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Quantitative measures for the management and comparison of annotated genomes

BACKGROUND: The ever-increasing number of sequenced and annotated genomes has made management of their annotations a significant undertaking, especially for large eukaryotic genomes containing many thousands of genes. Typically, changes in gene and transcript numbers are used to summarize changes fr...

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Detalles Bibliográficos
Autores principales: Eilbeck, Karen, Moore, Barry, Holt, Carson, Yandell, Mark
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653490/
https://www.ncbi.nlm.nih.gov/pubmed/19236712
http://dx.doi.org/10.1186/1471-2105-10-67
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author Eilbeck, Karen
Moore, Barry
Holt, Carson
Yandell, Mark
author_facet Eilbeck, Karen
Moore, Barry
Holt, Carson
Yandell, Mark
author_sort Eilbeck, Karen
collection PubMed
description BACKGROUND: The ever-increasing number of sequenced and annotated genomes has made management of their annotations a significant undertaking, especially for large eukaryotic genomes containing many thousands of genes. Typically, changes in gene and transcript numbers are used to summarize changes from release to release, but these measures say nothing about changes to individual annotations, nor do they provide any means to identify annotations in need of manual review. RESULTS: In response, we have developed a suite of quantitative measures to better characterize changes to a genome's annotations between releases, and to prioritize problematic annotations for manual review. We have applied these measures to the annotations of five eukaryotic genomes over multiple releases – H. sapiens, M. musculus, D. melanogaster, A. gambiae, and C. elegans. CONCLUSION: Our results provide the first detailed, historical overview of how these genomes' annotations have changed over the years, and demonstrate the usefulness of these measures for genome annotation management.
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spelling pubmed-26534902009-03-10 Quantitative measures for the management and comparison of annotated genomes Eilbeck, Karen Moore, Barry Holt, Carson Yandell, Mark BMC Bioinformatics Methodology Article BACKGROUND: The ever-increasing number of sequenced and annotated genomes has made management of their annotations a significant undertaking, especially for large eukaryotic genomes containing many thousands of genes. Typically, changes in gene and transcript numbers are used to summarize changes from release to release, but these measures say nothing about changes to individual annotations, nor do they provide any means to identify annotations in need of manual review. RESULTS: In response, we have developed a suite of quantitative measures to better characterize changes to a genome's annotations between releases, and to prioritize problematic annotations for manual review. We have applied these measures to the annotations of five eukaryotic genomes over multiple releases – H. sapiens, M. musculus, D. melanogaster, A. gambiae, and C. elegans. CONCLUSION: Our results provide the first detailed, historical overview of how these genomes' annotations have changed over the years, and demonstrate the usefulness of these measures for genome annotation management. BioMed Central 2009-02-23 /pmc/articles/PMC2653490/ /pubmed/19236712 http://dx.doi.org/10.1186/1471-2105-10-67 Text en Copyright © 2009 Eilbeck 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 Methodology Article
Eilbeck, Karen
Moore, Barry
Holt, Carson
Yandell, Mark
Quantitative measures for the management and comparison of annotated genomes
title Quantitative measures for the management and comparison of annotated genomes
title_full Quantitative measures for the management and comparison of annotated genomes
title_fullStr Quantitative measures for the management and comparison of annotated genomes
title_full_unstemmed Quantitative measures for the management and comparison of annotated genomes
title_short Quantitative measures for the management and comparison of annotated genomes
title_sort quantitative measures for the management and comparison of annotated genomes
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653490/
https://www.ncbi.nlm.nih.gov/pubmed/19236712
http://dx.doi.org/10.1186/1471-2105-10-67
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