/evs026

A new database (GCD) on genome composition for eukaryote and prokaryote genome sequences and their initial analyses

Kirill Kryukov, Kenta Sumiyama, Kazuho Ikeo, Takashi Gojobori, Naruya Saitou^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

11 Scopus citations

Abstract

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/.

Original language	English (US)
Pages (from-to)	501-512
Number of pages	12
Journal	Genome biology and evolution
Volume	4
Issue number	4
DOIs	https://doi.org/10.1093/gbe/evs026
State	Published - Jan 1 2012
Externally published	Yes

Keywords

Alignment-free sequence comparison
GCD
Oligonucleotide frequency

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics

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10.1093/gbe/evs026

Cite this

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abstract = "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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AU - Sumiyama, Kenta

AU - Ikeo, Kazuho

AU - Gojobori, Takashi

AU - Saitou, Naruya

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AB - 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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KW - Oligonucleotide frequency

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A new database (GCD) on genome composition for eukaryote and prokaryote genome sequences and their initial analyses

Abstract

Keywords

ASJC Scopus subject areas

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