A New Database (GCD) on Genome Composition for Eukaryote and Prokaryote Genome Sequences and Their Initial Analyses

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. Frequencie...

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Autores principales: Kryukov, Kirill, Sumiyama, Kenta, Ikeo, Kazuho, Gojobori, Takashi, Saitou, Naruya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Research Articles
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342873/
https://www.ncbi.nlm.nih.gov/pubmed/22417913
http://dx.doi.org/10.1093/gbe/evs026
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author Kryukov, Kirill
Sumiyama, Kenta
Ikeo, Kazuho
Gojobori, Takashi
Saitou, Naruya
author_facet Kryukov, Kirill
Sumiyama, Kenta
Ikeo, Kazuho
Gojobori, Takashi
Saitou, Naruya
author_sort Kryukov, Kirill
collection PubMed
description 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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spelling pubmed-33428732012-05-04 A New Database (GCD) on Genome Composition for Eukaryote and Prokaryote Genome Sequences and Their Initial Analyses Kryukov, Kirill Sumiyama, Kenta Ikeo, Kazuho Gojobori, Takashi Saitou, Naruya Genome Biol Evol Research Articles 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/. Oxford University Press 2012 2012-03-14 /pmc/articles/PMC3342873/ /pubmed/22417913 http://dx.doi.org/10.1093/gbe/evs026 Text en © The Author(s) 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Articles
Kryukov, Kirill
Sumiyama, Kenta
Ikeo, Kazuho
Gojobori, Takashi
Saitou, Naruya
A New Database (GCD) on Genome Composition for Eukaryote and Prokaryote Genome Sequences and Their Initial Analyses
title A New Database (GCD) on Genome Composition for Eukaryote and Prokaryote Genome Sequences and Their Initial Analyses
title_full A New Database (GCD) on Genome Composition for Eukaryote and Prokaryote Genome Sequences and Their Initial Analyses
title_fullStr A New Database (GCD) on Genome Composition for Eukaryote and Prokaryote Genome Sequences and Their Initial Analyses
title_full_unstemmed A New Database (GCD) on Genome Composition for Eukaryote and Prokaryote Genome Sequences and Their Initial Analyses
title_short A New Database (GCD) on Genome Composition for Eukaryote and Prokaryote Genome Sequences and Their Initial Analyses
title_sort new database (gcd) on genome composition for eukaryote and prokaryote genome sequences and their initial analyses
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342873/
https://www.ncbi.nlm.nih.gov/pubmed/22417913
http://dx.doi.org/10.1093/gbe/evs026
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