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Gene family assignment-free comparative genomics

BACKGROUND: The comparison of relative gene orders between two genomes offers deep insights into functional correlations of genes and the evolutionary relationships between the corresponding organisms. Methods for gene order analyses often require prior knowledge of homologies between all genes of t...

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Detalles Bibliográficos
Autores principales: Doerr, Daniel, Thévenin, Annelyse, Stoye, Jens
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526435/
https://www.ncbi.nlm.nih.gov/pubmed/23281826
http://dx.doi.org/10.1186/1471-2105-13-S19-S3
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author Doerr, Daniel
Thévenin, Annelyse
Stoye, Jens
author_facet Doerr, Daniel
Thévenin, Annelyse
Stoye, Jens
author_sort Doerr, Daniel
collection PubMed
description BACKGROUND: The comparison of relative gene orders between two genomes offers deep insights into functional correlations of genes and the evolutionary relationships between the corresponding organisms. Methods for gene order analyses often require prior knowledge of homologies between all genes of the genomic dataset. Since such information is hard to obtain, it is common to predict homologous groups based on sequence similarity. These hypothetical groups of homologous genes are called gene families. RESULTS: This manuscript promotes a new branch of gene order studies in which prior assignment of gene families is not required. As a case study, we present a new similarity measure between pairs of genomes that is related to the breakpoint distance. We propose an exact and a heuristic algorithm for its computation. We evaluate our methods on a dataset comprising 12 γ-proteobacteria from the literature. CONCLUSIONS: In evaluating our algorithms, we show that the exact algorithm is suitable for computations on small genomes. Moreover, the results of our heuristic are close to those of the exact algorithm. In general, we demonstrate that gene order studies can be improved by direct, gene family assignment-free comparisons.
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spelling pubmed-35264352013-01-10 Gene family assignment-free comparative genomics Doerr, Daniel Thévenin, Annelyse Stoye, Jens BMC Bioinformatics Proceedings BACKGROUND: The comparison of relative gene orders between two genomes offers deep insights into functional correlations of genes and the evolutionary relationships between the corresponding organisms. Methods for gene order analyses often require prior knowledge of homologies between all genes of the genomic dataset. Since such information is hard to obtain, it is common to predict homologous groups based on sequence similarity. These hypothetical groups of homologous genes are called gene families. RESULTS: This manuscript promotes a new branch of gene order studies in which prior assignment of gene families is not required. As a case study, we present a new similarity measure between pairs of genomes that is related to the breakpoint distance. We propose an exact and a heuristic algorithm for its computation. We evaluate our methods on a dataset comprising 12 γ-proteobacteria from the literature. CONCLUSIONS: In evaluating our algorithms, we show that the exact algorithm is suitable for computations on small genomes. Moreover, the results of our heuristic are close to those of the exact algorithm. In general, we demonstrate that gene order studies can be improved by direct, gene family assignment-free comparisons. BioMed Central 2012-12-19 /pmc/articles/PMC3526435/ /pubmed/23281826 http://dx.doi.org/10.1186/1471-2105-13-S19-S3 Text en Copyright ©2012 Doerr et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Proceedings
Doerr, Daniel
Thévenin, Annelyse
Stoye, Jens
Gene family assignment-free comparative genomics
title Gene family assignment-free comparative genomics
title_full Gene family assignment-free comparative genomics
title_fullStr Gene family assignment-free comparative genomics
title_full_unstemmed Gene family assignment-free comparative genomics
title_short Gene family assignment-free comparative genomics
title_sort gene family assignment-free comparative genomics
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526435/
https://www.ncbi.nlm.nih.gov/pubmed/23281826
http://dx.doi.org/10.1186/1471-2105-13-S19-S3
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