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Modeling and comparing the organization of circular genomes

Motivation: Most prokaryotic genomes are circular with a single chromosome (called circular genomes), which consist of bacteria and archaea. Orthologous genes (abbreviated as orthologs) are genes directly evolved from an ancestor gene, and can be traced through different species in evolution. Shared...

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Autores principales: Shieh, Grace S., Zheng, Shurong, Johnson, Richard A., Chang, Yi-Feng, Shimizu, Kunio, Wang, Chia-Chang, Tang, Sen-Lin
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065686/
https://www.ncbi.nlm.nih.gov/pubmed/21278186
http://dx.doi.org/10.1093/bioinformatics/btr049
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author Shieh, Grace S.
Zheng, Shurong
Johnson, Richard A.
Chang, Yi-Feng
Shimizu, Kunio
Wang, Chia-Chang
Tang, Sen-Lin
author_facet Shieh, Grace S.
Zheng, Shurong
Johnson, Richard A.
Chang, Yi-Feng
Shimizu, Kunio
Wang, Chia-Chang
Tang, Sen-Lin
author_sort Shieh, Grace S.
collection PubMed
description Motivation: Most prokaryotic genomes are circular with a single chromosome (called circular genomes), which consist of bacteria and archaea. Orthologous genes (abbreviated as orthologs) are genes directly evolved from an ancestor gene, and can be traced through different species in evolution. Shared orthologs between bacterial genomes have been used to measure their genome evolution. Here, organization of circular genomes is analyzed via distributions of shared orthologs between genomes. However, these distributions are often asymmetric and bimodal; to date, there is no joint distribution to model such data. This motivated us to develop a family of bivariate distributions with generalized von Mises marginals (BGVM) and its statistical inference. Results: A new measure based on circular grade correlation and the fraction of shared orthologs is proposed for association between circular genomes, and a visualization tool developed to depict genome structure similarity. The proposed procedures are applied to eight pairs of prokaryotes separated from domain down to species, and 13 mycoplasma bacteria that are mammalian pathogens belonging to the same genus. We close with remarks on further applications to many features of genomic organization, e.g. shared transcription factor binding sites, between any pair of circular genomes. Thus, the proposed procedures may be applied to identifying conserved chromosome backbones, among others, for genome construction in synthetic biology. Availability: All codes of the BGVM procedures and 1000+ prokaryotic genomes are available at http://www.stat.sinica.edu.tw/∼gshieh/bgvm.htm. Contact: gshieh@stat.sinica.edu.tw Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-30656862011-03-30 Modeling and comparing the organization of circular genomes Shieh, Grace S. Zheng, Shurong Johnson, Richard A. Chang, Yi-Feng Shimizu, Kunio Wang, Chia-Chang Tang, Sen-Lin Bioinformatics Original Papers Motivation: Most prokaryotic genomes are circular with a single chromosome (called circular genomes), which consist of bacteria and archaea. Orthologous genes (abbreviated as orthologs) are genes directly evolved from an ancestor gene, and can be traced through different species in evolution. Shared orthologs between bacterial genomes have been used to measure their genome evolution. Here, organization of circular genomes is analyzed via distributions of shared orthologs between genomes. However, these distributions are often asymmetric and bimodal; to date, there is no joint distribution to model such data. This motivated us to develop a family of bivariate distributions with generalized von Mises marginals (BGVM) and its statistical inference. Results: A new measure based on circular grade correlation and the fraction of shared orthologs is proposed for association between circular genomes, and a visualization tool developed to depict genome structure similarity. The proposed procedures are applied to eight pairs of prokaryotes separated from domain down to species, and 13 mycoplasma bacteria that are mammalian pathogens belonging to the same genus. We close with remarks on further applications to many features of genomic organization, e.g. shared transcription factor binding sites, between any pair of circular genomes. Thus, the proposed procedures may be applied to identifying conserved chromosome backbones, among others, for genome construction in synthetic biology. Availability: All codes of the BGVM procedures and 1000+ prokaryotic genomes are available at http://www.stat.sinica.edu.tw/∼gshieh/bgvm.htm. Contact: gshieh@stat.sinica.edu.tw Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2011-04-01 2011-01-28 /pmc/articles/PMC3065686/ /pubmed/21278186 http://dx.doi.org/10.1093/bioinformatics/btr049 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Papers
Shieh, Grace S.
Zheng, Shurong
Johnson, Richard A.
Chang, Yi-Feng
Shimizu, Kunio
Wang, Chia-Chang
Tang, Sen-Lin
Modeling and comparing the organization of circular genomes
title Modeling and comparing the organization of circular genomes
title_full Modeling and comparing the organization of circular genomes
title_fullStr Modeling and comparing the organization of circular genomes
title_full_unstemmed Modeling and comparing the organization of circular genomes
title_short Modeling and comparing the organization of circular genomes
title_sort modeling and comparing the organization of circular genomes
topic Original Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065686/
https://www.ncbi.nlm.nih.gov/pubmed/21278186
http://dx.doi.org/10.1093/bioinformatics/btr049
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